- phenixbb - phenix-online.org

RMSD Dihedrals
by J. Fleming 29 Mar '10

29 Mar '10

Hi all, I'm working on a ~3 angstrom structure of a protein with approximately 800 residues. The structure is mostly helical with interspersed turns. I've been using Phenix exclusively for the refinements and have a model that I believe to be pretty good with the exception of the dihedrals (see attached). I've looked at and employed some of the general suggestions for low resolution structures here: http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Refinement#Refi… I tried using "discard_psi_phi=False" but it only resulted in a change dihedrals of +0.10 with minimal changes to Ramachandran outliers. I'm unsure how to proceed and would love to hear any thoughts/opinions/suggestions. Thanks for all the help! -Jon

2 1

Re: [phenixbb] h_bonds restraints
by Maia Cherney 28 Mar '10

28 Mar '10

Hi Boaz, The problem is with the distance between 2 waters and not the Mg-water distance. These 2 waters belong to the Mg coordination, still they should be at a h_b distance from one another. I got around this problem by setting my custom restraints, but I think the program should take care of this. Maia Boaz Shaanan wrote: > Hi Maia, > > Can I make two comments concerning the distance restraints that you're > struggling with: > 1) I don't know the resolution your structure, nor do I know the way > Phenix treats the distance restraints internally, but I guess it's > similar to the way it is in CNS. That is, there is a value for the > restaint (2.1-2.2 A in your case) and there should be a number for the > tolerance of that distance (or its s.d.) which the user can decide on, > depending on the resolution. It is possible that Phenix is clever > enough to figure out this tolerance from the resolution and the > complete set of restraints, I'm not sure. > > 2) I wouldn't worry too much about the validation (as in fact Pavel > has alluded to). If your water molecules in the Mg+2 coordination > sphere "insist" on being closer to the metal than you expect, despite > all your efforts, then this is it. The RCSBpeople and validation > process should know about standard and deviation and resolution. In > the worst case your deposited structure will have a comment/remark put > in your deposited PDB saying perhaps that the Mg-water distances are > shorter by that much from the norm. > > That's my 2p worth thought. > > Cheers, > > Boaz > > ----- Original Message ----- > From: Maia Cherney <chern(a)ualberta.ca> > Date: Sunday, March 28, 2010 14:14 > Subject: Re: [phenixbb] h_bonds restraints > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > > > Hi Pavel, > > > > I have waters that are part of the Mg2+ coordination. They > > should be at > > ~2.1A from Mg2+. At the same time, they should be at a hydrogen- > > bonding > > distance from each other (minimum 2.2A otherwise the validation > > at the > > PDB complains). The two waters after refinement without > > restraints had > > closer (2.12A) distance between them, so I managed to restrain > > the > > distance to 2.23A using pdb_interpretation. But my question was, > > should > > not the refinement automatically restrain close distances > > between any > > atoms, including waters? (By the way, I picked them manually). > > > > Maia > > > > Pavel Afonine wrote: > > > Hi Maia, > > > > > > I'm not sure I understand the question. If you have that > > specific > > > water in your structure already (and you run phenix.refine > > with > > > "ordered_solvent=false"), then changing the > > h_bond_min_mac or > > > h_bond_min_sol will not change anything since these parameters > > are > > > used in water update. > > > > > > However, if you are at the stage of water picking and the > > distance > > > between Mg2+ and prospective water peak is 2.2A then the water > > will be > > > placed there (providing that the corresponding peak satisfies > > the > > > other criteria). > > > > > > Could you please explain what exactly the problem is, and then > > I will > > > try my best to give you the solution? > > > > > > Thanks! > > > Pavel. > > > > > > > > > On 3/27/10 5:23 PM, Maia Cherney wrote: > > >> Hi Pavel, > > >> what is h_bond_min_mac and h_bond_min_sol. > > >> > > >> which one should I change to 2.2 so that it will not affect > > the > > >> coordination distances of Mg2+ (around 2A)? > > >> > > >> Maia > > >> > > >> Pavel Afonine wrote: > > >>> Hi Maia, > > >>> > > >>>> I have done the things that you suggested, > > >>> > > >>> great! > > >>> > > >>>> and I have all the restraints for the Mg2+ and I see those > > 2 > > >>>> waters, but they are at 2.12A distance. > > >>> > > >>> Are these two waters located in the centers of corresponding > > density > > >>> peaks? If this is the case then I don't see the subject of > > your > > >>> worries. If this is not the case (these waters are off the > > peaks) > > >>> then edit the file that defines restraints for water-Mg2+ > > interactions.>>> > > >>>> I think there should be some general restraints that should > > keep > > >>>> h_bonds at least at > 2.2A. > > >>> > > >>> Yes. You wrote it yourself in your previous email: > > >>> > > >>> h_bond_min_mac = 1.8 > > >>> h_bond_min_sol = 1.8 > > >>> h_bond_max = 3.2 > > >>> > > >>> Just change the values to what you like! > > >>> > > >>>> That is why I asked you about those defaults (1.8A etc). > > Why are > > >>>> they at 1.8A? Should not they be at least at 2.2A? > > >>> > > >>> Honestly, I don't remember why I put these values (this is > > pretty > > >>> old code in phenix.refine that I wrote several years ago). > > All I > > >>> recall is that I had a reason for this. I probably need to > > run > > >>> through the whole PDB and see how the density peaks (actual, > > >>> residual, omit-residual) are distributed w.r.t. > > macromolecule, and > > >>> write it somewhere for the future reference. This could be a > > project > > >>> for a few weeks, but it will definitely yield a rock-solid > > >>> conclusion about "good" distances. Meanwhile feel free to > > edit the > > >>> available parameters. > > >>> > > >>> By the way, this is what CNS is using: > > >>> > > >>> {* minimum distance between water and any atom *} > > >>> {===>} min=2.6; > > >>> {* maximum distance between water and any atom *} > > >>> {===>} max=4.0; > > >>> > > >>> {* minimum hydrogen bonding distance between water and O or > > N *} > > >>> {===>} hmin=2.0; > > >>> {* maximum hydrogen bonding distance between water and O or > > N *} > > >>> {===>} hmax=3.2; > > >>> > > >>> Pavel. > > >>> > > >>> _______________________________________________ > > >>> phenixbb mailing list > > >>> phenixbb(a)phenix-online.org > > >>> http://phenix-online.org/mailman/listinfo/phenixbb > > >>> > > >>> > > >> _______________________________________________ > > >> phenixbb mailing list > > >> phenixbb(a)phenix-online.org > > >> http://phenix-online.org/mailman/listinfo/phenixbb > > > _______________________________________________ > > > phenixbb mailing list > > > phenixbb(a)phenix-online.org > > > http://phenix-online.org/mailman/listinfo/phenixbb > > > > > > > > _______________________________________________ > > phenixbb mailing list > > phenixbb(a)phenix-online.org > > http://phenix-online.org/mailman/listinfo/phenixbb > > > > > Boaz Shaanan, Ph.D. > Dept. of Life Sciences > Ben-Gurion University of the Negev > Beer-Sheva 84105 > Israel > Phone: 972-8-647-2220 ; Fax: 646-1710 > Skype: boaz.shaanan > > ‎

1 0

Re: [phenixbb] Twinning Refinement
by Eric Larson 28 Mar '10

28 Mar '10

Dear Joe, It is not uncommon for proteins to crystallize in different crystal forms when in complex with different substrates or inhibitors. Trust that the absurdly high R factors (38% in the lowest resolution shell!?!?) despite the great lengths you went through with error models, etc. and the fact that scalepack is trying to throw out 20% of your data is a hint that you may be in the wrong spacegroup. Also, most of your "systematic absences" have an I/sig >2.5 and so probably are not absent. Were the predictions falling on spots during integration? This may provide another clue. I think you need to go back to HKL and reprocess pretending that you don't know that the crystals are "well characterized". You may have a new crystal form. good luck, Eric __________________________ Eric Larson, PhD MSGPP Consortium Department of Biochemistry Box 357742 University of Washington Seattle, WA 98195 > Date: Fri, 26 Mar 2010 05:13:07 +0000 > From: Joseph Brock <joeylives2ride(a)hotmail.com> > To: <phenixbb(a)phenix-online.org> > Subject: [phenixbb] Twinning Refinement > Message-ID: <SNT120-W557FCF7E111C0FEA167769B230(a)phx.gbl> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Phenix Users, > > I'm currently using version: > Version: 1.4 > Release tag: 3 > cctbx tag: 2008_12_07_1353 > Platform: mac-intel-osx osx-10.5.6 > > I am working on characterising substrate/inhibitor interactions of a protein, the structure has been solved many times so its unit cell dimensions, contents (1 molecule per ASU) and space group (P3121) are well characterized. > > However, I have recently encountered several crystals that appear exhibit merohedral twinning, and am having trouble converging the R-factors to reasonable levels. The details of one such data set is described below: > > Diffraction to ~1.9A was recorded using a high and low resolution pass of 180? each. When processed with HKL2000 separately or together, Scalepack wanted to reject huge amounts of my data (~20%). I was forced to increase the error scale factor to 2 and adjust my error model to the very high R-factors of the low-resolution shells. The summary table from my final round of scalepack is: > Shell Lower Upper Average Average Norm. Linear Square > limit Angstrom I error stat. Chi**2 R-fac R-fac > 50.00 4.09 7648.3 1498.7 182.7 1.030 0.376 0.424 > 4.09 3.25 3885.1 568.9 64.1 1.410 0.416 0.480 > 3.25 2.84 1609.7 225.0 26.1 1.227 0.451 0.517 > 2.84 2.58 807.9 97.1 25.3 1.958 0.439 0.561 > 2.58 2.39 496.6 59.7 22.0 1.060 0.257 0.268 > 2.39 2.25 335.5 53.0 18.1 0.717 0.275 0.238 > 2.25 2.14 221.7 19.0 17.4 2.389 0.354 0.298 > 2.14 2.05 143.1 19.5 17.5 1.537 0.459 0.351 > 2.05 1.97 87.0 20.2 17.1 1.079 0.663 0.480 > 1.97 1.90 54.6 20.3 16.7 1.073 0.990 0.696 > All reflections 1588.3 269.2 41.9 1.350 0.400 0.444 > > In addition, many systematic absences appear to be present: > > Intensities of systematic absences > h k l Intensity Sigma I/Sigma > > 0 0 5 177.7 56.7 3.1 > 0 0 7 255.5 70.6 3.6 > 0 0 8 264.8 73.2 3.6 > 0 0 10 595.0 164.2 3.6 > 0 0 11 2343.5 1289.9 1.8 > 0 0 13 321.3 125.4 2.6 > 0 0 14 66.5 21.8 3.1 > 0 0 16 238.0 76.3 3.1 > 0 0 17 394.3 109.1 3.6 > 0 0 19 13.0 7.1 1.8 > 0 0 20 650.1 179.5 3.6 > 0 0 22 199.6 55.6 3.6 > 0 0 23 953.9 372.0 2.6 > 0 0 25 192.2 62.2 3.1 > 0 0 26 1038.7 405.0 2.6 > 0 0 28 96.3 28.9 3.3 > 0 0 29 2303.0 897.0 2.6 > 0 0 31 12.0 11.5 1.0 > 0 0 32 1622.4 516.5 3.1 > 0 0 34 11.5 13.8 0.8 > 0 0 35 22.8 14.8 1.5 > 0 0 37 27.9 18.0 1.5 > 0 0 38 154.3 45.6 3.4 > 0 0 40 55.8 27.8 2.0 > 0 0 41 35.5 23.7 1.5 > 0 0 43 -25.3 34.4 -0.7 > 0 0 44 67.7 32.1 2.1 > > > > The data has an overall completeness of 99.7%. > > When I run the data trough xtriage, it tells me: > > Statistics depending on twin laws > ----------------------------------------------------------------- > | Operator | type | R obs. | Britton alpha | H alpha | ML alpha | > ----------------------------------------------------------------- > | -h,-k,l | M | 0.307 | 0.301 | 0.256 | 0.022 | > ----------------------------------------------------------------- > > Patterson analyses > - Largest peak height : 5.288 > (corresponding p value : 0.86552) > > > The largest off-origin peak in the Patterson function is 5.29% of the > height of the origin peak. No significant pseudotranslation is detected. > > The results of the L-test indicate that the intensity statistics > are significantly different than is expected from good to reasonable, > untwinned data. > As there are twin laws possible given the crystal symmetry, twinning could > be the reason for the departure of the intensity statistics from normality. > It might be worthwhile carrying out refinement with a twin specific target function. > > I also estimated the twin fraction with the following server: > > http://nihserver.mbi.ucla.edu/Twinning/ > > And found it to about 20% (using data from 6-3A). > > After phasing the data with rigid body refinement in Refmac with intensity based twin refinement (brings both R-factors to ~36%), I have tried doing a twin refinement with Phenix: > > %phenix.refine model.pdb data.mtz twin_law="-h,-k,l" strategy=rigid_body+individual_sites+group_adp > > > The R_factors consistently diverge to the following values: > > Final R-work = 0.3392, R-free = 0.4360 > > Simulated annealing/TLS/ordered solvent/messing with wxc/wxu weights does not seem to improve the situation. I have also tried this with and without prior detwinning with the CCP4 program "Detwin", with similar results. > > Reindexing to -h,-k,l gives similar R-factors after rigid body refinement but after refinement with Phenix, things get even worse: > Final R-work = 0.3919, R-free = 0.5059 > > I was surprised to see that the fit to the map using both indexing conventions are comparable even though this should effectively reverse the hand of the structure. I assume this is because twin refinement is basically doing the job of "partial reindexing" on those parts of the lattice which are twinned? > > I have been working on this for about a week now and can't for the life of me find a way forward. If anyone can offer any suggestions It would greatly be appreciated. Im slowly beginning to lose my sanity.... > > BTW I don't think my problems stem from misindexing, although the beam was wondering all over the place during this block of data collection, I have previously solved another structure at the same d and xbeam ybeam values without any trouble. > > Sorry about the v.long post. Thought it would be better to give too much information rather than not enough =) > > Many thanks for all your suggestions in advance and for everything I > have learned from this community in the past. Cheers, > > Joe > PhD student. > > > > > > > > > > > > > > > > > > > > _________________________________________________________________ > Get personal with Windows. Download a free gift for your PC. > http://experience.windows.com >

4 11

Re: [phenixbb] pointer distances
by Maia Cherney 26 Mar '10

26 Mar '10

Thank you, Paul. There is also difference in recording water. Should it be ATOM or HETATM? Phenix makes it HETATM, but coot makes it ATOM. Here is an example that was saved after adding one water molecule in coot (after refinement in phenix). HETATM10472 O HOH S1252 75.727 6.379 70.023 1.00 31.17 O HETATM10473 O HOH S1253 40.692 -0.062 54.840 1.00 37.64 O TER 10474 HOH S1253 ATOM 10475 O HOH S1254 75.842 2.043 56.024 1.00 35.64 O TER 10476 HOH S1254 END Maia Paul Emsley wrote: > Maia Cherney wrote: >> Hi Paul, >> >> Coot saves pdb files with TER card. The problem is the TER card takes >> the next atom number. >> >> >> ATOM 2303 C4 ADP A 288 33.070 4.240 14.161 1.00 >> 11.08 C TER 2304 ADP A 288 ATOM 2305 O >> SER B -1 >> >> The same model after phenix gives no number to the TER card. >> >> ATOM 2303 C4 ADP A 288 33.070 4.240 14.161 1.00 >> 11.08 C >> TER >> ATOM 2304 O SER B -1 >> >> >> As a result, the number of atoms in the pdb files is different. That >> is confusing. Could you please fix this problem. >> >> Maia >> >> > > > Hi Maia, > > It seems to us that this is an issue with Phenix, not Coot or mmdb. > > Have a look here: > > http://www.wwpdb.org/documentation/format32/sect9.html#TER > > "The serial number of the TER record is one number greater than the > serial number of the ATOM/HETATM preceding the TER" > > Regards, > Paul. > > > > >

1 1

Twinning Refinement
by Joseph Brock 25 Mar '10

25 Mar '10

Dear Phenix Users, I'm currently using version: Version: 1.4 Release tag: 3 cctbx tag: 2008_12_07_1353 Platform: mac-intel-osx osx-10.5.6 I am working on characterising substrate/inhibitor interactions of a protein, the structure has been solved many times so its unit cell dimensions, contents (1 molecule per ASU) and space group (P3121) are well characterized. However, I have recently encountered several crystals that appear exhibit merohedral twinning, and am having trouble converging the R-factors to reasonable levels. The details of one such data set is described below: Diffraction to ~1.9A was recorded using a high and low resolution pass of 180º each. When processed with HKL2000 separately or together, Scalepack wanted to reject huge amounts of my data (~20%). I was forced to increase the error scale factor to 2 and adjust my error model to the very high R-factors of the low-resolution shells. The summary table from my final round of scalepack is: Shell Lower Upper Average Average Norm. Linear Square limit Angstrom I error stat. Chi**2 R-fac R-fac 50.00 4.09 7648.3 1498.7 182.7 1.030 0.376 0.424 4.09 3.25 3885.1 568.9 64.1 1.410 0.416 0.480 3.25 2.84 1609.7 225.0 26.1 1.227 0.451 0.517 2.84 2.58 807.9 97.1 25.3 1.958 0.439 0.561 2.58 2.39 496.6 59.7 22.0 1.060 0.257 0.268 2.39 2.25 335.5 53.0 18.1 0.717 0.275 0.238 2.25 2.14 221.7 19.0 17.4 2.389 0.354 0.298 2.14 2.05 143.1 19.5 17.5 1.537 0.459 0.351 2.05 1.97 87.0 20.2 17.1 1.079 0.663 0.480 1.97 1.90 54.6 20.3 16.7 1.073 0.990 0.696 All reflections 1588.3 269.2 41.9 1.350 0.400 0.444 In addition, many systematic absences appear to be present: Intensities of systematic absences h k l Intensity Sigma I/Sigma 0 0 5 177.7 56.7 3.1 0 0 7 255.5 70.6 3.6 0 0 8 264.8 73.2 3.6 0 0 10 595.0 164.2 3.6 0 0 11 2343.5 1289.9 1.8 0 0 13 321.3 125.4 2.6 0 0 14 66.5 21.8 3.1 0 0 16 238.0 76.3 3.1 0 0 17 394.3 109.1 3.6 0 0 19 13.0 7.1 1.8 0 0 20 650.1 179.5 3.6 0 0 22 199.6 55.6 3.6 0 0 23 953.9 372.0 2.6 0 0 25 192.2 62.2 3.1 0 0 26 1038.7 405.0 2.6 0 0 28 96.3 28.9 3.3 0 0 29 2303.0 897.0 2.6 0 0 31 12.0 11.5 1.0 0 0 32 1622.4 516.5 3.1 0 0 34 11.5 13.8 0.8 0 0 35 22.8 14.8 1.5 0 0 37 27.9 18.0 1.5 0 0 38 154.3 45.6 3.4 0 0 40 55.8 27.8 2.0 0 0 41 35.5 23.7 1.5 0 0 43 -25.3 34.4 -0.7 0 0 44 67.7 32.1 2.1 The data has an overall completeness of 99.7%. When I run the data trough xtriage, it tells me: Statistics depending on twin laws ----------------------------------------------------------------- | Operator | type | R obs. | Britton alpha | H alpha | ML alpha | ----------------------------------------------------------------- | -h,-k,l | M | 0.307 | 0.301 | 0.256 | 0.022 | ----------------------------------------------------------------- Patterson analyses - Largest peak height : 5.288 (corresponding p value : 0.86552) The largest off-origin peak in the Patterson function is 5.29% of the height of the origin peak. No significant pseudotranslation is detected. The results of the L-test indicate that the intensity statistics are significantly different than is expected from good to reasonable, untwinned data. As there are twin laws possible given the crystal symmetry, twinning could be the reason for the departure of the intensity statistics from normality. It might be worthwhile carrying out refinement with a twin specific target function. I also estimated the twin fraction with the following server: http://nihserver.mbi.ucla.edu/Twinning/ And found it to about 20% (using data from 6-3A). After phasing the data with rigid body refinement in Refmac with intensity based twin refinement (brings both R-factors to ~36%), I have tried doing a twin refinement with Phenix: %phenix.refine model.pdb data.mtz twin_law="-h,-k,l" strategy=rigid_body+individual_sites+group_adp The R_factors consistently diverge to the following values: Final R-work = 0.3392, R-free = 0.4360 Simulated annealing/TLS/ordered solvent/messing with wxc/wxu weights does not seem to improve the situation. I have also tried this with and without prior detwinning with the CCP4 program "Detwin", with similar results. Reindexing to -h,-k,l gives similar R-factors after rigid body refinement but after refinement with Phenix, things get even worse: Final R-work = 0.3919, R-free = 0.5059 I was surprised to see that the fit to the map using both indexing conventions are comparable even though this should effectively reverse the hand of the structure. I assume this is because twin refinement is basically doing the job of "partial reindexing" on those parts of the lattice which are twinned? I have been working on this for about a week now and can't for the life of me find a way forward. If anyone can offer any suggestions It would greatly be appreciated. Im slowly beginning to lose my sanity.... BTW I don't think my problems stem from misindexing, although the beam was wondering all over the place during this block of data collection, I have previously solved another structure at the same d and xbeam ybeam values without any trouble. Sorry about the v.long post. Thought it would be better to give too much information rather than not enough =) Many thanks for all your suggestions in advance and for everything I have learned from this community in the past. Cheers, Joe PhD student. _________________________________________________________________ Get personal with Windows. Download a free gift for your PC. http://experience.windows.com

4 4

project defaults ncs.params not read or overridden/overwritten by GUI?
by hari jayaram 25 Mar '10

25 Mar '10

Hi I am quite sure I am doing something wrong , but the refinement seems to always re-determine the NCS definitions despite it being set in the ncs.params file in the project defaults directory. Here is what I did: 1. I set the NCS groups definition in the GUI to go from residues 35:445 , 2. I check that using the view pick . Everything looks fine 3. I click the Green update and exit button 4. I look at the ncs.params file in the project defaults directory and it indeed reflects the changes . 5. I start the refinement from the GUI and the ncs section seems to have been reset to 26:450 . I even tried adding the ncs.params file to the Input files section, but to no avail. The ncs seems to always get re-determined and I end up getting an excessive distance stoppage of refinement. I even made sure I dont have the Find NCS restraints automatically button checked. Any idea why I cannot get the gui run refinement to remember my ncs definitions. Thanks in advance Hari

4 7

FreeR label?
by J. Fleming 24 Mar '10

24 Mar '10

Hello all, I used AutoSol to generate a model from my Se-Met crystal. I then used this output model, overall_best.pdb, for AutoBuild1 in which I extended the data to include a set of native data. At this point I took the exptl_fobs_phases_freeR_flags.mtz output and used it with a different model that I believe to be accurate to carry out AutoBuild2. The problem I'm having is that I can't run Refmac/Phenix refinements on the output from AutoBuild2: overall_best.pdb and overall_best_denmod_map_coeffs.mtz. Both pieces of software say the FreeR labels are missing although in the AutoBuild2 output PDB there is a FreeR test set count of ~2,000. When I list all labels in Refmac I see: F FP P PHIM W FOMM Using these labels doesn't work for refinement. I used default settings for AutoSol/AutoBuild except for the number of Se-Met sites and of course the f' and f'' etc. I'm assuming the problem is with the MTZ but I'm not sure where to troubleshoot. Does anyone have any thoughts? Thanks in advance, Jon

2 1

OS X PowerPC builds
by Ben Eisenbraun 24 Mar '10

24 Mar '10

Hi PHENIXians, I'm updating our nightly build, and I noticed that there are no current builds for OS X PowerPC. Are the PowerPC builds going to be discontinued? I searched the mailing list, but I didn't see an announcement. Thanks. -ben -- | Ben Eisenbraun | Software Sysadmin | | Structural Biology Grid | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |

3 2

Bulk solvent scaling & unstructured protein
by Mads Beich-Frandsen 24 Mar '10

24 Mar '10

Hi all, I have a P1-crystal and data (quite anisotropic to 2.85Å, 90% complete) of a partly unstructured protein, of which some 35% of the sequence is intrinsically unstructured. The structure has been solved by molecular replacement, and it has been refined to Rw/Rf 20/26 with Phenix. As expected, not much of the predicted unstructured region show clear density. The oligomeric protein packs in layers facing oneanother, leaving the unstructured parts 'packing' towards eachother, in what appears as huge solvent-channels. My question is now: Is there an approach to optimizing bulk solvent scaling in Phenix, keeping with the thought, that 30-35% of my protein sequence should be present where Phenix assigns bulk solvent. Thank you! -And any other tricks and tips will much appreciated! Rgds., Mads ------------------------------ Mads Beich-Frandsen Department of Structural and Computational Biology Max F. Perutz Laboratories University of Vienna Campus Vienna Biocenter 5 A-1030 Vienna Austria E-mail: mads.beich-frandsen(a)univie.ac.at Phone: +43-1-4277-52225 Fax: +43-1-4277-9522 Web: http://www.mfpl.ac.at/index.php?cid=58

2 1

where to find phenix.phaser 2.2.3 documentation on keywords
by Bjørn Panyella Pedersen 24 Mar '10

24 Mar '10

Dear list I am struggling to find the documentation for Phaser 2.2.3 (as part of phenix.phaser v1.6.289), and more specifically the list of allowed keywords and what their significance is. In my hands the PACK keyword is no longer allowed in v2.2.3 (works fine in v2.1.4) while two alternatives: SELECT CUTOFF DISTANCE and QUICK are suggested instead. However I cannot find any details on what these do. Ultimately I want to allow packing clashes beyond the default of 10. A google-search only give me hits on the Phaser homepage with documentation for v.2.1 (http://www-structmed.cimr.cam.ac.uk/phaser/documentation/index.html), and the phenix.phaser documentation (http://www.phenix-online.org/documentation/phaser.htm) does not include a keyword-list. Hope somebody can help with this simple problem. Best Bjørn -- Bjørn Panyella Pedersen, PhD Postdoc PUMPKIN, Centre for Membrane Pumps in Cells and Disease University of Aarhus, Dept. Molecular Biology Gustav Wieds Vej 10C DK-8000 Aarhus C, Denmark Phone: +45 89425261 E-mail: bjopp(a)bioxray.au.dk http://www.bioxray.au.dk

3 2

question about autosol
by crystallogrphy 22 Mar '10

22 Mar '10

Hi, When I run phenix.autosol with this scripts (phenix.autosol data=output-anomalous.sca input_phase_file=AutoMR_run_10_/MR.1.mtz input_phase_labels="F PHIC FOM" f_prime=-8.13 f_double_prime=5.61 kp-zntb.seq atom_type=Zn), the job is terminated by the error message. Does anyone know what I should do? I am using Phenix-1.5 version. Floating-point error (Python and libc call stacks above) This crash may be due to a problem in any imported Python module, including modules which are not part of the cctbx project. To disable the traps leading to this message, define these environment variables (e.g. assign the value 1): BOOST_ADAPTBX_FPE_DEFAULT BOOST_ADAPTBX_SIGNALS_DEFAULT This will NOT solve the problem, just mask it, but may allow you to proceed in case it is not critical.

2 1

help with geometry target weight
by Brown, Breann 18 Mar '10

18 Mar '10

I am currently refining a structure at 2.4A resolution. I would like to increase the geometry target weight during refinement, however when I decrease wxc_scale (to 0.25 or 0.1) there is no change in the bond deviations or R factors compared to refinement with the default wxc_scale. I noticed in the refinement logfile under XYZ refinement wc=0. This does not change when I change the wc value in the command line (wc=2.0 for example) as suggested in a previous email. I also see no change when I use the optimize_wxc=true command. Examples of the command line input and output log files are below. I am currently using version 1.6-289 and would appreciate any help in resolving this issue as it seems the geometry is not being properly weighted during refinement. Thanks, Breann Breann L. Brown Department of Molecular Pharmacology, Physiology and Biotechnology Brown University Box GE-3 Providence, RI 02912 >phenix.refine data.mtz model.pdb ligand.cif twin_law strategy=tls+individual_adp tls.params main.ncs=true wxc_scale=0.1 wc=2.0 ========================== Target weights: x-ray data ========================= |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.000000 wxc_scale = 0.100 wc = 0.000 | | angle between x-ray and geometry gradient vectors: None (deg) | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 11.057053 wxu_scale = 2.160 wu = 1.000 | | angle between Xray and ADP gradient vectors: 143.484 (deg) | |-----------------------------------------------------------------------------| ------------------------------------------------------------------------ stage angl bond chir dihe plan repu geom_target 0 : 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 1_bss: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 1_adp: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 2_bss: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 2_adp: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 3_bss: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 3_adp: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 4_bss: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 4_adp: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 5_bss: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 5_adp: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 6_bss: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 6_adp: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 7_bss: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 7_adp: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 8_bss: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 8_adp: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 9_bss: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 9_adp: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 10_bss: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 10_adp: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 10_bss: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 ------------------------------------------------------------------------ Maximal deviations: stage angl bond chir dihe plan repu |grad| 0 : 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 1_bss: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 1_adp: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 2_bss: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 2_adp: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 3_bss: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 3_adp: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 4_bss: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 4_adp: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 5_bss: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 5_adp: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 6_bss: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 6_adp: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 7_bss: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 7_adp: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 8_bss: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 8_adp: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 9_bss: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 9_adp: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 10_bss: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 10_adp: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 10_bss: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 -----Original Message----- From: phenixbb-bounces(a)phenix-online.org [mailto:[email protected]] On Behalf Of Pavel Afonine Sent: Tuesday, February 23, 2010 1:40 PM To: PHENIX user mailing list Subject: Re: [phenixbb] weights optimization, add hydrogens Hi Ursula, > I am refining a 2.0 A structure in Phenix using mostly the graphical > interface. The maps are very good and the R factors are low > (0.208/0.173). But the geometry is not so great with bond deviations > of 0.208 and Angle deviations of 1.85. What is the best thing to do > to try to improve the geometry. Should I try to optimize the weights? the R-factors seem good indeed. Yes, Although the angle deviations seem ok to me, I'm concerned about the bond deviations... Yes, you can try two things: - increase the restraints strength by increasing the corresponding weight: from the command line: "wc=VALUE", where VALUE is a number somewhat larger than 1.0; from the GUI: Refinement settings -> All parameters -> Refinement target weights... -> Stereochemistry weight scale - Run automatic weight optimization (note, this may take a while to run): from the command line: use keyword: "optimize_wxc=true"; from the GUI: Refinement settings -> All parameters -> Refinement target weights... -> Optimize X-ray/stereochemistry weight Alternatively, you can send me your PDB and data file and I will tell you what exactly is not right and how to fix it. Pavel.

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Re: [phenixbb] phenix.simple_ncs_from_pdb output... OMAT?
by Thomas C. Terwilliger 17 Mar '10

17 Mar '10

Hi Francis, No, I don't think it is the same as OMAT format.Here is the format from phenix.simple_ncs_from_pdb (identical to the format from resolve): (Mapping molecule j onto molecule 1) (As input) Operator # 1 New X-prime= 1.0000 X + 0.0000 Y + 0.0000 Z + 0.0000 New Y-prime= 0.0000 X + 1.0000 Y + 0.0000 Z + 0.0000 New Z-prime= 0.0000 X + 0.0000 Y + 1.0000 Z + 0.0000 Approximate center_of_mass of this object (from center_of_mass of object 1 and NC symmetry) is -28.39 18.81 -16.36 Operator # 2 New X-prime= -1.0000 X + -0.0035 Y + -0.0040 Z + -4.1335 New Y-prime= 0.0043 X + -0.1070 Y + -0.9943 Z +-21.6192 New Z-prime= 0.0031 X + -0.9943 Y + 0.1070 Z +-19.2559 Approximate center_of_mass of this object (from center_of_mass of object 1 and NC symmetry) is 24.44 -7.12 -39.79 would be represnted as: rota_matrix 1.0000 0.0000 0.0000 rota_matrix 0.0000 1.0000 0.0000 rota_matrix 0.0000 0.0000 1.0000 tran_orth 0.0000 0.0000 0.0000 center_orth -28.3915 18.8125 -16.3621 rota_matrix -1.0000 -0.0035 -0.0040 rota_matrix 0.0043 -0.1070 -0.9943 rota_matrix 0.0031 -0.9943 0.1070 tran_orth -4.1335 -21.6192 -19.2559 center_orth 24.4419 -7.1171 -39.7930 This is in contrast to OMAT: O/RAVE Format OMAT r11 r21 r31 (note that the rotation matrix is r12 r22 r32 transposed with respect to CCP4 r13 r23 r33 or conventional matrix format) t1 t2 t3 where x' = r11 x + r12 y + r13 z + t1 y' = r21 x + r22 y + r23 z + t2 z' = r31 x + r32 y + r33 z + t3 I hope that helps! -Tom T >> Is the output rota_matrix (x3), and tran_orth(x1) in OMAT format? >> >> Thanks >> >> F >> >> --------------------------------------------- >> Francis Reyes M.Sc. >> 215 UCB >> University of Colorado at Boulder >> >> gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D >> >> 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D >> >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

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phenix.simple_ncs_from_pdb output... OMAT?
by Francis E Reyes 17 Mar '10

17 Mar '10

Is the output rota_matrix (x3), and tran_orth(x1) in OMAT format? Thanks F --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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phenix.refine + metal ions
by Ralf W. Grosse-Kunstleve 17 Mar '10

17 Mar '10

George Phillips wrote: > I second Maia's 'request' to get proper scattering factors into Phenix > for metal ions! Metallobiochemists need love, too. Dear Metalimolbocheists, Available in phenix build 1.6.1-343 or higher. Example: HETATM 711 ZN ZN A1400 -1.928 -11.394 -27.827 1.00 17.21 ZN2+ ^^ Put the charge here To be sure it works, in the phenix.refine output, look for: Number of scattering types: 6 Type Number sf(0) Zn2+ 2 28.00 <<<<<< HERE S 13 16.00 Na 2 11.00 O 240 8.00 N 113 7.00 C 442 6.00 sf(0) = scattering factor at diffraction angle 0. Note: phenix.refine does not infer the charge from the atom name. It has to appear in the PDB charge columns 79-80 as shown above. Ralf

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program to display space group symmetry in three dimensions
by Karthik S 16 Mar '10

16 Mar '10

Hi, I was looking around for programs that display space group symmetry information and could not find any but perhaps i am lost for valuable or relevant keywords. I found two references TABLES and CRYST, but are there other alternatives that are more recent, or that can run on more common hardware? TABLES: http://scripts.iucr.org/cgi-bin/paper?S0021889887086060 CRYST: http://scripts.iucr.org/cgi-bin/paper?S0021889889007168 -- Karthik Graduate student Biophysics, U-M

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Number of atoms and average b-factors for specific chain IDs (with the option of specifying multiple chain IDs).
by Francis E Reyes 15 Mar '10

15 Mar '10

Is there anyway to get this quickly? Either by phenix util, web util, or whatever? Thanks! FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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gtk error
by Rafael Counago 15 Mar '10

15 Mar '10

Dear all, I am running PHENIX on ubunut (karmic koala, 32 bits). On start up I am getting the following message: Gtk-Message: Failed to load module "canberra-gtk-module": libcanberra-gtk-module.so: cannot open shared object file: No such file or directory Any ideas how to solve this issue? Another question... is there a way to automatically search the old messages from the bb? Cheers, Rafael. -- Rafael Couñago Research Fellow Department of Biochemistry University of Otago 710 Cumberland St Dunedin, New Zealand ph: (03) 479 5148

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Gap between R and Rfree
by Young-Jin Cho 13 Mar '10

13 Mar '10

Hi everyone, I recently got a diffraction data and am trying to refine it. The question is whatever I did the gap between R and Rfree stay far away: .2140/.2982 around 2.5 A resolution. (water added and isotropic(individual_adp) and so on). Although I am redoing with many different approaches, if anyone can give me any comments or suggestions, it would be helpful. Thanks in advance, Young-Jin

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Low resolution structure
by Kendall Nettles 13 Mar '10

13 Mar '10

I have a few questions related to a 3.5 angstrom structure. I have one helix that I am having trouble placing accurately. It does have a cysteine that disulfide bonds with the same residue in a symmetry related molecule. Can I restrain this distance during a rigid body refinement of the helix? How do I do this? What kind of parameters would be appropriate for the disulfide? My second question is whether someone can suggest appropriate distance_ideal, sigma, and slack for hydrogen bond restraints for a helix? Also, I have a 2 angstrom structure of this part of the complex for reference. Thanks! Kendall Nettles

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Re: [phenixbb] phenix gui freezes
by John Berrisford 12 Mar '10

12 Mar '10

Dear All Thanks for the suggestions on how to solve my GUI freezing issues. It looks like it was a communication problem with coot that was causing my problems. Editing App.py as below solved my problem. Adding a preference setting to do this would be useful. Thanks again John Message: 3 Date: Thu, 11 Mar 2010 09:48:29 -0500 From: Nathaniel Echols <NEchols(a)lbl.gov> To: PHENIX user mailing list <phenixbb(a)phenix-online.org> Subject: Re: [phenixbb] phenix gui freezes Message-ID: <49B2EAFF-6882-4118-8322-E3949BA490DE(a)lbl.gov> Content-Type: text/plain; charset=us-ascii I have one other thought - the GUI listens on a socket for incoming commands from Coot (this isn't used very much at present). Apparently this caused problems on Linux with the old GUI, which also used Python sockets. If something goes wrong here, it could certainly take down the entire program. To fix this, edit the file $PHENIX/phenix/wxGUI2/App.py, and comment out this line (in 1.6): self.start_xmlrpc_server() (if you're new to python, a comment starts with '#'.) I will add a preferences setting to do this. I can also try slowing down the GUI updates while a process is running (using detached processes should also take care of this). -- John Berrisford Medical Research Council Mitochondrial Biology Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-mbu.cam.ac.uk TEL: +44 (01223) 252918

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naming of refinement runs
by John Berrisford 12 Mar '10

12 Mar '10

Dear All I've been running multiple refinement runs and they are named sequentially. I'm looking for a method to name the refinement runs with the GUI. I understand that I can edit the output file names, but is there anyway to give the refinement runs a title to describe the run as there is in CCP4i? I was thinking along the lines of eg. "Refine_10 - 20 cycles ADP scale 2...." Thanks John -- John Berrisford Medical Research Council Mitochondrial Biology Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-mbu.cam.ac.uk TEL: +44 (01223) 252918

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Custom ligand - confirming the correct scattering definition
by George Phillips 12 Mar '10

12 Mar '10

Pavel, I am following up on this question of the oxidation state of metals. It is important to deal with this properly to get the most out of the data and to able to show difference maps in papers that make sense. Where are the scattering factors stored (it1992's for example)? One could hack an oxidation state in for the standard numbers to get it right (ugly but effective). Alternatively, maybe the scattering factor tables and element id's could be expanded? Is this all hard coded or are there libraries or tables that are parsed? THanks for any comments, as always. George N. Phillips, Jr., Ph.D. Professor of Biochemistry and of Computer Sciences University of Wisconsin-Madison 433 Babcock Dr. Madison, Wi 53706 Phone/FAX (608) 263-6140 Hi Andy, currently phenix.refine will not make difference between say "Fe" and "Fe+2". So if you see some artifacts at mFo-DFc map around your Fe, that might be explained by not taking "+2" into account. Refining occupancy of Fe would fix the map appearance (most likely), but I would not do that, since it will rather hide the problem than properly address it (and of course it would be misleading too). Regarding "n_gaussian table": it is just a dynamic approximation to the standard scattering factor table (mostly done to optimize runtime; the accuracy is not compromised). For more details see: Grosse-Kunstleve RW, Sauter NK, Adams PD: cctbx news Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3:22-31. Pavel. On 11/25/09 12:37 PM, Andy Torelli wrote: > To the Phenix group: > > I've created a .cif file for a ligand that includes metal atoms. The > metal atoms are defined in the .cif file with their element name, but in > actuality, they should be defined according to their oxidation state so > that the correct scattering parameters are used during refinement. > > In CNS, this meant choosing an "atom type" that would be parsed to > match the correct scattering definition listed in the scatter.lib file. > I see that phenix uses the n_gaussian table for scattering values. > Where can I view this and the other scattering table options? Like CNS, > do I just need to use the name of the element with the correct > oxidation state from the table (e.g. "Fe+2") in my .cif file to ensure > that the correct scattering definition is used during refinement and map > calculation? > > Thanks, > -Andy Torelli > > _______________________________________________ > phenixbb mailing list > phenixbb at phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb > Previous message: [phenixbb] Custom ligand - confirming the correct scattering definition Next message: [phenixbb] Confused by the output from Phenix autobuild jobs Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] More information about the phenixbb mailing list George N. Phillips, Jr., Ph.D. Professor of Biochemistry and of Computer Sciences University of Wisconsin-Madison 433 Babcock Dr. Madison, Wi 53706 Phone/FAX (608) 263-6142

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composite omit map command phenix 16
by John Bruning 11 Mar '10

11 Mar '10

Hi, How can I generate a composite omit map from the command line in Phenix16? Thanks, John

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March 15, 2010 deadline- User proposal submission for Collaborative Crystallography at BCSB
by Banumathi Sankaran 11 Mar '10

11 Mar '10

Dear Users, The deadline for May/June 2010 Collaborative Crystallography proposals will be *Mar 15, 2010. * ------------------------------------------------------------------------ Through the Collaborative Crystallography Program (CC) at the Advanced Light Source (ALS), scientists can send protein crystals to Berkeley Center for Structural Biology (BCSB) staff researchers for data collection and analysis. The CC Program can provide a number of benefits to researchers: * Obtain high quality data and analysis through collaborating with expert beamline researchers; * Rapid turn around on projects; and * Reduced travel costs. To apply, please submit a proposal through the ALS General User proposal review process for beamtime allocation. Proposals are reviewed and ranked by the Proposal Study Panel, and beamtime is allocated accordingly. BCSB staff schedule the CC projects on Beamlines 5.0.1 and 5.0.2 to fit into the available resources. Only non-proprietary projects will be accepted. As a condition of participation, BCSB staff researchers who participate in data collection and/or analysis must be appropriately acknowledged - typically being included as authors on publications and in PDB depositions. Please consult the website for additional information at: http://bcsb.als.lbl.gov/wiki/index.php/Collaborative_Crystallography ----------------------------------------------------------------------------------------- How To Apply: To learn more, go to: http://www.als.lbl.gov/als/quickguide/becomealsuser.html To submit a proposal, go to: http://alsusweb.lbl.gov/. Scroll down to "*Structural Biology beamlines (includes protein SAXS)*" and click on "New Proposal." Enter your proposal information, with attention to the following details: * For question 3/First choice, select "5.0.1 (Monochromatic);" for question 3/Second choice, select "5.0.2 (MAD)." * Check box (yes) in response to question (7) "Do you want collaborative crystallography (beamline 5.0.1 or 5.0.2 only) * In question 4, please describe a specific research project with a clear end point. In order to request CC time for May/June 2010 allocation period, proposals must be submitted by *March 15, 2010.* The deadline for CC proposals for the time period July/August 2010 will be May 15, 2010. Regards, Banumathi Sankaran

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does phenix.refine ignore F-obs, SIGF-obs?
by Scott Classen 11 Mar '10

11 Mar '10

Hi All, I have an mtz file that has: I-obs SIGI-obs F-obs SIGF-obs I want phenix.refine to use F-obs and SIGF-obs, but even though I provide : labels = "F-obs,SIGF-obs" I think phenix.refine is seeing the I-obs,SIGI-obs and recalculating the structure factors from those values instead of using the Fs that I provide in the mtz. Is this the case? Other than stripping the I-obs,SIGI-obs from the input mtz, is there a way to force phenix to use my structure factors? Thanks, Scott ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Scott Classen, Ph.D. SIBYLS Beamline 12.3.1 http://bl1231.als.lbl.gov Advanced Light Source Lawrence Berkeley National Laboratory 1 Cyclotron Rd MS6R2100 Berkeley, CA 94720 C) 510.206.4418 O) 510.495.2697 Beamline) 510.495.2134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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phenix gui freezes
by John Berrisford 11 Mar '10

11 Mar '10

Dear All A little while ago I posted a message about the GUI freezing on linux systems, either run remotely (centos) or locally (ubuntu system). I never received a solution and I'm still having this problem despite upgrading to version 1.6. On my ubuntu system the GUI seems to freeze either when the screen saver comes on (set to turn the screen off) or I switch desktop - although not everytime I do this. The freezing GUI means that I have to force quit phenix after every refinement run (I haven't tried other tasks) and that the freeR is not reported to the GUI (not a major problem). Thankfully in version 1.6 the configuration and results for each refinement run are recorded and I can retrieve this information by loading a job through job history - a big improvement over version 1.5. Anyone else having this problem and does anyone know a solution? Thanks John -- John Berrisford Medical Research Council Mitochondrial Biology Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-mbu.cam.ac.uk TEL: +44 (01223) 252918

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Re: [phenixbb] does phenix.refine ignore F-obs, SIGF-obs?
by Scott Classen 11 Mar '10

11 Mar '10

Here are some excerpts from the phenix.refine log file: Resolution range: 44.4024 1.8604 Completeness in resolution range: 0.995991 Completeness with d_max=infinity: 0.995862 Number of F-obs in resolution range: 92411 Number of F-obs <= 0: 3322 Refinement resolution range: d_max = 44.4024 d_min = 1.8604 Fobs statistics after all cutoffs applied: Miller array info: None Observation type: xray.amplitude Type of data: double, size=89089 Type of sigmas: double, size=89089 Number of Miller indices: 89089 Anomalous flag: False Systematic absences: 0 Centric reflections: 11672 Resolution range: 44.4024 1.8604 Completeness in resolution range: 0.960187 Completeness with d_max=infinity: 0.960063 This implies to me that phenix.refine is throwing out my very weak reflections. It appears that completeness goes from 99.6% to 96.0% Then further down in the log file I see: ============================== Outliers rejection ============================= Distribution of F-obs values before outliers rejection: 0.126 - 28.714 : 65519 28.714 - 57.302 : 13850 57.302 - 85.890 : 5625 85.890 - 114.478 : 2515 114.478 - 143.066 : 991 143.066 - 171.654 : 393 171.654 - 200.242 : 128 200.242 - 228.830 : 49 228.830 - 257.418 : 12 257.418 - 286.006 : 7 basic_wilson_outliers = 0 extreme_wilson_outliers = 0 beamstop_shadow_outliers = 0 model_based_outliers = 1 total = 1 Distribution of F-obs values after outliers rejection: 0.126 - 28.714 : 65519 28.714 - 57.302 : 13850 57.302 - 85.890 : 5624 85.890 - 114.478 : 2515 114.478 - 143.066 : 991 143.066 - 171.654 : 393 171.654 - 200.242 : 128 200.242 - 228.830 : 49 228.830 - 257.418 : 12 257.418 - 286.006 : 7 which makes it look like nothing is being rejected? So what is it? in the header of the resulting pdb file: REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.860 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.402 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.03 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.02 REMARK 3 NUMBER OF REFLECTIONS : 89088 which implies that indeed some reflections are being rejected. My hunch is that if F-obs = SIGF-obs then the reflection is rejected. Thanks, Scott

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Re: [phenixbb] phenixbb Digest, Vol 52, Issue 12
by Kay Diederichs 11 Mar '10

11 Mar '10

Am 11.03.2010 23:51, schrieb phenixbb-request(a)phenix-online.org: > Message: 4 > Date: Wed, 10 Mar 2010 16:52:35 -0500 > From: Nathaniel Echols<NEchols(a)lbl.gov> > To: PHENIX user mailing list<phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] autosol interface bug? selinux conflict? > Message-ID:<6BE2BD93-F43C-4D37-AD91-9F31BCE2C6F1(a)lbl.gov> > Content-Type: text/plain; charset=us-ascii > > On Mar 10, 2010, at 4:37 PM, Kay Diederichs wrote: >> > I wonder >> > - why do Fortran binaries give a SElinux problem, and C++ binaries don't? > Because we bundle the Intel Fortran shared libraries (which are required by SOLVE) with the binary installers. > if you simply link with -static-intel then you don't have to distribute those libraries. HTH, Kay

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Additional residue info in coot
by Brown, Breann 11 Mar '10

11 Mar '10

Hello, I am currently refining a model of a zinc-binding protein and after refinement there is additional positive Fo-Fc density at the zinc site. This is the fourth independent structure of this particular protein solved in my lab so we are confident the metal is in fact zinc. I noticed that after refinement the "residue info" in Coot has two lines for the zinc atom. The first line reads "G/121 ZN/ZN 1.00 44.30" while the second line reads G/121 ZN/ 0.00 0.00. The occupancy for the second line cannot be changed and it only appears after refinement. I carried out the same refinement using a previously solved structure of the same protein and the extra residue info line was not present. My question is where does this extra line in the residue info come from and could the zero occupancy be causing additional Fo-Fc density at the metal site? Thanks, Breann Breann L. Brown Page Laboratory Department of Molecular Pharmacology, Physiology and Biotechnology Brown University Providence, RI 02912

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Re: [phenixbb] autosol interface bug? selinux conflict?
by Kay Diederichs 10 Mar '10

10 Mar '10

Am 11.03.2010 07:00, schrieb phenixbb-request(a)phenix-online.org: > Message: 1 > Date: Wed, 10 Mar 2010 09:28:36 -0500 > From: Nathaniel Echols<NEchols(a)lbl.gov> > To: PHENIX user mailing list<phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] autosol interface bug? selinux conflict? > Message-ID:<E0B9BF9F-C96B-4F45-9D02-CC16197AFFF0(a)lbl.gov> > Content-Type: text/plain; charset=us-ascii > > On Mar 9, 2010, at 6:03 PM, Stuart Endo-Streeter wrote: >> After this repetitive route got autosol running, I ran into some kind of >> selinux security warning that blocked autosol and caused it to crash. I >> seem to have fixed that issue by switching temporarily to permissive mode, >> but disabling security to run phenix hardly seems the appropriate solution. >> I didn't manage to catch the autosol error message, I will try to recreate >> it later tonight if needed. > > SELinux breaks the Fortran binaries we distribute. There are two things to try: > > 1. If you installed to /usr/local, try installing to your home directory instead (if this is your computer rather than a shared system). For example: > > computer:~> ./install --prefix=/home/nat/software > > I don't know if this will help or not, but it's worth a try. I wonder - why do Fortran binaries give a SElinux problem, and C++ binaries don't? - does the phenix installer script treat (i.e. label) C++ binaries in any special way which cannot be done for other binaries? If it is known that SElinux is the problem, then this already half of the solution. In general, these problems can easily be found and fixed (on RedHat-derived distros at least) by labelling libraries and binaries in a specific way which is suggested by the output of the SEtroubleshoot- daemon (to be found in /var/log/messages). If that daemon doesn't run, you may have to install it with "yum install setroubleshoot-server". HTH, Kay

2 1

python issues
by Patrick Loll 10 Mar '10

10 Mar '10

Hi, This is really a ccp4-provoked question, but it relates to phaser & cctbx (I think), so I'll try here as well: After an install of ccp4 on a MacBook Pro running Snow Leopard and on a MacPro running Leopard, the command: source /sw*/bin/init.csh (where /sw* is either /sw64 on the machine running 10.6, or /sw on the machine running 10.5) gives the error: ******************************************* Fatal Error: Incomplete libtbx environment! ******************************************* Please re-run the libtbx/configure.py command. If I go to ...ccp4.../src/phaser/phaser-2.1.4/libtbx/ and type python configure.py Then it tells me that the md5 module is deprecated, and that the cool kids use hashlib instead. Does this mean that I need to go to an earlier version of python? Will that mess up other things? Curiously, one machines giving this problem has python 2.5.1, while the other has 2.6. However, I currently have python 2.5.1 running on another machine (albeit with a slightly earlier version of ccp4) and it doesn't give me this problem. Ideas? Thanks, Pat --------------------------------------------------------------------------------------- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pat.loll(a)drexelmed.edu

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Re: [phenixbb] autosol interface bug? selinux conflict?
by Nathaniel Echols 10 Mar '10

10 Mar '10

On Mar 9, 2010, at 6:03 PM, Stuart Endo-Streeter wrote: > Problem is, column labels are selected. "i_obs sigma" is showing in the > label field for each dataset. Clicking on the field to try to re-select > makes no difference, I still get the same error message. If I load just a > single anomalous dataset in addition to the native dataset, usually autosol > will run, sometimes not. It does not matter which anomalous dataset I am > using. If I load the native and only one of the anomalous datasets it > usually works. If I then repeat the process of adding a single anomalous > dataset, running autosol, aborting the run, then adding the next dataset, > eventually I can add all the datasets and start autosol. I'm not sure what to suggest, because I can't reproduce this (with 1.6 or the latest code), nor could I find anything in the code that indicates how it happens. Could you please send me a screenshot of the GUI before you click Run? > After this repetitive route got autosol running, I ran into some kind of > selinux security warning that blocked autosol and caused it to crash. I > seem to have fixed that issue by switching temporarily to permissive mode, > but disabling security to run phenix hardly seems the appropriate solution. > I didn't manage to catch the autosol error message, I will try to recreate > it later tonight if needed. SELinux breaks the Fortran binaries we distribute. There are two things to try: 1. If you installed to /usr/local, try installing to your home directory instead (if this is your computer rather than a shared system). For example: computer:~> ./install --prefix=/home/nat/software I don't know if this will help or not, but it's worth a try. 2. Install from source. This will take several hours, so if you have multiple cores we recommend adding the flag "--nproc=8" (or whatever) when you run the install script. If you have access to the Intel Fortran compiler we recommend installing and configuring that (I think the build script will switch to using it automatically), since g77/gfortran produce binaries that are *much* slower. This problem should go away in a few months when we purge the last FORTRAN code from PHENIX. -------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 NEchols(a)lbl.gov

1 0

autosol interface bug? selinux conflict?
by Stuart Endo-Streeter 09 Mar '10

09 Mar '10

Dear board... I am trying to run autosol with a native dataset and a mad experiment to extend the phases. Unfortunately I cannot even begin the actual process (without some weird convolutions) because phenix keeps giving the following message: "You must select a column label to use in each reflection file. If no labels are shown in the drop-down menu, it may not be a valid format." Problem is, column labels are selected. "i_obs sigma" is showing in the label field for each dataset. Clicking on the field to try to re-select makes no difference, I still get the same error message. If I load just a single anomalous dataset in addition to the native dataset, usually autosol will run, sometimes not. It does not matter which anomalous dataset I am using. If I load the native and only one of the anomalous datasets it usually works. If I then repeat the process of adding a single anomalous dataset, running autosol, aborting the run, then adding the next dataset, eventually I can add all the datasets and start autosol. After this repetitive route got autosol running, I ran into some kind of selinux security warning that blocked autosol and caused it to crash. I seem to have fixed that issue by switching temporarily to permissive mode, but disabling security to run phenix hardly seems the appropriate solution. I didn't manage to catch the autosol error message, I will try to recreate it later tonight if needed. My system is CentOS 5.4, gui is KDE, phenix is v1.6, installed just yesterday. Any suggestions/clues would be appreciated. Stuart Endo-Streeter ________________________________ Stuart Endo-Streeter, Ph.D Dept. Computer Science Duke University Medical Center 3245 French Family Sciences Building 919-660-4018 stuart.endostreeter(a)duke.edu

1 0

anisotropic refinement water hydrogens and gui
by Christian Roth 09 Mar '10

09 Mar '10

Dear all, I did an anisotropic refinement with the gui for a 1.6 Ang. structure I think this is quite O.K. as the R-values seems to be reasonable(14/18.8). But for comparison I want exclude waters and hydrogens explicitly from the anistropic refinement. One could do this in the command line mode via adp.individual.anisotropic ="not water and not element H. I started from the gui and modified the .eff directly by icnluding: adp { individual { isotropic = None anisotropic = "not water and not element H" In the output pdb all waters have an anisou flag. So I assume phenix refined them anisotropically. How do I have to modify the .eff file to exclude the waters from the anisotropic refinement. I would like to use the gui, because you get this nice summary output with all statistics. Phenix started optionally anisotropic refinement at 1.7 Ang. As far as I understand one should keep in mind that the data to parameter ration should have certain value of app. 3 or 4. But restraints as paramters are not as solid as experimental data. Is this 1.7 Ang. borderline a rule of thumb, is there a strict rule at which point I could refine anisotropic, or maybe mixed isotropic anisotropic. Best regards Christian

3 2

phenix.refine and multi-metals centers
by Carlos Frazao 09 Mar '10

09 Mar '10

Hi I have a doubt on the refinement of e doubled metal center. I know that: 1) one may fix the metals to their actual positions by using e.g. refine.sites.individual="not element Fe" 2) one may use "phenix.metal_coordination my.pdb" to obtain a dictionary for the actual metals coordinations but how does phenix.refine handels metal-to-metal interactions? How should one set the refinement of a metallo protein with a two metals centre, in order not to bias the final result (metal to metal distances) ? Thanks a lot, Carlos -- ************************************** Dr. Carlos Frazao Structural Biology Laboratory - Macromolecular Crystallography Unit ITQB-UNL, Av Republica, Apartado 127 2781-901 Oeiras, Portugal Phone: (351)-214469666 FAX: (351)-214433644 e-mail: frazao(a)itqb.unl.pt www.itqb.unl.pt

2 1

molprobity todo list and coot integration in linux
by hari jayaram 09 Mar '10

09 Mar '10

Hi, Is a difference in the way the GUI molprobity TODO list is displayed between linux and Mac OSX . I am running 1.6.289 on both ...and have coot with scheme and python scripting installed, On mac OSX , phenix starts up coot with the molecule and maps loaded after a phenix.validate and a TO-DO list in a separate GUI window In Linux these separate To-do list windows dont seem to open . ..I have looked everywhere and the dont seem burried behind something else, Is there some setting I need to toggle to have these popup , sortable todo lists for molprobity assisted rebuilding on Linux systems? Thanks for your help Hari

2 2

Autosol + MR
by Manoj saxena 07 Mar '10

07 Mar '10

Hi, I have partial solution from MR on a crystal with dimensions 52.729 60.364 142.908 90.00 90.00 90.00 P 21 21 21. I have SAD data from another crystal with dimension 53.860 61.470 142.492 90.00 90.00 90.00 P 21 21 21. My question is can I treat both as isomorphous and combine data from both of them and use my MR as model with Autosol. What is the maximum difference in unit cell dimensions allowed to consider two unit cell isomorphous? If you can point to some references/examples that will be highly appreciated. Thanks a lot. Marusa

2 1

phenix.reduce segmentation fault with -trim option on Snow leopard Mac OSX
by hari jayaram 04 Mar '10

04 Mar '10

Hi I am running the phenix.reduce with the -trim option and getting a segmentation fault with phenix version 1.6.289 I will remove the molprobity introduced hydrogens using pdbtools ..but thought I will write in with this Thanks Hari $ phenix.reduce s3-3_2.1_refmac0-coot-15_refmac0FH.pdb -trim > s3-3_2.1_refmac0-coot-15_refmac0FnoH.pdb reduce: version 3.15 11/6/2009, Copyright 1997-2009, J. Michael Word Processing file: "s3-3_2.1_refmac0-coot-15_refmac0FH.pdb" Segmentation fault

2 1

coot integration require coot with python?
by hari jayaram 03 Mar '10

03 Mar '10

Hi Is it likely that the phenix-coot integration with the new GUI requires a python infused coot ?. Although I have set the coot path correctly nothing happens after coot launches . I am using the ccp4 6.1.3 coot 0.6 (revision 2540) [with guile 1.8.3 embedded] and phenix 1.6.289 on OSX snow leopard 10.6.2. I know the ccp4 coot does not come with python scripting support ...the pymol integration seems fine , but coot just sits there with an empty window after a phenix.validate run. Any ideas on how to have them talking to each other? Thanks Hari

4 5

autosol and NCS
by hli＠uci.edu 03 Mar '10

03 Mar '10

I have solved a structure by MR with Phaser. There are 4 copies of molecules per ASU. Parts of the search model are not agreeable with the new structure leading to messy density in some regions. Now a set of SAD data has been collected. I want to run Autosol (MRSAD) to combine the SAD and model phases, doing density modification including the NCS. Can I run simple_ncs_from_pdb to get the NCS operators from the MR solution pdb file and use them for Autosol? Thanks for help. Huiying UC Irvine

2 1

Phaser phasing power statistics
by Daqi Tu 03 Mar '10

03 Mar '10

Hi, I was trying to find phasing power statistics from phenix.autosol log file but couldn't. My structure was phased by Phaser SAD module in phenix.autosol, all I could find was figure of merit. I then ran Phaser SAD within CCP4 and still could not find phasing power statistics from its log. Does anyone know if Phaser SAD generates phasing power statistics in its log file at all? Thanks. Daqi Tu Postdoc Eck lab Harvard medical school

2 1

SAD + Xray = ???
by J. Fleming 02 Mar '10

02 Mar '10

Hi, I have a set of Se-Met SAD data, high resolution x-ray data, and a protein sequence. Is there a way to combine these data sets in Phenix and carry out an autobuild? I saw a section in the manual about MRSAD but that requires a starting model. I've used the SAD data alone to generate a model but I'd like to use both data sets together. Thanks for your thoughts, -Jon

2 1

ICCBM13 - Call for abstracts now open!
by Valerie Pye 02 Mar '10

02 Mar '10

Apologies for this being off topic - but may be of general interest: * * * * *13th International Conference on the Crystallisation of Biological Macromolecules* Trinity College Dublin, Ireland 12th – 16th September 2010 *Crystallization Workshop* – 9th – 12th September 2010 Call for Abstracts Now Open <http://www.iccbm13.ie/abstracts.html> The *13th International Conference on the Crystallisation of Biological Macromolecules* (*ICCBM13 <http://www.iccbm13.ie/>*) is the meeting of choice to learn about the latest research and developments in biomacromolecular crystallogenesis for structure-function-rational design applications. At ICCBM13 leading academic and pharmaceutical scientists will report on challenging systems to include macromolecular complexes and membrane proteins with an emphasis on novel practical as well as mechanistic aspects of crystallogenesis. To cater to the needs of the individual wanting to learn how to grow crystals or to acquire new crystallisation skills, the Conference is preceded by a *Workshop <http://www.iccbm13.ie/workshop.html>* devoted to hands-on instruction on select aspects of macromolecule production and crystal growth. The Conference will be held at *Trinity College Dublin <http://www.tcd.ie/>, Ireland* from the 12th to the 16th September 2010. Convenient and affordable housing is available on and around Trinity College. The campus is situated in the heart of Ireland’s capital city and is surrounded by a diversity of restaurants, pubs, theatres and other points of interests. *Scholarships <http://www.iccbm13.ie/scholarships.html>* are available to Graduate Students and Postdoctoral Fellows. Additional information is available at *www.iccbm13.ie* *ICCBM13 Congress Secretariat* T: + 353 (0) 1 400 3626 F: + 353 (0) 1 400 3692 E: info(a)iccbm13.ie W: www.iccbm13.ie *C/O Keynote PCO* Suite 26, Anglesea House, Blackrock Co. Dublin, Ireland www.keynotepco.ie

1 0

twin refinement
by subhash bihani 02 Mar '10

02 Mar '10

Hi i am refining a protein strucutre with space group P61. Intesity statistics doesnot suggest any twining but refmac and phenix xtriage suggest a twin operator with fraction 0.48. when refined with this twin operator R factors come dowm by 3-5% and also map looks much better. but upon closer inspceion it seems that maps are heavily biased toward the model in both refmac and phenix ( I have mutated one lysine to his and it changed the map to cover his). my question is why twin refinement maps are biased and what are the ways to overcome this. my second question is how to decide whether to use twin refinement or not. is it depends on R factor statistics or we have to check some other parameters. thanks in advance subhash bihani scientific officer Bhabha Atomic Research Centre Trombay-400085 Mumbai(M.S.) India Ph. +912594688 (o) +919322191020 -- Subhash Bihani Scientific Officer Solid State Physics Division Bhabha Atomic Research Centre Trombay, Mumbai-85 Ph. 25594688 (o) alternate email: subhashbihani(a)yahoo.co.in

2 1

NCS restraints
by Mirek Cygler 28 Feb '10

28 Feb '10

Hi, I have NCS symmetry in my crystal and wouldlike to use it during the refinement. What is the strength of the restraints for the backbone, for the sidechains? How can I control these restraints? Thanks, Mirek

3 2

Clarification on ADPs in PDB files for TLS refinement ?
by Phil Jeffrey 27 Feb '10

27 Feb '10

Hi, Having a discussion with a colleague yesterday on differences in Phenix and Refmac representations of TLS B-factors in the PDB file I came across two different definitions for what the PDB ANISOU U's correspond to as written by Phenix: 1. From necat.chem.cornell.edu/workshops/.../WK04_PavelAfonine.pdf on p.20 U(TOTAL)= U(ATOM) + U(TLS) + U(CRYST) and only U(atom) + U(tls) is stored in the PDB ANISOU card. 2. From http://proteincrystallography.org/ccp4bb/message8948.html "Utotal = Utls + Ulocal + Ucryst. So, the ANISOU records always contain Utotal and ATOM records contain isotropic equivalent of Utotal" Which is not the same thing. I suspect it's #1. Am I right ? I would think that U(cryst) is potentially a non-zero contribution to atomic ANISOU values but is actually applied before the TLS/Anisotropic B-factors are refined. As a tie-breaker between #1 and #2 the program documentation suggest that it is just U(tls)+U(atom) but the paragraph that nominally explains it is not short of of inconsistencies, referring to the ANISOU record as having the "the total B-factor (B_tls + B_individual)" whereas they're not only not B's (they are U's) but it's also not the *total* U or B by its own definitions. IMHO it would warrant a rewrite for clarity since B and U are used interchangeably and "total" has variable usage. Phil Jeffrey Princeton

5 5

Re: [phenixbb] Map after refinement
by Xuewu Zhang 26 Feb '10

26 Feb '10

To Paul, No, I used the mtz format map file in coot. TO Pavel, I will send you the files tomorrow. The command I used is the simplest one: phenix.refine input.pdb input.mtz. By the way, the same thing happened to one of my colleagues here a while ago. She solved the problem by updating to the then new 1.5 version. Thanks you guys for the quick replies. Xuewu Zhang UT Southwestern Medical Center On Fri, Feb 26, 2010 at 4:29 PM, <phenixbb-request(a)phenix-online.org> wrote: > Send phenixbb mailing list submissions to > phenixbb(a)phenix-online.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://phenix-online.org/mailman/listinfo/phenixbb > or, via email, send a message with subject or body 'help' to > phenixbb-request(a)phenix-online.org > > You can reach the person managing the list at > phenixbb-owner(a)phenix-online.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of phenixbb digest..." > > > Today's Topics: > > 1. Int'l Workshop on Macromolecular Crystallography - South > America (Alejandro Buschiazzo) > 2. Re: Gap between R and Rfree (Felix Frolow) > 3. Re: Map after refinement (Xuewu Zhang) > 4. Re: Map after refinement (Paul Adams) > 5. Re: Map after refinement (Pavel Afonine) > 6. weaker density in maps (David Garboczi) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 26 Feb 2010 18:17:06 -0200 > From: Alejandro Buschiazzo <alebus(a)pasteur.edu.uy> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: [phenixbb] Int'l Workshop on Macromolecular Crystallography - > South America > Message-ID: <4B882C42.9080701(a)pasteur.edu.uy> > Content-Type: text/plain; charset=windows-1252; format=flowed > > Dear colleagues, > > just a reminder, we're close to the deadline for applications. Details > below. > > Thank you! > > > ----------------------------------------------------------------------------------------------------------------------- > > *International Workshop ?Macromolecular Crystallography : Introduction > and Applications"* > > *April 26 - May 7, 2010* > > *Institut Pasteur de Montevideo* > > *Uruguay* > > The principal aim of this course, is to give intense hands-on training > in all main aspects of macromolecular 3D structure determination by X > ray diffraction. > > The course will include lectures delivered by a number of > international experts in the discipline, linked to hands-on > experimental work and demonstrations. > > Special emphasis will be given to : > > * Experiment design : manual and robotic crystallogenesis of > macromolecules, X ray diffraction of single crystals, data collection > * Diffraction data processing > * Model refinement and structural analysis > > > *ACTIVITY INTENDED FOR* > > * Graduate Students (MSc and PhD) > * Postdocs > * Young Research Scientists > > > *APPLICATION REQUIREMENTS* > > Candidates should send the following information : > > 1. -Short CV (including age, current position, scientific interests, > publications) > 2. -Letter of motivation (the applicant should stress how > Macromolecular Crystallography is included in her/his ongoing > scientific project) > 3. -Reference letter from the apllicant's supervisor > > > *SCHOLARSHIPS* > > Inscription fees are fully covered for all accepted students. > Applicants from abroad with no financial support, are welcome to apply > for a lodging and per diem expenses scholarship. This should be > inlcuded as a separate document at the time of application. A limited > number of traveling aids will be available: arguments backing this > request should be duly explained, to be evaluated on a case by case > basis. > > *APPLICATION DEADLINE* > > All applications should be received until March 7 2010. They should be > sent as a single pdf document to : crystallography(a)pasteur.edu.uy > > *ORGANIZERS* > > Dr. Alejandro Buschiazzo > Unidad de Cristalograf?a de Prote?nas > Institut Pasteur de Montevideo > > Dr. Pedro Alzari > Departamento de Biolog?a Estructural y Qu?mica > Institut Pasteur de Paris > > Dr. William Shepard > Proxima 2 > Synchrotron Soleil > > For further information, please E-mail to crystallography(a)pasteur.edu.uy > > The official language of the course will be english. > > Detailed information is available at: > http://www.pasteur.edu.uy/mxcourse Please check for regular updates of > the program. > > *FUNDING* > > RIIP, AMSUD/PASTEUR, IP MONTEVIDEO (URUGUAY INNOVA), CeBEM > > This International Workshop is part of the activities of the Center of > Structural Biology of Mercosur (Centro de Biolog?a Estructural del > Mercosur - CeBEM) > > > > > -- > Alejandro Buschiazzo, PhD > Research Scientist > Laboratory of Protein Crystallography > Pasteur Institute of Montevideo > Mataojo 2020 > Montevideo 11400 > URUGUAY > > Phone: +5982 5220910 int. 120 > Fax: +5982 5224185 > > > > ------------------------------ > > Message: 2 > Date: Fri, 26 Feb 2010 22:18:33 +0200 > From: Felix Frolow <mbfrolow(a)post.tau.ac.il> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] Gap between R and Rfree > Message-ID: <F52C4FE8-AE34-4C23-B74E-A923995E5831(a)post.tau.ac.il> > Content-Type: text/plain; charset=us-ascii > > Yea Phil, You have got them > I was accused several years ago for over-fitting Rfree !!!!!!! > The bad thing is that to publish you have to avoid arguing with these > post-crystallography era referees. > Today they ask meaningless question " I am novice to crystallography, teach > me how to minimize Rfree" > Tomorrow they referee you papers and make meaningless remarks about gap > between R and Rfree > " Your R factor is 17% and Rfree is 24%, it rase question" > geeeeek!!!!!! what question????? > Dr Felix Frolow > Professor of Structural Biology and Biotechnology > Department of Molecular Microbiology > and Biotechnology > Tel Aviv University 69978, Israel > > Acta Crystallographica D, co-editor > > e-mail: mbfrolow(a)post.tau.ac.il > Tel: ++972 3640 8723 > Fax: ++972 3640 9407 > Cellular: ++972 547 459 608 > > On Feb 26, 2010, at 11:30 , Phil Evans wrote: > > > > > I do worry a bit about the fetishisation of R-factors, to the point where > I get the impression that some people think that the object of refinement is > minimisation of Rfree. The aim is to produce the "best" model consistent > with the data, and the most important tool is looking at the maps on the > graphics, in conjunction with validation tools analysing consistency with > what we know about stereochemistry (Ramachandran, rotamers, bumps etc). Also > is your model consistent with your initial experimental phased map, if > available? The Rfree is a useful guide, but no more than that. > > > > My (admittedly superficial) experience of changing weights, freeR > selection, resolution limits, NCS, etc in refinement is that often you can > spend some time doing this, maybe improve the R-factors a bit, but end up > with a model which is indistinguishable from the previous model when > superimposed on it. > > > > I'm fed up with referees telling me my structure must be wrong because > the Rfree is "too high" (and I haven't followed their particular pet > protocol), when I know that it is essentially correct, and as good as I can > make it. > > > > Phil > > > > > > On 26 Feb 2010, at 01:49, Pavel Afonine wrote: > > > >> Hi Simon, > >> > >> the next available PHENIX nightly build will have this command: > >> > >> phenix.r_factor_statistics > >> > >> This will output a plain text histograms for Rwork, Rfree and > Rfree-Rwork. For example: > >> > >> *** > >> phenix.r_factor_statistics 2.5 left_offset=0.2 right_offset=0.2 n_bins=5 > >> Command used: > >> > >> phenix.r_factor_statistics 2.500 left_offset=0.200 right_offset=0.200 > n_bins=5 > >> > >> > >> Histogram of Rwork for models in PDB at resolution 2.30-2.70 A: > >> 0.115 - 0.168 : 149 > >> 0.168 - 0.220 : 2998 > >> 0.220 - 0.273 : 1879 > >> 0.273 - 0.325 : 67 > >> 0.325 - 0.378 : 2 > >> Histogram of Rfree for models in PDB at resolution 2.30-2.70 A: > >> 0.146 - 0.210 : 116 > >> 0.210 - 0.274 : 3288 > >> 0.274 - 0.337 : 1664 > >> 0.337 - 0.401 : 26 > >> 0.401 - 0.465 : 1 > >> Histogram of Rfree-Rwork for all model in PDB at resolution 2.30-2.70 A: > >> 0.001 - 0.021 : 233 > >> 0.021 - 0.041 : 1412 > >> 0.041 - 0.060 : 2180 > >> 0.060 - 0.080 : 1045 > >> 0.080 - 0.100 : 225 > >> Number of structures considered: 5095 > >> *** > >> > >> and running it without arguments will take all structures. > >> > >> Pavel. > >> > >> > >> > >> On 2/25/10 2:01 PM, Simon Kolstoe wrote: > >>> oh yes please Pavel (command line polygon/statistics overview) - could > the output be a pdf or ps rather than just starting up the GUI? > >>> > >>> Simon > >>> > >>> > >>> > >>> On 25 Feb 2010, at 19:39, Pavel Afonine wrote: > >>> > >>>> Hi Francis, > >>>> > >>>> in PHENIX GUI: "Validation" -> "PDB Statistics Overview" > >>>> > >>>> or: > >>>> > >>>> in PHENIX GUI: "Validation" -> "POLYGON" > >>>> > >>>> The underlying idea is published here: > >>>> > >>>> Crystallographic model quality at a glance. L. Urzhumtseva, P. V. > Afonine, P. D. Adams, A. Urzhumtsev Acta Cryst. D65, 297-300 (2009) > >>>> > >>>> I can add a command line version if anyone is interested. > >>>> > >>>> Pavel. > >>>> > >>>> > >>>> > >>>> On 2/25/10 9:45 AM, Francis E Reyes wrote: > >>>>> Pavel > >>>>> > >>>>> What phenix utility produces such information? > >>>>> Thx > >>>>> > >>>>> FR > >>>>> > >>>>> On Feb 25, 2010, at 10:43 AM, Pavel Afonine <PAfonine(a)lbl.gov> > wrote: > >>>>> > >>>>>> Hi Young-Jin, > >>>>>> > >>>>>> the distribution of R-factors for all structures in PDB refined at > resolutions between 2.4 and 2.6 A is following: > >>>>>> > >>>>>> Histogram of Rwork for all model in PDB at resolution 2.40-2.60: > >>>>>> 0.115 - 0.141 : 5 > >>>>>> 0.141 - 0.168 : 69 > >>>>>> 0.168 - 0.194 : 414 > >>>>>> 0.194 - 0.220 : 955 <<<<< your structure > >>>>>> 0.220 - 0.246 : 695 > >>>>>> 0.246 - 0.273 : 153 > >>>>>> 0.273 - 0.299 : 25 > >>>>>> 0.299 - 0.325 : 5 > >>>>>> 0.325 - 0.352 : 0 > >>>>>> 0.352 - 0.378 : 1 > >>>>>> Histogram of Rfree for all model in PDB at resolution 2.40-2.60: > >>>>>> 0.146 - 0.178 : 3 > >>>>>> 0.178 - 0.210 : 41 > >>>>>> 0.210 - 0.242 : 404 > >>>>>> 0.242 - 0.274 : 1104 > >>>>>> 0.274 - 0.305 : 653 <<<<< your structure > >>>>>> 0.305 - 0.337 : 108 > >>>>>> 0.337 - 0.369 : 8 > >>>>>> 0.369 - 0.401 : 0 > >>>>>> 0.401 - 0.433 : 0 > >>>>>> 0.433 - 0.465 : 1 > >>>>>> Histogram of Rfree-Rwork for all model in PDB at resolution > 2.40-2.60: > >>>>>> 0.002 - 0.012 : 28 > >>>>>> 0.012 - 0.022 : 83 > >>>>>> 0.022 - 0.031 : 232 > >>>>>> 0.031 - 0.041 : 430 > >>>>>> 0.041 - 0.051 : 458 > >>>>>> 0.051 - 0.061 : 493 > >>>>>> 0.061 - 0.071 : 298 > >>>>>> 0.071 - 0.080 : 186 > >>>>>> 0.080 - 0.090 : 85 <<<<< your structure > >>>>>> 0.090 - 0.100 : 29 > >>>>>> > >>>>>> which I interpret as your Rwork is most likely good as well as > Rfree, but the gap Rfree-Rwork is too large meaning possible overfitting. > >>>>>> > >>>>>> A few tips: > >>>>>> - if you have NCS - use it in refinement; > >>>>>> - optimize refinement target weights: a) automatically: > "optimize_wxc=true optimize_wxu=true", or b) manually using wxc_scale and > wxu_scale parameters; > >>>>>> - make sure you use the latest PHENIX version. > >>>>>> > >>>>>> Let me now if you have any questions. > >>>>>> > >>>>>> Pavel. > >>>>>> > >>>>>> > >>>>>> On 2/25/10 9:17 AM, Young-Jin Cho wrote: > >>>>>>> Hi everyone, > >>>>>>> I recently got a diffraction data and am trying to refine it. The > question is whatever I did the gap between R and Rfree stay far away: > .2140/.2982 around 2.5 A resolution. (water added and > isotropic(individual_adp) and so on). > >>>>>>> Although I am redoing with many different approaches, if anyone can > give me any comments or suggestions, it would be helpful. > >>>>>>> > >>>>>>> Thanks in advance, > >>>>>>> > >>>>>>> Young-Jin > >>>>>>> > >>>>>>> > >>>>>>> _______________________________________________ > >>>>>>> phenixbb mailing list > >>>>>>> phenixbb(a)phenix-online.org > >>>>>>> http://phenix-online.org/mailman/listinfo/phenixbb > >>>>>>> > >>>>>> _______________________________________________ > >>>>>> phenixbb mailing list > >>>>>> phenixbb(a)phenix-online.org > >>>>>> http://phenix-online.org/mailman/listinfo/phenixbb > >>>>> _______________________________________________ > >>>>> phenixbb mailing list > >>>>> phenixbb(a)phenix-online.org > >>>>> http://phenix-online.org/mailman/listinfo/phenixbb > >>>> _______________________________________________ > >>>> phenixbb mailing list > >>>> phenixbb(a)phenix-online.org > >>>> http://phenix-online.org/mailman/listinfo/phenixbb > >>> > >>> _______________________________________________ > >>> phenixbb mailing list > >>> phenixbb(a)phenix-online.org > >>> http://phenix-online.org/mailman/listinfo/phenixbb > >> _______________________________________________ > >> phenixbb mailing list > >> phenixbb(a)phenix-online.org > >> http://phenix-online.org/mailman/listinfo/phenixbb > > > > _______________________________________________ > > phenixbb mailing list > > phenixbb(a)phenix-online.org > > http://phenix-online.org/mailman/listinfo/phenixbb > > > > ------------------------------ > > Message: 3 > Date: Fri, 26 Feb 2010 14:31:26 -0600 > From: Xuewu Zhang <xuewu.zhang(a)gmail.com> > To: phenixbb(a)phenix-online.org > Subject: Re: [phenixbb] Map after refinement > Message-ID: > <926abad51002261231g71b81d30o48b7ab63f41ba820(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Phenix developers/gurus, > I got a SAD structure, the experimental map (overall_best_denmod..mtz) from > Autosol looks great. I then built the model and used phenix.refine to > refine > the model using the "exptl_fobs....mtz", which worked well as shown by the > lowered Rfree. However, the map from the refinement makes no sense at all, > totally featureless. Using the same refined model and mtz, > phenix.model_vs_data did make the right map. I have tried both phenix 1.5 > and 1.6. Any clue? > Thanks, > Xuewu Zhang > UT Southwestern Medical Center >

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Re: [phenixbb] Map after refinement
by Xuewu Zhang 26 Feb '10

26 Feb '10

Hi Phenix developers/gurus, I got a SAD structure, the experimental map (overall_best_denmod..mtz) from Autosol looks great. I then built the model and used phenix.refine to refine the model using the "exptl_fobs....mtz", which worked well as shown by the lowered Rfree. However, the map from the refinement makes no sense at all, totally featureless. Using the same refined model and mtz, phenix.model_vs_data did make the right map. I have tried both phenix 1.5 and 1.6. Any clue? Thanks, Xuewu Zhang UT Southwestern Medical Center

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Int'l Workshop on Macromolecular Crystallography - South America
by Alejandro Buschiazzo 26 Feb '10

26 Feb '10

Dear colleagues, just a reminder, we're close to the deadline for applications. Details below. Thank you! ----------------------------------------------------------------------------------------------------------------------- *International Workshop “Macromolecular Crystallography : Introduction and Applications"* *April 26 - May 7, 2010* *Institut Pasteur de Montevideo* *Uruguay* The principal aim of this course, is to give intense hands-on training in all main aspects of macromolecular 3D structure determination by X ray diffraction. The course will include lectures delivered by a number of international experts in the discipline, linked to hands-on experimental work and demonstrations. Special emphasis will be given to : * Experiment design : manual and robotic crystallogenesis of macromolecules, X ray diffraction of single crystals, data collection * Diffraction data processing * Model refinement and structural analysis *ACTIVITY INTENDED FOR* * Graduate Students (MSc and PhD) * Postdocs * Young Research Scientists *APPLICATION REQUIREMENTS* Candidates should send the following information : 1. -Short CV (including age, current position, scientific interests, publications) 2. -Letter of motivation (the applicant should stress how Macromolecular Crystallography is included in her/his ongoing scientific project) 3. -Reference letter from the apllicant's supervisor *SCHOLARSHIPS* Inscription fees are fully covered for all accepted students. Applicants from abroad with no financial support, are welcome to apply for a lodging and per diem expenses scholarship. This should be inlcuded as a separate document at the time of application. A limited number of traveling aids will be available: arguments backing this request should be duly explained, to be evaluated on a case by case basis. *APPLICATION DEADLINE* All applications should be received until March 7 2010. They should be sent as a single pdf document to : crystallography(a)pasteur.edu.uy *ORGANIZERS* Dr. Alejandro Buschiazzo Unidad de Cristalografía de Proteínas Institut Pasteur de Montevideo Dr. Pedro Alzari Departamento de Biología Estructural y Química Institut Pasteur de Paris Dr. William Shepard Proxima 2 Synchrotron Soleil For further information, please E-mail to crystallography(a)pasteur.edu.uy The official language of the course will be english. Detailed information is available at: http://www.pasteur.edu.uy/mxcourse Please check for regular updates of the program. *FUNDING* RIIP, AMSUD/PASTEUR, IP MONTEVIDEO (URUGUAY INNOVA), CeBEM This International Workshop is part of the activities of the Center of Structural Biology of Mercosur (Centro de Biología Estructural del Mercosur - CeBEM) -- Alejandro Buschiazzo, PhD Research Scientist Laboratory of Protein Crystallography Pasteur Institute of Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +5982 5220910 int. 120 Fax: +5982 5224185

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