- phenixbb - phenix-online.org

PHENIX refine: detached sidechain atoms
by Oliver King 25 Jun '10

25 Jun '10

Hi All, I've noticed that when refining a model in phenix.refine using a PDB file from Refmac, the sidechain atoms of certain residues become detached from the rest of the molecule and appear to float on their own, at least when viewing in Coot. I think this is down to the format of the PDB file. For example the atoms of a Leu residue from a phenix.refine file which displays well is of the form: ATOM 1 N LEU A 8 50.022 -34.247 -5.817 1.00 58.12 N ATOM 2 CA LEU A 8 49.788 -34.905 -4.539 1.00 55.84 C ATOM 3 C LEU A 8 48.339 -35.358 -4.348 1.00 60.39 C ATOM 4 O LEU A 8 48.008 -36.016 -3.360 1.00 68.40 O ATOM 5 CB LEU A 8 50.219 -34.011 -3.373 1.00 57.98 C ATOM 6 CG LEU A 8 51.690 -34.126 -2.975 1.00 65.66 C ATOM 7 CD1 LEU A 8 52.014 -33.170 -1.836 1.00 59.99 C ATOM 8 CD2 LEU A 8 52.020 -35.566 -2.594 1.00 68.57 C where as from a Refmac PDB which also behaves well, it is of the form: ATOM 1 N LEU A 8 50.453 -35.722 -5.617 1.00 20.00 N ATOM 2 CA LEU A 8 49.649 -35.131 -4.482 1.00 20.00 C ATOM 3 CB LEU A 8 50.190 -33.735 -4.147 1.00 20.00 C ATOM 4 CG LEU A 8 51.461 -33.755 -3.275 1.00 20.00 C ATOM 5 CD1 LEU A 8 52.556 -32.768 -3.741 1.00 20.00 C ATOM 6 CD2 LEU A 8 51.082 -33.546 -1.799 1.00 20.00 C ATOM 7 C LEU A 8 48.166 -35.063 -4.824 1.00 20.00 C ATOM 8 O LEU A 8 47.822 -34.257 -5.568 1.00 20.00 O but after refinement in phenix it becomes ATOM 1 N LEU A 8 50.734 -35.936 -5.935 1.00 54.45 N ATOM 2 CA LEU A 8 49.846 -35.185 -4.892 1.00 51.89 C ATOM 3 CB LEU A 8 50.377 -33.761 -4.516 1.00 51.22 C ATOM 4 CG LEU A 8 51.550 -33.730 -3.431 1.00 59.27 C ATOM 5 CD1 LEU A 8 52.457 -32.407 -3.635 1.00 60.88 C ATOM 6 CD2 LEU A 8 51.120 -34.090 -1.879 1.00 55.50 C ATOM 7 C LEU A 8 48.268 -35.042 -5.221 1.00 47.92 C ATOM 8 O LEU A 8 47.989 -34.282 -6.195 1.00 47.32 O and the CD2 atom is now too far away to be part of the residue in Coot Is there an easy way to convert a PDB from Refmac into one which will behave itself when put through phenix.refine? I've tried using phenix.pdb_tools and also putting the model through Molprobity and hoping that that the output would be corrected. Thanks, Olly King

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Defining planarity for Phenix.refine
by Peter Grey 23 Jun '10

23 Jun '10

Dear all, I have an RNA/Protein big complex at low resolution (roughly 4A). I would like to have the base pairs in the RNA as close as possible to ideal base pairs. I added restraints for distances between base pair hydrogen-bonding atoms but this is not enough to ensure that the bases will be in the same plane. Could you suggest how to define for Phenix.refine this planarity ? I am grateful for your advice, Peter

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Re: [phenixbb] AutoMR:Multi-subunit model
by S. Saif Hasan 22 Jun '10

22 Jun '10

Hello, Thanks. When I use the PDB structure with 8 polypeptides as the search model and specify the 8 sequences together, I get this warning from AutoMR- "ASYMMETRIC UNIT TOO FULL (scattering from ensembles =1.82 of total scattering)- TOTAL SCATTERING INCREASED: To get rid of this warning message do one of the following: (1) Increasing the scattering in the ASU (keyword COMPOSITION) because you have more scattering than you thought (2) Decrease the number of ensembles you are packing into the ASU (keywords SOLUTION and SEARCH)" Could this be a problem in missing some additional prosthetic groups ? I did not specify any non-protein groups but the search model has them. -- S. Saif Hasan Graduate Student Department of Biological Sciences Hockmeyer Hall of Structural Biology Purdue University 240 S. Martin Jischke Drive West Lafayette, IN 47907 Quoting "Thomas C. Terwilliger" <terwilliger(a)lanl.gov>: > Hi Saif, > > If I understand you correctly, you can specify the search model with 8 > polypeptides as one PDB file and all 8 sequences (separated by blank lines > or lines starting with ">" in one sequence file. Also component 1 can be > all 8 polypeptides and copies=1. > > All the best, > Tom T > > >> Hello, > >> > >> I have a membrane protein complex made up of 8 different polypeptides > >> present in > >> two copies each (16mer). The asymmetric unit is the octamer, as > determined > >> from > >> previous crystallographic studies. To carry out molecular replacement > with > >> the > >> phases from the published structure in AutoMR, should I specify the > >> coordinates > >> of the search model and its overall sequence identity as one file or > >> should I > >> break it down for each subunit ? Also, for the asymmetric unit contents, > >> should > >> I specify the sequence or mass of each subunit separately (as component > 1, > >> 2 and > >> so on) keeping the number of copies fixed at 1 ? There is no NCS. > >> > >> Thanks. > >> -- > >> S. Saif Hasan > >> > >> Graduate Student > >> Department of Biological Sciences > >> Hockmeyer Hall of Structural Biology > >> Purdue University > >> 240 S. Martin Jischke Drive > >> West Lafayette, IN 47907 > >> > >> > >> > >> > >> > >> _______________________________________________ > >> 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 >

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AutoMR:Multi-subunit model
by S. Saif Hasan 22 Jun '10

22 Jun '10

Hello, I have a membrane protein complex made up of 8 different polypeptides present in two copies each (16mer). The asymmetric unit is the octamer, as determined from previous crystallographic studies. To carry out molecular replacement with the phases from the published structure in AutoMR, should I specify the coordinates of the search model and its overall sequence identity as one file or should I break it down for each subunit ? Also, for the asymmetric unit contents, should I specify the sequence or mass of each subunit separately (as component 1, 2 and so on) keeping the number of copies fixed at 1 ? There is no NCS. Thanks. -- S. Saif Hasan Graduate Student Department of Biological Sciences Hockmeyer Hall of Structural Biology Purdue University 240 S. Martin Jischke Drive West Lafayette, IN 47907

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secondary restraints
by Jianghai Zhu 21 Jun '10

21 Jun '10

Hi, I am using secondary restraints in the phenix.refine. I got the following error message. hydrogen_bonds_from_selections: incomplete non-PRO residues in helix. "(chain 'A' and resseq 141:143) and (altloc 'A' or altloc ' ') and name H" => 0 donors "(chain 'A' and resseq 141:143) and (altloc 'A' or altloc ' ') and name O" => 3 acceptors hydrogen_bonds_from_selections: incomplete non-PRO residues in helix. "(chain 'A' and resseq 160:162) and (altloc 'A' or altloc ' ') and name H" => 0 donors "(chain 'A' and resseq 160:162) and (altloc 'A' or altloc ' ') and name O" => 3 acceptors hydrogen_bonds_from_selections: incomplete non-PRO residues in helix. "(chain 'A' and resseq 242:244) and (altloc 'A' or altloc ' ') and name H" => 0 donors "(chain 'A' and resseq 242:244) and (altloc 'A' or altloc ' ') and name O" => 3 acceptors hydrogen_bonds_from_selections: incomplete non-PRO residues in helix. "(chain 'A' and resseq 360:363) and (altloc 'A' or altloc ' ') and name H" => 0 donors "(chain 'A' and resseq 360:363) and (altloc 'A' or altloc ' ') and name O" => 4 acceptors hydrogen_bonds_from_selections: incomplete non-PRO residues in helix. "(chain 'A' and resseq 387:389) and (altloc 'A' or altloc ' ') and name H" => 0 donors "(chain 'A' and resseq 387:389) and (altloc 'A' or altloc ' ') and name O" => 3 acceptors hydrogen_bonds_from_selections: incomplete non-PRO residues in helix. "(chain 'A' and resseq 455:457) and (altloc 'A' or altloc ' ') and name H" => 0 donors "(chain 'A' and resseq 455:457) and (altloc 'A' or altloc ' ') and name O" => 3 acceptors hydrogen_bonds_from_selections: incomplete non-PRO residues in helix. "(chain 'B' and resseq 143:152) and (altloc 'A' or altloc ' ') and name H" => 0 donors "(chain 'B' and resseq 143:152) and (altloc 'A' or altloc ' ') and name O" => 10 acceptors hydrogen_bonds_from_selections: incomplete non-PRO residues in helix. "(chain 'B' and resseq 156:165) and (altloc 'A' or altloc ' ') and name H" => 0 donors "(chain 'B' and resseq 156:165) and (altloc 'A' or altloc ' ') and name O" => 10 acceptors hydrogen_bonds_from_selections: incomplete non-PRO residues in helix. "(chain 'B' and resseq 190:193) and (altloc 'A' or altloc ' ') and name H" => 1 donors "(chain 'B' and resseq 190:193) and (altloc 'A' or altloc ' ') and name O" => 4 acceptors hydrogen_bonds_from_selections: incomplete non-PRO residues in helix. "(chain 'B' and resseq 222:227) and (altloc 'A' or altloc ' ') and name H" => 0 donors "(chain 'B' and resseq 222:227) and (altloc 'A' or altloc ' ') and name O" => 6 acceptors hydrogen_bonds_from_selections: incomplete non-PRO residues in helix. "(chain 'B' and resseq 243:251) and (altloc 'A' or altloc ' ') and name H" => 0 donors "(chain 'B' and resseq 243:251) and (altloc 'A' or altloc ' ') and name O" => 9 acceptors hydrogen_bonds_from_selections: incomplete non-PRO residues in helix. "(chain 'B' and resseq 253:256) and (altloc 'A' or altloc ' ') and name H" => 0 donors "(chain 'B' and resseq 253:256) and (altloc 'A' or altloc ' ') and name O" => 4 acceptors hydrogen_bonds_from_selections: incomplete non-PRO residues in helix. "(chain 'B' and resseq 278:282) and (altloc 'A' or altloc ' ') and name H" => 0 donors "(chain 'B' and resseq 278:282) and (altloc 'A' or altloc ' ') and name O" => 5 acceptors hydrogen_bonds_from_selections: incomplete non-PRO residues in helix. "(chain 'B' and resseq 301:305) and (altloc 'A' or altloc ' ') and name H" => 0 donors "(chain 'B' and resseq 301:305) and (altloc 'A' or altloc ' ') and name O" => 5 acceptors hydrogen_bonds_from_selections: incomplete non-PRO residues in helix. "(chain 'B' and resseq 311:321) and (altloc 'A' or altloc ' ') and name H" => 0 donors "(chain 'B' and resseq 311:321) and (altloc 'A' or altloc ' ') and name O" => 11 acceptors Traceback (most recent call last): File "/nfs/home/jzhu/phenix/phenix-1.6.2-432/phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/nfs/home/jzhu/phenix/phenix-1.6.2-432/phenix/phenix/refinement/command_line.py", line 71, in run overwrite = command_line_interpreter.command_line.options.overwrite) File "/nfs/home/jzhu/phenix/phenix-1.6.2-432/phenix/phenix/refinement/driver.py", line 121, in __init__ h_bond_table = self.sec_str.get_bonds_table(log=log) File "/nfs/home/jzhu/phenix/phenix-1.6.2-432/cctbx_project/mmtbx/secondary_structure.py", line 1023, in get_bonds_table log=log) File "/nfs/home/jzhu/phenix/phenix-1.6.2-432/cctbx_project/mmtbx/secondary_structure.py", line 444, in hydrogen_bonds_from_selections ss_type="helix") File "/nfs/home/jzhu/phenix/phenix-1.6.2-432/cctbx_project/mmtbx/secondary_structure.py", line 652, in _donors_and_acceptors donor_isel.insert(k, n_atoms) IndexError: Index out of range. How do I fix it? Thanks. -- Jianghai

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how to extend R-free set
by Robert Immormino 21 Jun '10

21 Jun '10

Hi, Hopefully I'm just missing something obvious.... I'm trying to copy the Rfree set from an old set of data, to a new mutant structure....and extend to higher resolution. I've tried: phenix.reflection_file_converter old.mtz --label="R-free-flags" new.sca --label="i_obs,sigma" --mtz new.mtz and several other combination, but I am still failing to get phenix to read multiple data files and output the desired mtz. I can get just the Rfree flags or the I and SigI, but not both. I also tried with phenix.refine phenix.refine --dry-run old.pdb old.mtz new.sca ligands.cif refinement.input.xray_data.labels="i_obs,sigma" refinement.input.xray_data.r_free_flags.label="R-free-flags" This seems closer, but I get the error: Sorry: R-free flags not compatible with F-obs array: missing flag for 492 F-obs selected for refinement: Thanks, -bob

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find_all_ligands vs. ligand_identification
by Mark A Saper 21 Jun '10

21 Jun '10

Could someone explain the difference between the GUI "ligand_identification" routine and the documented command line "find_all_ligands". The latter appears to have more flexible input parameters. I'm not sure the GUI for ligand_identification is working correctly. Thanks, Mark _________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry University of Michigan Biophysics, 3040 Chemistry Building 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. saper(a)umich.edu phone (734) 764-3353 fax (734) 764-3323 http://www.biochem.med.umich.edu/?q=saper http://www.strucbio.umich.edu/

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LAST CHANCE TO REGISTER FOR DIFFRACTION METHODS GRC
by A Leslie 21 Jun '10

21 Jun '10

The biannual Gordon Conference on Diffraction Methods in Structural Biology will be held at Bates College in Lewiston, Maine from 18-23rd July. The program covers all aspects of macromolecular structure solution from crystallization to structure solution and refinement and includes sessions on complementary techniques and the potential of free electron lasers. Many of the leading methods developers will be present and the format of the meeting, with free afternoons, provides ample opportunities for informal discussions. The registration deadline is *** THIS COMING SUNDAY, 27th June *** = ======================================================================== Limited funds are still available to support new student and postdoctoral applications, contact andrew(a)mrc-lmb.cam.ac.uk for details. = ======================================================================== Further details, including a full program and details on the application procedure can be obtained from: http://www.grc.org/programs.aspx?year=2010&program=diffrac We hope to see you there ! Andrew Leslie (Chair) & Ana Gonzalez (Vice Chair) Outline Program Diffraction Methods in Structural Biology, 18-23rd July 2010, Bates College, Lewiston, Maine Sunday pm: Macromolecular Structures, Pushing the boundaries Discussion leader: Michael Rossmann 1. ABC Transporters: Doug Rees 2. The Spliceosome : Kyoshi Nagai Monday am: Crystallisation and the diffraction experiment Discussion leader: Bob Sweet 1. Nanolitre crystallisation: Seth Harris 2. Twinning and disorder: Todd Yeates 3. Simulating the diffraction experiment: James Holton 4. Microcrystallography: Gwyndaf Evans Monday pm: Radiation damage and data collection strategies Discussion leader: Vivian Stojanoff 1. Radiation damage, experimental: Martin Weik 2. Microbeams: Yanhui Zou 3. Testing data collection strategies with the Pilatus: Marcus Mueller Tues am: Synchrotron developments and automated data processing Discussion leader: Thomas Schneider 1. Synchrotrons, latest developments: Sean Mc Sweeney 2. Synchrotrons, latest developments: Janet Smith 3. Data processing with Xia2/CHEF: Graeme Winter 4. Data processing with AUTOPROC: Clemens Vonrhein Tues pm: Complementary techniques Discussion leader: Ana Gonzales 1. Electron tomography: Sriram Subramaniam 2. SAXS: Hiro Tsuruta 3. Spectroscopy: Carrie Wilmot Weds am: Structure solution and refinement Discussion leader: Paul Adams 1. SAD Phasing: Randy Read 2. Molecular replacement with BALBES: Garib Murshudov 3. PHENIX: Tom Terwilliger 4. TLS: Ethan Merritt Weds pm: Challenging problems/Membrane Proteins Discussion leader: Michael Wiener 1. Using cubic lipidic phase: Martin Caffrey 2. Membrane Proteins: Stephen White 3. Heterogeneity, low solubility and low resolution: structural pursuit on the ternary Myddosome complex in Toll-like receptor signaling: Hao Wu Thurs am: Selected Posters and Map improvement and Model building Discussion leader: Tassos Perrakis 1. COOT: Paul Emsley 2. Modelling nucleic acids: Johan Hattne Thursday pm: Future Methods, FELs, Diffraction imaging Discussion leader: Ed Lattman 1. Opportunities fof membrane protein analysis with FELs: Petra Fromme 2. Single particle imaging with pulsed hard Xray lasers: Anton Barty 3. Femtosecond nanocrystallography of membrane proteins using LCSL: John Spence

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"Open in Coot" not working on 1.6.1-357
by Ben Eisenbraun 19 Jun '10

19 Jun '10

Howdy PHENIXians, I can't seem to get the "Open in Coot" option to work in PHENIX. I tested version 1.6.1-357 on 32 and 64-bit linux as well as the OS X Intel version, and while Coot will open, it won't display the working data. 'phenix.find_coot_command' works fine from the command line. On the linux machines, when Coot opens, it doesn't have the "Connected to PHENIX" button. On the OS X Intel machine, it does have the button, but it still won't display the working data. Any ideas? -ben -- | Ben Eisenbraun | Software Sysadmin | | Structural Biology Grid | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |

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is derivative data useful for looking for the missingpart of the model?
by Jacob Keller 16 Jun '10

16 Jun '10

> Hi Fengyun, > > How have you determined whether you in fact have the full-length protein > in your crystals? It sounds like, from your statistics, that everything is > already modelled--it seems hard to believe that 80% of the whole protein > would give such good R values. Do others agree? > > You could run some of your crystals on a gel next to a sample which is > known to be full-length, and you could get the answer. > > Jacob > > ******************************************* > Jacob Pearson Keller > Northwestern University > Medical Scientist Training Program > Dallos Laboratory > F. Searle 1-240 > 2240 Campus Drive > Evanston IL 60208 > lab: 847.491.2438 > cel: 773.608.9185 > email: j-keller2(a)northwestern.edu > ******************************************* > > ----- Original Message ----- > From: <fn1(a)rice.edu> > To: <phenixbb(a)phenix-online.org> > Sent: Tuesday, June 15, 2010 5:59 PM > Subject: [phenixbb] is derivative data useful for looking for the > missingpart of the model? > > >> Hi everyone, >> >> I got a partial model, consisting of 80% of the whole molecule, from the >> molecular replacement. The native data reflects to 2.3 A, and now the >> R/Rfree= 0.22/0.28. My problem is that the missing part of the model is >> important for us, but there is not any density for this region now. >> >> Meantime, we have several heavy atom derivative data. My question is >> that if refine the model against the derivative data, will the heavy >> atom appear in the difference map if existing? Any suggestions on how to >> use the derivative data to locate the missing part of model? >> >> Thanks in advance! >> Regards, >> Fengyun >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >

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phaser spacegroup within phenix
by John M. Berrisford 16 Jun '10

16 Jun '10

Hello I've just spotted a discrepancy between phenix run from ccp4i and from the phenix GUI regarding spacegroup selection run phaser runs. Within the CCP4 GUI you can specify the space group for a phaser molecular replacement run to be the space group of the mtz or a sub-space group (i.e P222 or P212121 etc...). For some reason this isn't as obvious within the phenix GUI. I have an mtz processed in P21 and when I load it into the phenix phaser GUI it tells me its P21 (P 1 21 1) and gives me no other options. However, when I run the molecular replacement job it decides that the space group could be either P2 or P21 and runs both - which in my case runs in P2 and gives a partial solution, not the full solution I would expect in P21. A bit annoying as I know my space group is actually P21. After a few minutes of head scratching, the only way I found to fix it to run in P21 is to enter the "other settings" menu and select "none" within "alternative space groups". I guess this is what your suppose to do, but its not obvious. Can the phenix GUI be changed so that its as obvious as the ccp4 GUI as to what is actually going to run when you press "run". Thanks John I'm running phenix 1.6.1 on OS X. -- 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 1223 252882

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Re: [phenixbb] phaser spacegroup within phenix
by John M. Berrisford 16 Jun '10

16 Jun '10

Hi Nat I don't think its a bug, just phaser getting a little bit confused. Phaser ran in both P2 and P21 using the phenix default, not P21 - the space group of the mtz. This default is probably the right thing to do if you don't know the space group of your crystal, but then you wouldn't have scaled the mtz in P21. In my case the reason phaser failed to find a solution is that the P2 solution had a higher initial LLG than the P21 solution while finding the first copy of 4 in my A.U.. So phaser picked P2 to continue the molecular replacement and subsequently stopped due to clashes during packing. John On Tue, Jun 15, 2010 at 8:45 AM, John M. Berrisford <jmb(a)mrc-mbu.cam.ac.uk>wrote: > > I have an mtz processed in P21 and when I load it into the phenix phaser > > GUI it tells me its P21 (P 1 21 1) and gives me no other options. However, > > when I run the molecular replacement job it decides that the space group > > could be either P2 or P21 and runs both - which in my case runs in P2 and > > gives a partial solution, not the full solution I would expect in P21. A bit > > annoying as I know my space group is actually P21. > > After a few minutes of head scratching, the only way I found to fix it to > > run in P21 is to enter the "other settings" menu and select "none" within > > "alternative space groups". I guess this is what your suppose to do, but its > > not obvious. > Point taken - I'll move this to the main window (and label it more clearly - sorry). The result you're describing sounds like it might be a bug, though; shouldn't Phaser try P21 as well and get the full solution, instead of settling for P2? This is what I would expect for the default behavior. -Nat -- 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 1223 252882

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Re: [phenixbb] is derivative data useful for looking for the missing part of the model?
by Thomas C. Terwilliger 16 Jun '10

16 Jun '10

Hi Francis, Yes, you can do that. It requires one extra step to do the combination. You need to make a script like the one below (see https://solve.lanl.gov/Resolve/html_resolve_manual/resolve_sample_scripts.h…): All the best, Tom T Merging phase sets with different origins You can merge phase sets with different origins with this script. It uses an FFT convolution to find the best allowed offset between the maps calculated with the two phase sets. Merging the files REQUIRES HL coefficients (see above for generating them if you do not have them). Note: the FP and SIGFP in the output file will come from the hklin file NOT the hklmerge file: phenix.resolve <<EOD hklin random_1_hl.mtz ! File with target map (fixed) labin FP=FP PHIB=PHIM FOM=FOMM HLA=HLAM HLB=HLBM HLC=HLCM HLD=HLDM hklmerge random_2_hl.mtz ! File to be offset labmerge FP=FP PHIB=PHIM FOM=FOMM HLA=HLAM HLB=HLBM HLC=HLCM HLD=HLDM hkl_offset_file resolve_off.mtz ! The hklmerge file, offset all by itself hkl_merge_file resolve_merge.mtz ! The hklmerge file offset, then merged with hklin EOD >> Thanks so much!It looks promising. >> If I have two or more derivative data and want to combine all these >> information. Can I just do MRSAD individually for each dataset, and >> combine them? >> >> >> ÒýÓÃ Nathaniel Echols <nechols(a)lbl.gov>£º >> >>> On Tue, Jun 15, 2010 at 4:03 PM, Francis E Reyes >>> <Francis.Reyes(a)colorado.edu >>>> wrote: >>> >>>> Using the model to find the heavy atom sites and then calculating >>>> phases on >>>> those sites (without model) might help. ( I believe phenix will output >>>> a >>>> phase combined map (model + experimental phases)). >>>> >>> >>> Correct, this is the default behavior if you provide a model directly to >>> AutoSol (or Phaser). There is however a semi-automatic way to use the >>> model >>> phases to find sites without biasing the experimental map; see the >>> documentation here: >>> >>> https://www.phenix-online.org/version_docs/1.6.2-432/autosol.htm#anch126 >>> >>> (The AutoBuild step is optional - you could just look at the >>> density-modified map after AutoSol is done.) >>> >>> -Nat >>> >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

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is derivative data useful for looking for the missing part of the model?
by fn1＠rice.edu 16 Jun '10

16 Jun '10

Hi everyone, I got a partial model, consisting of 80% of the whole molecule, from the molecular replacement. The native data reflects to 2.3 A, and now the R/Rfree= 0.22/0.28. My problem is that the missing part of the model is important for us, but there is not any density for this region now. Meantime, we have several heavy atom derivative data. My question is that if refine the model against the derivative data, will the heavy atom appear in the difference map if existing? Any suggestions on how to use the derivative data to locate the missing part of model? Thanks in advance! Regards, Fengyun

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Re: [phenixbb] input sharp phases into phenix.autosol
by Thomas C. Terwilliger 15 Jun '10

15 Jun '10

Hi Michael, If I understand correctly, you want to take a file that has experimental phases, density modify it, and autobuild a model. Plus you want to take the inverse hand of the phases and do the same thing. For the first part you have two easy options: phenix.autobuild my_exptl_phases.mtz my_seq.dat ha_file=my_ha_file phenix.build_model my_exptl_phases.mtz my_seq.dat ha_file=my_ha_file These do more or less the same thing, but build_model is a lot faster (but not quite as good), and requires version 1.6.2-242 or higher. For phases from sharp, you will want to specify the columns of data to be used for FP SIGFP PHIB FOM HLA HLB HLC HLD for each method above. (The way to specify these are different in the two methods. For autobuild you just list the column labels to be used for the above items with labels="myFP mySIGFP myPHIB myFOM myHLA myHLB myHLC myHLD", and for build_model you specify a regular labin line: labin="FP=myFP SIGFP=mySIGFP...etc" For the second part, flipping the hand of a file with experimental phases...I am not sure if we have a tool for that. Perhaps someone else can comment. All best, Tom T >> Hi, >> >> I hope what I want to do is not considered a crime :-) Is there a way to >> input phases e.i. from sharp into phenix.autosol (preferably the command >> line version) to run resolve with both hands and autobuild for a SAD or >> SIRAS case? >> >> Thanks! >> Michael >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

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input sharp phases into phenix.autosol
by Michael Hothorn 14 Jun '10

14 Jun '10

Hi, I hope what I want to do is not considered a crime :-) Is there a way to input phases e.i. from sharp into phenix.autosol (preferably the command line version) to run resolve with both hands and autobuild for a SAD or SIRAS case? Thanks! Michael

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Diffraction Methods GRC, Registration deadline is 27th June
by andrew＠mrc-lmb.cam.ac.uk 12 Jun '10

12 Jun '10

The biannual Gordon Conference on Diffraction Methods in Structural Biology will be held at Bates College in Lewiston, Maine from 18-23rd July. The program covers all aspects of macromolecular structure solution from crystallization to structure solution and refinement and includes sessions on complementary techniques and the potential of free electron lasers. Many of the leading methods developers will be present and the format of the meeting, with free afternoons, provides ample opportunities for informal discussions. The registration deadline is 27th June, so please apply soon ! ========================================================================= Limited funds are available to support new student and postdoctoral applications, contact andrew(a)mrc-lmb.cam.ac.uk for details. ========================================================================= Further details, including a full program and details on the application procedure can be obtained from: http://www.grc.org/programs.aspx?year=2010&program=diffrac We hope to see you there ! Andrew Leslie (Chair) & Ana Gonzalez (Vice Chair) Outline Program Diffraction Methods in Structural Biology, 18-23rd July 2010, Bates College, Lewiston, Maine Sunday pm: Macromolecular Structures, Pushing the boundaries Discussion leader: Michael Rossmann 1. ABC Transporters: Doug Rees 2. The Spliceosome : Kyoshi Nagai Monday am: Crystallisation and the diffraction experiment Discussion leader: TBA 1. Nanolitre crystallisation: Seth Harris 2. Twinning and disorder: Todd Yeates 3. Simulating the diffraction experiment: James Holton 4. Microcrystallography: Gwyndaf Evans Monday pm: Radiation damage and data collection strategies Discussion leader: Vivian Stojanoff 1. Radiation damage, experimental: TBA 2. Microbeams: Yanhui Zou 3. Testing data collection strategies with the Pilatus: Marcus Mueller Tues am: Synchrotron developments and automated data processing Discussion leader: Thomas Schneider 1. Synchrotrons, latest developments: Sean Mc Sweeney 2. Synchrotrons, latest developments: Janet Smith 3. Data processing with Xia2/CHEF: Graeme Winter 4. Data processing with AUTOPROC: Clemens Vonrhein Tues pm: Complementary techniques Discussion leader: Ana Gonzales 1. Electron tomography: Sriram Subramaniam 2. SAXS: Hiro Tsuruta 3. Spectroscopy: Carrie Wilmot Weds am: Structure solution and refinement Discussion leader: Paul Adams 1. SAD Phasing: Randy Read 2. Molecular replacement with BALBES: Garib Murshudov 3. PHENIX: Tom Terwilliger 4. TLS: Ethan Merritt Weds pm: Challenging problems/Membrane Proteins Discussion leader: TBC 1. Using cubic lipidic phase: Martin Caffrey 2. Membrane Proteins: Stephen White 3. Heterogeneity, low solubility and low resolution: structural pursuit on the ternary Myddosome complex in Toll-like receptor signaling: Hao Wu Thurs am: Selected Posters and Map improvement and Model building Discussion leader: Tassos Perrakis 1. COOT: Paul Emsley 2. Modelling nucleic acids: Johan Hattne Thursday pm: Future Methods, FELs, Diffraction imaging Discussion leader: Ed Lattman 1. Opportunities fof membrane protein analysis with FELs: Petra Fromme 2. Single particle imaging with pulsed hard Xray lasers: Anton Barty 3. Femtosecond nanocrystallography of membrane proteins using LCSL: John Spence

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Job Openings: Industrial Post Doc - Structure Based Drug Design Method R&D
by Lance Westerhoff 11 Jun '10

11 Jun '10

Hello All- Good news! We have the following new position available. We are particularly interested in folks who have experience with xray refinement method research and development, so I figured this list would probably be a good fit. Please contact me if you know of anyone who might be interested: ================= Contact: Dr. Lance M Westerhoff - careers(a)quantumbioinc.com Based at: QuantumBio Inc., 200 Innovation Boulevard, State College, PA 16803 On the Web: http://www.quantumbioinc.com/careers/ Job Purpose: Beginning immediately, QuantumBio Inc, headquartered adjacent to The Pennsylvania State University in State College, PA, is in need of a post doctoral computational Biochemist/Chemist interested in continuing his or her career within a dynamic, small-company environment. Under the direction of Dr. Lance M. Westerhoff, General Manager of QuantumBio, the successful candidate will work with both academic and industrial partners to help transition and validate the novel, quantum mechanically based structure-based drug discovery technologies recently developed in the academic laboratory of Dr. Kenneth M. Merz Jr. to QuantumBios product line. The successful candidate will be integral to this project and will focus his or her efforts on the research and software development aspects necessary to validate and deploy this novel technology across the pharmaceutical industry. The position requires the candidate to have a Ph.D. in Chemistry, Biochemistry, or related field along with experience with the methods and software in the field. Due to the limited number of new work visas available, only American citizens or candidates with valid work permits will be considered at this time. A willingness to publish is required, and experience with C++, high performance programming, or xray refinement methods is a plus. Opportunities for advancement may be available through additional SBIR/STTR-style projects, and industry-supported collaborations. Further, in addition to the research and development duties of the project, the position will afford the successful candidate with access to and experience with QuantumBio's industry partners including a number of pharmaceutical, biotech, and computational firms. To apply, submit cover letter, CV, and one or two representative publications to the Contact above. About QuantumBio: QuantumBio Inc is accelerating drug discovery efforts by providing pharmaceutical, biotechnology companies and life science research organizations with a next generation of Computer-Assisted Drug Design (CADD) and Computer-Assisted Molecular Modeling (CAMM) solutions based on the increased accuracy and power of quantum mechanics. These solutions include a number of options tailored to each customers specific requirements including software licensing, services, and customization. See http://www.quantumbioinc.com/ for more! ================= Thank you for your time! -Lance ____________________ Lance M. Westerhoff, Ph.D. General Manager QuantumBio Inc. WWW: http://www.quantumbioinc.com Email: lance(a)quantumbioinc.com Phone: 814-235-6908 Fax: 814-235-6909

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large coordinate and map shift after simulated annealing
by fn1＠rice.edu 11 Jun '10

11 Jun '10

Hi everyone, I am wondering why large coordinate shift could happen after simulated annealing (no rigid body refinement). Although it helps decreasing R values, it looks like the whole molecule shifts together by about 3 A. Is this normal? I read a post in previous phenixbb, but I still not understand it. Thank you very much! Regards, Fengyun

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Persistant high average B-factor.
by Joseph Brock 10 Jun '10

10 Jun '10

Dear Phenix users, I am currently using version 1.6.1-353 and I'm working on a 1.7A structure that has refined quite well using Individual_sites+individual_adp(isotropic)+occupanices+TLS: Final R-work = 0.1776, R-free = 0.2262 However, I noticed that the average B-factor reported by polygon with these settings was quite high ( < 0.1 of other structures with a similar resolution). Discovering I could not change the value of wxu_scale when using individual_adp+TLS, I went about trying to reduce the average B using the method described here: http://phenix-online.org/pipermail/phenixbb/2007-September/000511.html However, I still can't seem to reduce the average B-factor. I've just done a refinement with the following non-default (extreme) target weight settings: target_weights { wxc_scale = 1.5 fix_wxc = 2 fix_wxu = 0.1 (wxu_scale = 1) But if anything, reducing wxu to such low values makes the avergae B-even higher while concuretnly making the gap between R-values much worse: Final R-work = 0.1602, R-free = 0.2457 This suggests to me that I'm obviously over fitting the data but I'm at a loss on how to proceed. Should i just accept that the automatic scaling used for Phenix TLS wxu is doing a good job and that my structure actually does have an unusually high avergae B? I'm fitting two ligands into density, which is at several places ambiguous, so I would like the most unbiased difference density possible. Many thanks in advance, Joe. _________________________________________________________________ New, Used, Demo, Dealer or Private? Find it at CarPoint.com.au http://clk.atdmt.com/NMN/go/206222968/direct/01/

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Autobuild error message, please help!!!
by 신인철 10 Jun '10

10 Jun '10

Hi, everyone I have a problem in running phenix.automr I started AutoMR with the command: ---------------------------------------------------------------------------- ----- phenix.automr build=True data=ZZZZZZ_H-Nat_x22_P3221_from_P321.sca \ coords='1_SMsp.pdb 2_SMsp.pdb 3_SMsp.pdb 4_SMsp.pdb' \ identity='40 32 29 27' seq_file=ZZZZZZ_seq.dat input_seq_file=ZZZZZZ_seq.dat \ copies=4 ---------------------------------------------------------------------------- ------ AutoMR process seems to be done without any error but during autobuild process, I encounterd an error message as follows ---------------------------------------------------------------------------- ----- Re-using input PDB coordinates in build this cycle Running 3 parallel build jobs Standard build in parallel starting with refine.pdb_1 This is the first try at building this model Setting background=False as nproc=1 Try: 1 building 1 model Try: 2 building 1 model Try: 3 building 1 model Running up to 1 jobs in parallel... with total of 3 jobs Splitting work into 3 jobs and running 1 at a time with csh in /data1/disk02/icshin/UGI/MR/PHENIX_MR_8/AutoBuild_run_1_/TEMP0 Starting job 1... **************************************************************************** **** Failed to carry out AutoBuild_build_cycle: child process stderr output: command: 'csh /data1/disk02/icshin/ZZZ/MR/PHENIX_MR_8/AutoBuild_run_1_/TEMP0/RUN_FILE_1' icshin_com: No such file or directory. **************************************************************************** **** ---------------------------------------------------------------------------- ---------------------------------------------------------- What am I supposed to do? Please, help me! ------------------------------------------------------- Inchul Shin Structural Biology Lab. CALS. Seoul Nationl Univ.

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how-to change resolve keywords using phenix.multi_crystal_average
by Bjørn Panyella Pedersen 09 Jun '10

09 Jun '10

Dear board I am doing a difficult case of density modification. I get good results using resolve after optimising some keywords. I now want to use multicrystal averaging. This works ok in dmmulti, but I would like to combine it with resolve. For this I have tried phenix.multi_crystal_average, which also runs phenix.resolve, but it uses default keywords for resolve, and I can't find documentation on how to change these keywords. Current maps from phenix.multi_crystal_average are worse that the optimized resolve maps, and I believe this is because of the default resolve settings. Is it possible to control resolve keywords using phenix.multi_crystal_average? And how can I do it? Thanks in advance -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

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Re: [phenixbb] phenixbb Digest, Vol 55, Issue 7
by ak2197＠columbia.edu 08 Jun '10

08 Jun '10

Ok Alex Sent from my Verizon Wireless BlackBerry -----Original Message----- From: phenixbb-request(a)phenix-online.org Date: Mon, 07 Jun 2010 12:00:01 To: <phenixbb(a)phenix-online.org> Subject: phenixbb Digest, Vol 55, Issue 7 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. Robert Ng wants to stay in touch on LinkedIn (Robert Ng) ---------------------------------------------------------------------- Message: 1 Date: Mon, 7 Jun 2010 08:57:29 -0700 (PDT) From: Robert Ng <ubi(a)ufl.edu> To: PHENIX list <phenixbb(a)phenix-online.org> Subject: [phenixbb] Robert Ng wants to stay in touch on LinkedIn Message-ID: <1916754023.4088196.1275926249246.JavaMail.app(a)ech3-cdn13.prod> Content-Type: text/plain; charset="utf-8" LinkedIn ------------ PHENIX, I'd like to add you to my professional network on LinkedIn. - Robert Ng Robert Ng Graduate Research Assistant at Department of Biochemistry and Biophysics Gainesville, Florida Area Confirm that you know Robert Ng https://www.linkedin.com/e/isd/1366202655/UCksvc1y/ ------ (c) 2010, LinkedIn Corporation -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20100607/f95d09c5/a…> ------------------------------ _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb End of phenixbb Digest, Vol 55, Issue 7 ***************************************

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Robert Ng wants to stay in touch on LinkedIn
by Robert Ng 07 Jun '10

07 Jun '10

LinkedIn ------------ PHENIX, I'd like to add you to my professional network on LinkedIn. - Robert Ng Robert Ng Graduate Research Assistant at Department of Biochemistry and Biophysics Gainesville, Florida Area Confirm that you know Robert Ng https://www.linkedin.com/e/isd/1366202655/UCksvc1y/ ------ (c) 2010, LinkedIn Corporation

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A couple of questions regarding twinning
by Pietro Roversi 03 Jun '10

03 Jun '10

Dear all, A couple of questions regarding twinning: 1. The structure I work with has multiple twinning domains (4 to be exact, with pseudo-orthorhombic 222 symmetry induced by twinning in P1). I feed the autobuild script the operators using a keyord: input_files.refine_eff_file_list=mytwinrefinement.eff (see attached file) but only the last one seems to be used. Do I guess correctly that there is only provision for two domains adn therefore the last twinning definition overrides any previously defined one? If so, is there a way of specifying and using multiple twinning domains/operators? 2. Output structure factor amplitudes: are they detwinned? Are they detwinned before the density modification in resolve? and during it? Thanks for any clarification/suggestions Regards Pietro

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Re: [phenixbb] NAG-NAG description
by Chris Ulens 02 Jun '10

02 Jun '10

Thanks for the feedback. I would like to refine a NAG-NAG chain attached to residue Asn122 in my structure. There are 5 identical subunits. Could you verify my .params file? I get the following error: Empty atom selection refinement .pdb_interpretation.apply_cif_link.residue_selection_1="chain A and resname NAG and resid 122" Thanks. -Chris On 31 May 2010, at 21:34, Georg Mlynek wrote: > Dear Chris, this did it for me. > > > Create a file which you can call whatever you want even the extension > doesn't matter. E.g.: cif_link.params > > Put in this file your links: (Which Atom of residue1 will be > connected to > which Atom in residue2 is already defined in mon_lib_list.cif) > > > > refinement.pdb_interpretation.apply_cif_link { > data_link = NAG-ASN > residue_selection_1 = chain A and resname NAG and resid 500 > residue_selection_2 = chain A and resname ASN and resid 297 > } > refinement.pdb_interpretation.apply_cif_link { > data_link = BETA1-4 > residue_selection_1 = chain A and resname NAG and resid 500 > residue_selection_2 = chain A and resname NAG and resid 501 > } > refinement.pdb_interpretation.apply_cif_link { > data_link = BETA1-4 > residue_selection_1 = chain A and resname NAG and resid 501 > residue_selection_2 = chain A and resname BMA and resid 502 > } > refinement.pdb_interpretation.apply_cif_link { > data_link = ALPHA1-3. > > residue_selection_1 = chain A and resname BMA and resid 502 > residue_selection_2 = chain A and resname MAN and resid 503 > } > > 4) add this file in the GUI > > > Or run % phenix.refine model.pdb data.hkl cif_link.params > > > 5)Trouble shooting > > a)run iotbx.phil cif_link.params (this checks if the syntax is > right) > > b) check .eff file the links should be added there. You can also > check the . > geo file if you see anything strange. > > c)Having unknown to phenix.refine item in PDB file (novel ligand, > etc... > (BMA is also not there) ). phenix.refine uses the CCP4 Monomer > Library as > the source of stereochemical information for building geometry > restraints > and reporting statistics. If phenix.refine is unable to match an > item in > input PDB file against the Monomer Library it will stop with "Sorry" > message > explaining what to do and listing the problem atoms. If this > happened, it is > necessary to obtain a cif file (parameter file, describing unknown > molecule) > by either making it manually or having eLBOW program to generate it: > > phenix.elbow model.pdb --do-all --output=all_ligands > > this will ask eLBOW to inspect the model_new.pdb file, find all > unknown > items in it and create one cif file for them all_ligands.cif. > Alternatively, > one can specify a three-letters name for the unknown residue: > > phenix.elbow model.pdb --residue=MAN --output=man > > !Check the file if everything is ok! > > > Please correct if this is not ok, or there is an easier way now. > > Kind regards George. > > > -----Ursprüngliche Nachricht----- > Von: phenixbb-bounces(a)phenix-online.org > [mailto:[email protected]] Im Auftrag von Chris Ulens > Gesendet: Monday, May 31, 2010 9:14 PM > An: PHENIX user mailing list > Betreff: Re: [phenixbb] NAG-NAG description > > Dear glycobiologists and phenixfriends. > > I am trying to refine a NAG-NAG chain attached to an Asn122 in my > (pentameric) structure. > What is the proper description in the cif_link.params that is the > equivalent of the pdb description pasted below that phenix so kindly > ignores? > Also, what is the proper way to define the cif_link.params file in the > GUI? > > Thank you. > -Chris > > > LINK ND2 ASN A 122 C1 NAG A 834 1555 > 1555 1.37 > LINK O4 NAG A 834 C1 NAG A 835 1555 > 1555 1.43 > LINK ND2 ASN B 122 C1 NAG B 834 1555 > 1555 1.37 > LINK O4 NAG B 834 C1 NAG B 835 1555 > 1555 1.43 > LINK ND2 ASN C 122 C1 NAG C 834 1555 > 1555 1.37 > LINK O4 NAG C 834 C1 NAG C 835 1555 > 1555 1.43 > LINK ND2 ASN D 122 C1 NAG D 834 1555 > 1555 1.37 > LINK O4 NAG D 834 C1 NAG D 835 1555 > 1555 1.43 > LINK ND2 ASN E 122 C1 NAG E 834 1555 > 1555 1.37 > LINK O4 NAG E 834 C1 NAG E 835 1555 > 1555 1.43 > > --------------------------------------------------- > Chris Ulens, Ph.D. > Lab of Structural Neurobiology > Department of Molecular Cell Biology > Campus Gasthuisberg, ON1 > Herestraat 49, PB 601 > B-3000 Leuven > Belgium > e chris.ulens(a)med.kuleuven.be > t +32 16 345812 > f +32 16 345699 > w http://www.xtal.be > > _______________________________________________ > 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

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segmentation fault
by Harry M. Greenblatt 01 Jun '10

01 Jun '10

BS"D Dear All, We had the phenix 1.6.1 GUI running on a fedora core 12 machine; it was thought, for different reasons, that a kernel upgrade would address certain issues unrelated to phenix. The machine is now running 2.6.32.12-115.fc12 (64 bit) and phenix now gives a segmentation fault. Any suggestions? Thanks Harry ------------------------------------------------------------------------ - Harry M. Greenblatt Associate Staff Scientist Dept of Structural Biology harry.greenblatt(a)weizmann.ac.il Weizmann Institute of Science Phone: 972-8-934-3625 Rehovot, 76100 Facsimile: 972-8-934-4159 Israel

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Weight optimization
by Jianghai Zhu 29 May '10

29 May '10

Hi, I am using the optimize_wxc=true and optimize_wxu=true in my last refinement. The R and Rfree went down but the RMSDs were way too large. I wonder if phenix.refine still targets the geometry when it optimizes the R and Rfree. Here are the results from almost two identical runs except the weight optimization. 1) optimize_wxc = False optimize_wxu = False wxc_scale=0.08 wxu_scale=1.66 results: R=0.2294 R-free=0.2709 angl=1.087 bond=0.006 2) optimize_wxc = True optimize_wxu = True wxc_scale=0.08 wxu_scale=1.66 results: R=0.2141 R-free=0.2628 angl=2.894 bond=0.033 I am using the dev-412 version. Thanks. -- Jianghai

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offtopic: Problem with Pymol showing maps
by Tatyana Sysoeva 29 May '10

29 May '10

Hi all, if somebody is still not on the memorial day weekend, I have a short question off-topic for Pymol-users I have several maps from Phenix and want to draw some pictures in Pymol. I am opening the files, renamed to ccp4 or map, or not, and all I am getting is just a box, which is not even a unit cell boundary. If you know some nice simple program to do nice pictures of the electron densities- share your knowledge please! Sincerely Tanya

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Super: Rotation and translation
by J. Fleming 29 May '10

29 May '10

Hello, I've been using 'super' to align the c-alphas within one domain of two different models of the same protein while leaving the second domain to move freely. I can do this using: super (A and resid 1-100 and name ca), (B and resid 1-100 and name ca) What I would like to do is determine the rotation and translation of model B's second domain as it moves away from A's second domain. I can output a matrix after running super using: print cmd.get_object_matrix("A") How do I go from the matrix to an angle and distance? Thanks for any thoughts, Jon

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Re: [phenixbb] Autobuild submitted jobs
by Mark A Saper 27 May '10

27 May '10

Tom -- It turns out that each of the omit region's jobs submits another job, but that latter job is only the "test run_command" job. Why test the run_command if no subsequent jobs are submitted? Our solution, thanks to an extremely savvy cluster manager, was to install the qsub (Torque?) package on each of the computing nodes (117). Also we ran the top-level process on the head (scheduler) node, so as not to tie up a computing node while it waits for its sibling jobs (the omit regions) to finish the calculation. Overall wall-time with a separate node allocated for each omit region was about 50 minutes. Interestingly, although each node has 8 processors, the OMIT region jobs seems to only use one processor! Interestingly when phenix.refine jobs are run on my Macbook Pro, the operating system is savvy enough to spread it over 2 processors. -Mark ______________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry University of Michigan Biophysics, 3040 Chemistry Building 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. saper(a)umich.edu phone (734) 764-3353 fax (734) 764-3323 http://www.biochem.med.umich.edu/?q=saper http://www.strucbio.umich.edu/

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How to turn off mask optimization
by Schubert, Carsten [PRDUS] 26 May '10

26 May '10

Hi, Is there a way to turn off the mask optimization step in 393? I tried 'main.optimize_mask = False' but that does not work. The program spends a substantial amount of time in repeated mask optimizations and I am trying to shave off a couple minutes for each run... Cheers, Carsten

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Autobuild submitted jobs
by Mark A Saper 26 May '10

26 May '10

Dear Tom and colleagues, We're running Autobuild composite omit on a large cluster, each node has 8 processors. Autobuild submits jobs with the "run_command". And it appears that each of those jobs submit other jobs. Are the latter jobs necessary? That is, are there situtations where they wouldn't be submitted as separate jobs but run as subprocesses? Currently nodes in our cluster don't have capability of qsubing new jobs, but we are in the process of changing this. Thanks, Mark _________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry University of Michigan Biophysics, 3040 Chemistry Building 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. saper(a)umich.edu phone (734) 764-3353 fax (734) 764-3323 http://www.biochem.med.umich.edu/?q=saper http://www.strucbio.umich.edu/

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atom selection syntax for ALT atoms?
by Scott Classen 25 May '10

25 May '10

This is the selection for the atom I'm interested in: atom_selection_2 = "name OE1 and chain A and resname GLU and resseq 160" I want to try a refinement with an alternate conformation at GLU160 . Can someone please help me with the proper syntax. 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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PDB Deposition Question
by Alexander Hirschi 25 May '10

25 May '10

Hi all - I refined a structure using Phenix 1.4-3 and now I need to submit it to the PDB. When I try to run sfcheck on the .mtz that Phenix generated, sfcheck can't read the file. I also tried to convert the .mtz to .cns using phenix.reflection_file_converter. This time, sfcheck could "not find IOBS or FOBS in your file". Any advice would be greatly appreciated. -Alex

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Installation problem, please help
by Tiberman Danny 24 May '10

24 May '10

Hello, while trying to install I get the following Error message: "======================================================================== Installing from binary bundle ========================================================================== bundle file: bundle-1.6.1-357-intel-linux-2.6-x86_64.tar.gz PHENIX installation source directory set to: /root/phenix-installer-1.6.1-357 PHENIX installation target directory <PHENIX_LOC > set to: /usr/local/phenix-1.6.1-357 PHENIX installation build directory set to: <PHENIX_LOC > /build/intel-linux-2.6-x86_64 PHENIX temporary build directory set to: build-binary/intel-linux-2.6-x86_64/monst/tmp PHENIX installation log directory set to: build-binary/intel-linux-2.6-x86_64/monst/log ==== warning: "/usr/local/phenix-1.6.1-357" already exists ==== ==== warning: cannot determine installation time-stamp, proceeding ==== installing binary components removing existing files in build-binary/intel-linux-2.6-x86_64/monst/tmp/binary finding installed versions finding binary versions binary components up-to-date the binary package will not be installed setting environment configuring PHENIX components /root/phenix-installer-1.6.1-357/bin/install-from-binary: line 347: 19650 Floating point exception$PHENIX_BUILD/base/bin/python $PHENIX_LOC/cctbx_project/libtbx/configure.py --current_working_directory="$PHENIX_BUILD" $PHENIX_COMPONENTS >>$PHENIX_LOG/binary.log 2>&1 Error configuring: see /root/phenix-installer-1.6.1-357/build-binary/intel-linux-2.6-x86_64/monst/log/binary.log for details" Thanks

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Re: [phenixbb] Restraining altloc related atoms during refinement
by John Pascal 20 May '10

20 May '10

>I have my doubts about supporting NCS restraints of alternative >conformations; the two seem to be mutually exclusive. But maybe >I don't understand your situtation. Here are some more details on the refinement situation: it is possible for a piece of duplex DNA to be positioned in two conformations in the crystal, and it appears that both conformations are occupied with roughly the same occupancy. The sequence is not completely palindromic, so at some positions a different base is present depending on the random orientation of the DNA. However, the phosphate and ribose atoms occupy the same positions regardless of the orientation, and I want to enforce this. >I can see that NCS restraints of backbone atoms only are useful, >even if the residue names are different. >The trouble is that atoms in two chains need to be matched >unambiguously while allowing for chain breaks. >I could try to simply remove the requirement that the residue names >have to match and go by residue sequence number + insertion code >only. Would that work in your case? Yes, that sounds like it would work. >A potential downside is that people have to be careful >excluding non-matching sidechain atoms. Perhaps it could be that there is an override option after an error message. Thanks for your help. -John -- John Pascal, PhD ph 215.503.4596 Assistant Professor fx 215.923.2117 Thomas Jefferson University Biochemistry & Molecular Biology 233 South 10th Street, BLSB 804 Philadelphia, Pennsylvania 19107 ----- Forwarded message from John.Pascal(a)mail.jci.tju.edu ----- Date: Thu, 20 May 2010 11:54:33 -0400 From: John Pascal <John.Pascal(a)mail.jci.tju.edu> Reply-To: John Pascal <John.Pascal(a)mail.jci.tju.edu> Subject: Restraining altloc related atoms during refinement To: phenixbb(a)phenix-online.org Hello All, I would like to restrain the positions of ribose/phosphate atoms of altloc 'A' to the positions of those in altloc 'B'. Problem is, altloc A and altloc B are different residue types, so phenix.refine exits stating that there are no common atoms when I enter the following NCS-type restraint: selection: chain I and altloc A and resid 1 and (phosphate or ribose) restrain: chain I and altloc B and resid 1 and (phosphate or ribose) I am using the phenix GUI. Is there a better place to enter this type of restraint (rather than NCS) that does not care if a P atom is from a Cd or from a Gd residue type? thanks. Best, John -- John Pascal, PhD ph 215.503.4596 Assistant Professor fx 215.923.2117 Thomas Jefferson University Biochemistry & Molecular Biology 233 South 10th Street, BLSB 804 Philadelphia, Pennsylvania 19107 ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. ----- End forwarded message ----- ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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Restraining altloc related atoms during refinement
by John Pascal 20 May '10

20 May '10

Hello All, I would like to restrain the positions of ribose/phosphate atoms of altloc 'A' to the positions of those in altloc 'B'. Problem is, altloc A and altloc B are different residue types, so phenix.refine exits stating that there are no common atoms when I enter the following NCS-type restraint: selection: chain I and altloc A and resid 1 and (phosphate or ribose) restrain: chain I and altloc B and resid 1 and (phosphate or ribose) I am using the phenix GUI. Is there a better place to enter this type of restraint (rather than NCS) that does not care if a P atom is from a Cd or from a Gd residue type? thanks. Best, John -- John Pascal, PhD ph 215.503.4596 Assistant Professor fx 215.923.2117 Thomas Jefferson University Biochemistry & Molecular Biology 233 South 10th Street, BLSB 804 Philadelphia, Pennsylvania 19107 ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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Re: [phenixbb] all reflections are equal, but some more than others
by Frank von Delft 20 May '10

20 May '10

Are you sure? It's the sigma estimation he talked about, and that does assume it's the same foe both strong and weak, doesn't it? ----- Reply message ----- From: "Phil Evans" <pre(a)mrc-lmb.cam.ac.uk> Date: Wed, May 19, 2010 21:22 Subject: [phenixbb] all reflections are equal, but some more than others To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> If by "scaling" you mean scaling unmerged observations together, I don't think it is right that it assumes a unimodal intensity distribution. In refinement I believe the underlying distributions are assumed to be unimodal, but in data reduction scaling there is no such assumption. That scaling just assumes that the experiment (mainly the diffraction geometry) can be parameterised in such a way that reflections close together in reciprocal space and in measurement time have similar and parameterisable scales. This is independent of the intensity distribution. Phil On 19 May 2010, at 08:44, esko.oksanen(a)helsinki.fi wrote: > Frank, > > Having had a case of such hectic pseudosymmetry, it turns out that the problem originates already from the scaling that assumes a unimodal intensity distribution. The weak reflections then have their sigmas heavily overestimated and the strong ones overestimated. I had to scale the weak and strong reflections separately and ridig-body refine against the weak ones... Of course this type of problem has little to do with issue of treating negative intensities. > > Esko > > Quoting "Frank von Delft" <frank.vondelft(a)sgc.ox.ac.uk>: > >> The philosophical arguments are fine, but is Pavel not justified in asking for real cases where it matters? It's not like he hasn't spent time thinking about it, and it's not like the whole phenix community isn't sitting in his ear about their own favourite missing fix. >> >> I suppose what comes to mind is a case with hectic pseudotranslation causing half the reflections to be systematically almost but not quite zero. But then again, I understand that even if you don't toss the weak ones out, current algorithms don't deal with this well anyway, so it needs special treatment (for now: refine in smaller cell, then rigid-body refine in super-cell). >> >> phx. >> >> >> >> >> >> On 18/05/2010 18:33, Ed Pozharski wrote: >>> On Mon, 2010-05-17 at 16:20 -0700, Peter Zwart wrote: >>> >>>> You make it sound like it is a bad thing. The effect of restraint >>>> weights (ADP, geometry) has most likely a much bigger impact on the >>>> final structure then a small fraction of smallish intensities (*) >>>> >>> Peter, >>> >>> I think discarding data has to be justified. Two points: >>> >>> 1. The fraction of negative intensities is not necessarily small. It >>> depends on resolution cutoff (and you make an excellent point about >>> PTS), but looking at scalepack log-files I can tell that in my hands the >>> fraction is often 10% or more (DISCLAIMER: I belong to I/sigma=1 >>> resolution cutoff cult). >>> >>> 2. Just because these reflections are weak does not mean that they are >>> insignificant. Their contribution to the maps may be small (now I fear >>> another round of "fill-in missing Fobs with Fc for map calculation" >>> discussion), but keeping Fc close to zero for these reflections during >>> refinement seems to be just as important as to keep Fc close to whatever >>> values the strong reflections have. >>> >>> The weak reflections are not fundamentally worse than strong(er) >>> reflections in the same resolution range. They are measured with >>> roughly the same precision. Moreover, the practice of setting negative >>> intensities to zero and then ignoring them in refinement discards those >>> that are barely negative and leaves in those that were (quite randomly) >>> barely positive. >>> >>> You are absolutely right that other factors will have impact on the >>> model. But that does not mean that discarding weak data is justified. >>> Crystallographic refinement is a Rube Goldberg machine, and all the >>> components should be as good as we can make them. Perhaps there could >>> be something better than French&Wilson, but discarding negative >>> intensity reflections is hardly the solution. >>> >>> Cheers, >>> >>> Ed. >>> >>> PS. Personally I have no stake in this, since I always use truncate. >>> >>> >>> >> _______________________________________________ >> 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

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View DM map from AutoSol gui?
by Francis E Reyes 19 May '10

19 May '10

I'm not a GUI kind of person but today I'm messing around with it. After AutoSol (with build=False... errr AutoBuild unchecked), I have an opportunity to 'View sites and experimental map' in coot or PyMOL. Wouldn't it be more useful if the gui loaded the DM maps as well? 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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changing TLS groups mid refinement
by Scott Classen 19 May '10

19 May '10

Hello Phenixers, Are there any considerations to changing TLS groups mid refinement? Can I rest assured that after a few rounds of refinement with the new TLS definitions everything will sort itself out or should I do something drastic, like remove all the ANISOU records, reset B factors to some constant value, and start over? Thanks, Scott

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phenix distorts ligand
by Mustafa Koksal 18 May '10

18 May '10

Hi, I have a problem in phenix refinement at 2.25 A resolution, data is 80% complete. I have protein, water, and ions in the .PDB file, and a ligand molecule that is distorted during refinement. I generated the pdb (with H atoms) with ChemDraw3D, edited the atom names etc. I used phenix.elbow to generate the .CIF file. Here is the first problem: Ligand has trans double bonds, which are written out by phenix.elbow as single rotatable bonds although I had correct connect records and H atoms in the .PDB file. I ran phenix.refine, it distorted the ligand, making double bonds not planar and nearly cis. Here is what I have tried: I edited the .CIF file to change these torsion agles to be CONSTANT and 180 or 0 deg. Here is the second problem: phenix.refine still distorted the ligand. Here is what I have tried: I used optimize_wxc/wxu in phenix.refine to optimize the weight, to see if I overweighed the data. Here is the third problem: phenix.refine still distorted the ligand. Is there a way to solve this problem? Is there a way to tighten the constraints for the ligand only? I still do not understand why it even cannot keep the double bonds planar (and trans). I do not want to move back to good old CNS... Thanks to all, Mustafa -- Mustafa Koksal Postdoctoral Fellow University of Pennsylvania Department of Chemistry Roy and Diana Vagelos Laboratories Office: 2090 IAST Office Phone: (215) 898-2227 Mobile Phone: (267) 319-6443 Mail Address: 231 S. 34th St, Philadelphia 19104, USA -- "If you grant me a pen, I shall destroy swords and spears" Mawlana Jalal-ad-Din Rumi --

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geometry_restraints between sym mates?
by Scott Classen 18 May '10

18 May '10

Hi all, Is this possible? # on working model bond { atom_selection_1 = "name SM and chain M and resname SM and resseq 1" atom_selection_2 = "name OE1 and chain A and resname GLU and resseq 313" distance_ideal = 2.5 sigma = 0.2 } # on SYM mol bond { atom_selection_1 = "name SM and chain M and resname SM and resseq 1" atom_selection_2 = "name OE1 and chain A and resname GLU and resseq 285" distance_ideal = 2.5 sigma = 0.2 } I'll find out in a few minutes when I run it through phenix.refine, but I thought to ask anyways. Thanks, Scott

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Looking at omit maps in coot
by xaravich ivan 17 May '10

17 May '10

Hi, Again this is pretty novice and I would apologize in advance. I ran Simulated annealing omit map in PHENIX and it gave me a bunch of files. I started with a partially built model ( I would say most of it was built) and it gave me an edited pdb that I can open in coot but I the composite omit mtz file is not opening in coot. In fact I cannot open any mtz file from the phenix output /OMIT directory and cannot see any map. I am pretty clueless. Thanks, Ivan

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An easier explanation of the regions in omit map
by xaravich ivan 17 May '10

17 May '10

Hi Nat, So I have quite a few regions build by the SA_omit map of phenix. But How do I go about looking at these maps. What am I looking for here. Should I look at the regions where the occupancy was set zero in all these outputs and find if I could build some thing from one of the maps? I guess I am asking, How do I use this information to move forward in refinement? There are 24 regions map and .pdb output in the /OMIT directory. Thanks, Ivan On Fri, May 14, 2010 at 5:52 PM, Nathaniel Echols <nechols(a)lbl.gov> wrote: > On Fri, May 14, 2010 at 5:40 PM, xaravich ivan <xaravich.ivan(a)gmail.com>wrote: > >> Again this is pretty novice and I would apologize in advance. >> I ran Simulated annealing omit map in PHENIX and it gave me a bunch of >> files. I started with a partially built model ( I would say most of it was >> built) and it gave me an edited pdb that I can open in coot but I the >> composite omit mtz file is not opening in coot. In fact I cannot open any >> mtz file from the phenix output /OMIT directory and cannot see any map. >> I am pretty clueless. >> > > Some clarification: > > 1. Which version of Phenix, and which platform? > 2. GUI or command-line? > 3. If you're really making a composite omit map (as opposed to a simple > omit map, e.g. for a ligand), ignore the PDB file output by AutoBuild and > stick to the original. > > One common problem is that on Mac, if you try to open the MTZ file in Coot > (using the "Open MTZ", not auto-open), it will open a window to choose > column labels in the file, but it opens *behind* the main window, which you > need to move to the side temporarily. > > -Nat > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > >

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Building DNA
by Rajagopalan, Senapathy 15 May '10

15 May '10

Dear Phenix developers, I am solving a protein-dna complex and Autobuild is able to build both the protein as well as DNA chain (one at a time). However, when I try to do the refinement, I get an error saying "Phenix could not find the geometry restraints in the standard monomer library for one or more residues in the pdb file... DG: 6 copies, DA: 3 copies, DT: 43 copies". It seems like Autobuid uses the nomenclature DA, DC, DG and DT for the DNA bases while Phenix.Refine either doesn't like the nomenclature or the restraint files uses a different one. It still however lets me do the refinement...although I don't know if it just ignores the DNA part. Can someone enlighten me on this. Also, the nomenclature Coot seems to like is Ad, Cd, Gd, Td for the DNA and doesn't like the above phenix style. In order to manipulate in coot, I had to rename all the bases...is it possible to have a format that is compatible both in Phenix and Coot or am I missing something obvious here. Thanks and Have a great weekend! Sena Methodist. Leading Medicine. Recognized by U.S.News & World Report as an "Honor Roll" hospital Named to FORTUNE magazine's "100 Best Companies to Work For" list five years in a row Designated as a Magnet hospital for excellence in nursing Visit us at methodisthealth.com Follow us at twitter.com/MethodistHosp and www.facebook.com/methodisthospital ***CONFIDENTIALITY NOTICE*** This e-mail is the property of The Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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Improved refinement method for low resolution data
by Florian Nachon 14 May '10

14 May '10

Hi all, Axel Brunger just published a paper in Nature (http://www.nature.com/nature/journal/v464/n7292/abs/nature08892.html) about a new method to improve models despite low-resolution data. It is implemented in CNS 1.3. It might be a bit early, but is there any plan to implement that method in phenix? Florian.

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where do phenix.metal_coordination ideal bond lengths come from?
by Scott Classen 14 May '10

14 May '10

Hello, I have a structure with several water/carboxylate-coordinated metal ions and I am using phenix.metal_coordination to generate the restraints parameter file for phenix.refine. Can someone please tell me where phenix.metal_coordination is getting the ideal bond length/angle values from. Thanks, Scott Classen

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Gordon Conference on Diffraction Methods
by A Leslie 14 May '10

14 May '10

Just a reminder that there is still time to register for the Gordon Conference on Diffraction Methods in Structural Biology, that will be held at Bates College in Lewiston, Maine from 18-23rd July. The program (see below) covers all aspects of macromolecular crystallography, from crystallization to structure solution and refinement, and includes sessions on complementary techniques and the potential of free electron lasers. Many of the leading methods developers will be present and the format of the meeting, with free afternoons, provides ample opportunities for informal discussions. Further details, including a full program and details on the application procedure can be obtained from: http://www.grc.org/programs.aspx?year=2010&program=diffrac We hope to see you there ! Andrew Leslie (Chair) & Ana Gonzalez (Vice Chair) Outline Program: Sunday pm: Macromolecular Structures, Pushing the boundaries Discussion leader: Michael Rossmann 1. ABC Transporters: Doug Rees 2. The Spliceosome : Kyoshi Nagai Monday am: Crystallisation and the diffraction experiment Discussion leader: Zbyszek Dauter 1. Nanolitre crystallisation: Seth Harris 2. Twinning and disorder: Todd Yeates 3. Simulating the diffraction experiment: James Holton 4. Microcrystallography: Gwyndaf Evans Monday pm: Radiation damage and data collection strategies Discussion leader: Vivian Stojanoff 1. Radiation damage, experimental: Elspeth Garman 2. Microbeams: Yanhui Zou 3. Testing data collection strategies with the Pilatus: Marcus Mueller Tues am: Synchrotron developments and automated data processing Discussion leader: Thomas Schneider 1. Synchrotrons, latest developments: Sean Mc Sweeney 2. Synchrotrons, latest developments: Janet Smith 3. Data processing with Xia2/CHEF: Graeme Winter 4. Data processing with AUTOPROC: Clemens Vonrhein Tues pm: Complementary techniques Discussion leader: Ana Gonzales 1. Electron tomography: Sriram Subramaniam 2. SAXS: Hiro Tsuruta 3. Spectroscopy: Carrie Wilmot Weds am: Structure solution and refinement Discussion leader: Paul Adams 1. SAD Phasing: Randy Read 2. Molecular replacement with BALBES: Garib Murshudov 3. PHENIX: Tom Terwilliger 4. TLS: Ethan Merritt Weds pm: Challenging problems/Membrane Proteins Discussion leader: TBC 1. Using cubic lipidic phase: Martin Caffrey 2. Membrane Proteins: Stephen White 3. The Bacterial Ribosome: Venki Ramakrishnan Thurs am: Selected Posters and Map improvement and Model building Discussion leader: Tassos Perrakis 1. COOT: Paul Emsley 2. Modelling nucleic acids: Johan Hattne Thursday pm: Future Methods, FELs, Diffraction imaging Discussion leader: Ed Lattman 1. Anton Barty 2. Serial Crystallography: John Spence and Petra Fromme

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question about free energy calculation in protein complex
by crystallogrphy 14 May '10

14 May '10

Hi, I am trying to calculate the free energy of association for structure of a protein complexes based on the salt bridges, H-bonds and van der waals interaction? Does any one know how to do it? Thanks!

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