- phenixbb - phenix-online.org

Re: [phenixbb] Question/enhancement request for automated datafile conversion
by Ralf W. Grosse-Kunstleve 06 Feb '08

06 Feb '08

Hi Carsten, > The .sca file (or dtrek .ref) file gets automatically converted to a > mtz file with I-obs and SIGI-obs and refinement proceeds as expected. I > just noticed that in the following ...002.def file and in the 001.eff > file the parameter xray_data.observation_type is set to amplitude > instead of intensities. What is going on there, is phenix smart enough > to know when it deals with amplitudes vs. intensities? Did not seem to > have much effect on the refinement though when I switched this around, > which is surprising. That parameter wasn't actually used. I just removed it completely. Thanks for alerting us to this. > As an enhancement request: Would it be possible that the autoconversion > writes out a mtz file which contains BOTH amplitudes and intensities > instead of intensities and R-flags alone? OK, done! You will see the change in the next release (hopefully very soon). Ralf

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Question/enhancement request for automated datafile conversion
by Schubert, Carsten [PRDUS] 06 Feb '08

06 Feb '08

Hi, I noticed that there is a possible inconsistency in the handling of xray datafiles in phenix. For instance, we usually invoke phenix like this: phenix.refine my.sca my.pdb my.def The .sca file (or dtrek .ref) file gets automatically converted to a mtz file with I-obs and SIGI-obs and refinement proceeds as expected. I just noticed that in the following ...002.def file and in the 001.eff file the parameter xray_data.observation_type is set to amplitude instead of intensities. What is going on there, is phenix smart enough to know when it deals with amplitudes vs. intensities? Did not seem to have much effect on the refinement though when I switched this around, which is surprising. As an enhancement request: Would it be possible that the autoconversion writes out a mtz file which contains BOTH amplitudes and intensities instead of intensities and R-flags alone? Sometimes it happens that I need to go back to running phaser when the initial rigid body refinement does not grip. Since phaser just runs on amplitudes I need to add a couple of extra steps to get a file, which is useful for both programs. I think the underlying philosophy should be that once data has been imported into the phenix suite, from whichever entry point, it should be usable w/o conversion in all applications. Cheers, Carsten

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Question abount B-factor refinement - B-factors = 0
by Schubert, Carsten [PRDUS] 04 Feb '08

04 Feb '08

Hi, I have a question about B-factor refinement in phenix. This is a reiteration of one or two of threads with the same subject dating back to September last year: Initially, I noticed that the B-factors within a residue have quite a large spread, when one runs a temperature factor variance analysis as implemented in coot (Yes I read Pavel's response about this ...). This prompted me to actually look at the B-factors in the PDB file. I noticed that actually for quite a few residues one or more of the B-factors refines to 0.00 For instance one of the less extreme examples: ATOM 118 N HIS A 21 -28.768 35.430 2.317 1.00 4.73 N ATOM 119 CA HIS A 21 -27.357 35.565 2.625 1.00 0.00 C ATOM 120 C HIS A 21 -27.124 35.408 4.116 1.00 2.25 C ATOM 121 O HIS A 21 -28.072 35.360 4.902 1.00 7.73 O ATOM 122 CB HIS A 21 -26.853 36.940 2.186 1.00 8.10 C ATOM 123 CG HIS A 21 -27.610 38.078 2.799 1.00 11.18 C ATOM 124 ND1 HIS A 21 -28.733 38.624 2.216 1.00 17.18 N ATOM 125 CD2 HIS A 21 -27.418 38.759 3.955 1.00 13.28 C ATOM 126 CE1 HIS A 21 -29.194 39.600 2.979 1.00 25.70 C ATOM 127 NE2 HIS A 21 -28.414 39.701 4.041 1.00 12.79 N As background the data extends to 1.8A, with an I/I(s) of ~15 and ~2.5 in the highest shell, CHI^2 are all around 1+/ 0.1. The Wilson B is 11.3A^2 and R/Rfree 16.8/19.8%. This is homesource date, at the synchrotron I could probably push the resolution further out to better than 1.6A. No hydrogens were added, nor was TLS used. In order to get around the problem I initally reset all B-values to the Wilson-B, enabled wxc refinement (latest CCI-APPs) and refined ADPs only for 10 macrocycles. After a couple of cycles the B-factor distribution settled into the following, which looks fairly reasonable to me, except for the min values of 0.00: |-ADP statistics (Wilson B = 11.289)------------------------------------------| | Atom | Number of | Isotropic or equivalent| Anisotropy lmin/max | | type |iso aniso | min max mean | min max mean | | - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - - | | all : 2659 0 0.00 129.99 13.58 None None None | | all(noH): 2659 0 0.00 129.99 13.58 None None None | | Sol. : 390 0 0.35 56.99 27.75 None None None | | Mac. : 2269 0 0.00 129.99 11.14 None None None | | Hyd. : 0 0 None None None None None None | | - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | | Distribution of isotropic (or equivalent) ADP for non-H atoms: | | Bin# value range #atoms | Bin# value range #atoms | | 0: 0.000 - 12.999: 1778 | 5: 64.993 - 77.991: 17 | | 1: 12.999 - 25.997: 492 | 6: 77.991 - 90.990: 9 | | 2: 25.997 - 38.996: 210 | 7: 90.990 - 103.988: 4 | | 3: 38.996 - 51.994: 124 | 8: 103.988 - 116.987: 2 | | 4: 51.994 - 64.993: 19 | 9: 116.987 - 129.985: 4 | | =>continue=> | |-----------------------------------------------------------------------------| B-factors of 0 indicate to me that there is a problem, not sure how to tackle this in phenix at this point. Could there be a problem with the bulk-solvent scaling? Should I restrict the minimum B-factor to 1.0 (ugggh)? Or should I tighten the B-factor restraints? Cheers, Carsten

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Re: [phenixbb] Maps from twinned data
by Peter Zwart 04 Feb '08

04 Feb '08

Hi Mary, Can you try and download the latest cci_apps and recompute the maps with phenix.refine? I did make some updates since rc6 in the dewtinning code. Cheers Peter 2008/2/1, Mary Fitzgerald <mary.x.fitzgerald(a)gmail.com>: > Peter- > I've attached an image from coot. I loaded my model and then a cns > detwinned 3fo-2fc map (purple) and the 2fo-fc (blue) from phenix both are > contoured at 1.5. The 3fo-2fc is the only map have at the moment equivalent > to the 2fo-fc model although it had waters in the model. I have the > symmetry brought up and there's not a symmetry related molecule in the area. > I've been working with this model quite a while and have never seen density > there before. It shows up in a couple of other spots as well with nothing > appearing in the fo-fc maps, which I didn't show here. It looks as if I'm > missing part of my model in areas that there shouldn't be any model. > > Thanks, > Mary > > > On Feb 1, 2008 2:59 PM, Peter Zwart <PHZwart(a)lbl.gov> wrote: > > Can you send a picture of the density and/or the data and model so I > > can have a look. > > The detwinning is done differently and for twin fractions of 0.5 > > something weird mihgt be happening. > > > > Thanks > > > > Peter > > > > > > > > > > 2008/2/1, Mary Fitzgerald <mary.x.fitzgerald(a)gmail.com>: > > > > > > > > > I'm new to phenix and just installed Phenix 1.3 beta rc6. > > > > > > I've taken a data set that I've been refining in cns and am trying > > > phenix.refine. The data has a twinning fraction of 0.5. I'm seeing > what I > > > think is odd in the 2mFobs-DFmodel.map. If I'm reading the > documentation > > > correctly, this map should be detwinned (I also set > > > > refinement.twinning.detwin.map_types.aniso_correct=true), I > > > see alot of extra density where there is no model, nor a symmetry > related > > > molecule in coot. I don't see this extra density in my detwinned 2fofc > cns > > > maps. > > > > > > So, could the extra density I'm seeing be due to using a different > program > > > and it is detwinning the data differently. The extra density is from > the > > > twin???? > > > > > > Any input would be appreciated, > > > > > > Mary X. Fitzgerald > > > Postdoctoral Associate > > > Arnold Lab > > > > > > > > > _______________________________________________ > > > phenixbb mailing list > > > phenixbb(a)phenix-online.org > > > http://www.phenix-online.org/mailman/listinfo/phenixbb > > > > > > > > > > >

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Maps from twinned data
by Mary Fitzgerald 01 Feb '08

01 Feb '08

I'm new to phenix and just installed Phenix 1.3 beta rc6. I've taken a data set that I've been refining in cns and am trying phenix.refine. The data has a twinning fraction of 0.5. I'm seeing what I think is odd in the 2mFobs-DFmodel.map. If I'm reading the documentation correctly, this map should be detwinned (I also set refinement.twinning.detwin.map_types.aniso_correct=true), I see alot of extra density where there is no model, nor a symmetry related molecule in coot. I don't see this extra density in my detwinned 2fofc cns maps. So, could the extra density I'm seeing be due to using a different program and it is detwinning the data differently. The extra density is from the twin???? Any input would be appreciated, Mary X. Fitzgerald Postdoctoral Associate Arnold Lab

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phenix.refine & twin fraction
by Karolina Michalska 29 Jan '08

29 Jan '08

Dear all, Can onyone tell me how to introduce twin fraction to the refinement parameters? According to phenix.xtriage it should be 0.4 but phenix.refine uses 0.2. Thanks a lot, Karolina -- *********************************** Karolina Michalska, PhD Dept. of Crystallography Faculty of Chemistry A. Mickiewicz University ul. Grunwaldzka 6 60-780 Poznan, Poland ***********************************

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Re: [phenixbb] phenix.find_ncs and DANO
by Tom Terwilliger 24 Jan '08

24 Jan '08

Hi Bryan, >in principle, phenix.find_ncs should be fine with FP=DANO, right? I'm not quite clear on this, but yes, find_ncs wants a map, and you can give it any map coefficients with labin="labin FP=FP PHIB=PHIB FOM=FOM " >and - do i understand correctly that phenix only correlates the map with >the .pdb sites, and does not rotate the map about itself (like in getax, i >think)? Correct, find_ncs is looking for NCS in the heavy-atom sites as presented in a PDB file, or in a model as given in a PDB file, without rotating the map. Any crystallographic symmetry is automatically applied. >-bryan > >p.s: > >i can run phenix.find_ncs with FP=DANO, but seems that resolve wants it to >be FP as usual. It might be helpful if you could send me this example! I hope that helps! -Tom T Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB

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high resolution refinement with phenix.refine
by Pavel Afonine 22 Jan '08

22 Jan '08

Dear phenix.refine users: responding to Vijayalakshmi Janakiraman's questions about refinement at high resolution with phenix.refine, I finally documented this functionality of phenix.refine and supplied it with a small example. This paragraph (see attached HTML file) will be available as part of phenix.refine documentation in the next release of PHENIX and CCI Apps. *Important:* writing this text I assumed that the latest version of phenix.refine is used (currently, it is one from CCI Apps: /2008_01_09_2058/ , http://www.phenix-online.org/download/). Cheers, Pavel. >> I have a high resolution structure with NADP as ligand bound to it. >> I was using CNS to start with. Somehow the Rfree was always very >> high. But when I tried with default options of data= and model=, >> in phenix.refine with the whole data and the intial rigid body >> refined coordinates from CNS, the Rfactors came down to 31%. I have >> now decided to do refinements with phenix.refine. >> Do you suggest any protocol for refinement of structure at this high >> resolution starting from initial rigid body refinements? >> Since I would like to handle alternate conformations in the final >> steps. I am wondering if the 2007 July version could handle >> refinements of alternate conformations. >> Thanks, >> Viji

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Re: [phenixbb] Autosol Feedback and questions
by Tom Terwilliger 22 Jan '08

22 Jan '08

Hi Partha, At 03:53 AM 1/2/2008, you wrote: >Happy new year everybody, > >I had quite a bit of difficulty with a SAD dataset which also showed >Sulphur. Previously I had tried SHELEX to find sites, MLPHARE to >refine, AddSOLVE to find more , and both SOLVE and PHASER to solve >but it did not get to a point where I could do manual building. >Autosol worked beautifully, the input files were scalepack merged >data, ha.pdb (from addsolve step), and the sequence. PHASER to solve >and TEXTAL & RESOLVE with through build option. > >This actually leave me with some confusions / questions: > >1. When I compare the other "solutions", they look like the right >one, just not good enough. Where exactly is the autosol making a >difference? Is it the ability of of TEXTAL to build something more >meaningful when the solution is not good or number of iterations? Autosol uses the quality of the model built as a score, if any model is built (R-factor if < 0.40; number of residues built less 2 * number of chains otherwise).. If no model is built, it uses the standard 4 or 5 criteria that are printed out on the AutoSol wizard screen (CC and R-factor for density modification; skew of electron density histograms, FOM, CC of NCS). >2. How does PHASER know the different anomalous atoms? Does is use a >different scaling factor for SE and S? It can tell by the ratio of anomalous to real scattering corresponding to each atom. >3. I see that phenix.refine has been used in the internal runs, I >have used phenix.refine earlier. But after playing with the side >chains in Coot, when I tried to use the modified pdb file and >resolve.mtz, it complained about the good old Free_R flag. However, >it ran directly in Refmac. Is it a known problem or maybe I did >something stupid? I could do a dry run and change the read mtz and >not cns if that would solve the problem. As Pavel and Ralf have mentioned, this is because AutoSol has tossed a few (usually blank) reflections from your reflection file when it created the refinement file exptl_fobs_phases_freeR_flags_15.mtz # or something similar. Without the "_15" if from AutoBuild The solution is to either (1) use the refinement file from AutoSol (exptl_fobs_phases_freeR_flags_15.mtz), or to delete the MD5 remark record from the AutoSol/AutoBuild PDB file. >4. Lastly, is it possible to use multiple processors to run the job? As Pavel mentioned...we are thinking about this but do not have anything yet. -Tom T Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB

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Re: [phenixbb] Continue from an AutoBuild job abruptly killed
by Tom Terwilliger 22 Jan '08

22 Jan '08

Hi Miguel, I'm sorry for the slow response...you can continue AutoBuild by typing: phenix.autobuild run=1 if you were previously on run #1 and you want to continue it. All the best, Tom T At 02:24 AM 1/16/2008, you wrote: >Dear all, > >We had a problem with a machine running >AutoBuild, which resulting in the computer going >down and the AutoBuild job consequently killed. >I've tried to find out if there is a way to >continue the job (it had been running for four >days and still had a few hours to go I guess: a >pretty big unit cell) but I failed. I would >appreciate if someone could point to the >relevant pages in the manual/tutorials or give >me advice about how to do such a thing. If that's possible, of course. > >We're using the latest phenix (1.3b-rc6) and cci apps. > >Thank you! > > >Miguel >-- ><http://www.pangea.org/mol/spip.php?rubrique2>http://www.pangea.org/mol/spip.php?rubrique2 > >~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >Je suis de la mauvaise herbe, >Braves gens, braves gens, >Je pousse en liberté >Dans les jardins mal fréquentés! > >Georges Brassens >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://www.phenix-online.org/mailman/listinfo/phenixbb Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB

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Re: [phenixbb] picking Rfree set
by Peter Zwart 22 Jan '08

22 Jan '08

yes, it will. This is useful for when the data is twinned. P 2008/1/22, David Garboczi <dgarboczi(a)niaid.nih.gov>: > So, for instance, when addition of a ligand to a P212121 cell (1 mol) > changes the symmetry to P21 (almost same cell, but 2 mol), the > selection of the Rfree set from the P21 data by phenix.refine will > take the higher almost symmetry into account? > > Dave > > >btw3: the lattice symmetry is taken into account when choosing an free > >set in phenix.refine (unless specified otherwise). If all NCS > >rotational operators are approximately parallel to twin laws, you > >should be fine. > > > >P > > > > > > > > > > > >2008/1/22, Ralf W. Grosse-Kunstleve <rwgk(a)cci.lbl.gov>: > >> > Does phenix.refine take NCS into account when picking the Rfree set? > >> > Thin shells, or other strategy... > >> > >> The short answer is no. > >> We had long internal discussions about this without reaching a final > >> conclusion. In the long run we may integrate alternative R-free set > >> distributions in phenix.refine; in the meantime you have to use > >> an external program (e.g. dataman or sftools). > >> BTW 1: just to prove that we have thought about this subject, we have a > >> simple tool for "visualizing" distributions of R-free flags: > >> iotbx.r_free_flags_accumulation your.mtz > >> It writes a file with x,y pairs which you can plot with e.g. Excel > >> or any other 2D plotting program. > >> BTW 2: The free reflections aren't as free as one may think. When > >> using a maximum likelihood target (any program), the free reflections > >> are used in the estimatation of the error model. This estimation > >> becomes more tricky if the reflections are distributed in thin > >> shells. I.e. if you go to thin shells you may in fact account to some > >> degree for the NCS, but at the same time you compromise the error > >> model estimation. > >> Ralf > >> _______________________________________________ > >> phenixbb mailing list > >> phenixbb(a)phenix-online.org > >> http://www.phenix-online.org/mailman/listinfo/phenixbb > >> > >_______________________________________________ > >phenixbb mailing list > >phenixbb(a)phenix-online.org > >http://www.phenix-online.org/mailman/listinfo/phenixbb > > > -- > David N. Garboczi, PhD > Phone: 301-496-4773 > Investigator, Structural Biology Section (SBS) > Laboratory of Immunogenetics (LIG) > National Institute of Allergy and Infectious Diseases (NIAID) > National Institutes of Health (NIH) > Twinbrook 2/Room 110 > 12441 Parklawn Drive > Rockville, Maryland 20852-1742 > Fax: 301-402-0284 > Email: dgarboczi(a)niaid.nih.gov > > > > > The information in this e-mail and any of its attachments is > confidential and may contain sensitive information. It should not be > used by anyone who is not the original intended recipient. If you have > received this e-mail in error please inform the sender and delete it > from your mailbox or any other storage devices. The National Institute > of Allergy and Infectious Diseases (NIAID) shall not accept liability > for any statement made that are the sender's own and not expressly made > on behalf of the NIAID by one of its representatives. > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb >

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picking Rfree set
by David Garboczi 22 Jan '08

22 Jan '08

Does phenix.refine take NCS into account when picking the Rfree set? Thin shells, or other strategy... Dave --

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Re: [phenixbb] autosol : input_ncs_file
by Tom Terwilliger 22 Jan '08

22 Jan '08

Hi Bryan, No, autosol does not let you tell it what the NCS is with input_ncs_file. This is a good idea, however... -Tom T At 06:45 PM 1/15/2008, you wrote: >using PHENIX VERSION: 1.3b of 20-11-2007. > >does phenix.autosol use "input_ncs_file"? > >the documentation implies that phenix.autosol will take `input_ncs_file` >(at the 'find_ncs' entry, "input_ncs_file" is mentioned but no where >else), yet, i get a 'Sorry, unknown file or keyword:' message with no such >command line option listed. > >-bryan >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://www.phenix-online.org/mailman/listinfo/phenixbb Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB

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modify_start_model.adp.set_b_iso doesn't seem to work on PDB files with ANISOU cards
by Stephen Graham 21 Jan '08

21 Jan '08

Hi all, I just tried to reset my B values to the wilson B before TLS refinement (in an attampt to shake some model bias that I am sure is hiding somewhere in my temperature factors...). My start model was a TLS-refined PDB file from phenix.refine (hence with ANISOU cards). I issued the following command: > phenix.refine my_model.pdb my_data.mtz modify_start_model.adp.set_b_iso=60 output.prefix=my_model_resetB main.number_of_macro_cycles=0 As far as I can tell, this should reset my B values to 60 and then exit. However, when I look at the resultant PDB file the Bs for all the solvent molecules 60 but for the protein they are not; rather the protein Bs are almost identical to the starting PDB file. If I try to remove the TLS-derived ANISOU cards by adding the command line option "adp.convert_to_isotropic=true" the result is the same (except the output PDB file no longer has ANISOU cards). However, if I strip out the ANISOU cards from my starting pdb file and _then_ run the above command the resultant PDB file _does_ have the correct values for both protein and solvent. It seems like modify_start_model.adp.set_b_iso=60 does not work when atom has an ANISOU card. The behaviour I would *expect* would be for the adp be reset to an 'isotropic' 60 (i.e. set the diagonal elements to 1 and the off-diagonals to 0). Is this a bug, or am I doing something silly? Cheers, Stephen -- Dr Stephen Graham Nuffield Medical Fellow Division of Structural Biology Wellcome Trust Centre for Human Genetics Roosevelt Drive Oxford OX3 7BN United Kingdom Phone: +44 1865 287 549

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d_min_textal=
by Bryan W. Lepore 18 Jan '08

18 Jan '08

the documentation says : "Textal has an optimal high-resolution limit of 2.8 A" is that to say that resolutions != 2.8 are not optimal? -bryan

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Re: [phenixbb] disulfide bonds in phenix.refine
by Ralf W. Grosse-Kunstleve 18 Jan '08

18 Jan '08

Hi Allister, > 1) How do I specifically prevent a disulfide bond from being defined > between two sulfurs that are close together (I tried manipulating the > "disulfide_distance_cutoff" variable but this doesn't seem to stop a > disulfide being formed). If you set, e.g. disulfide_distance_cutoff=0.1 you shouldn't get any disulfide bonds anymore. I just tried it on a small structure and it worked as expected. > 2) How can I soften the restraint on the disulfide bond length for > specific cysteine residues. With the current phenix.refine you cannot edit the automatically determined disulfide bonds (sorry). However, you can use disulfide_distance_cutoff=0.1 to turn off the automatic bonds. Then use geometry_restraints.edits (see documentation at http://phenix-online.org/documentation/refinement.htm) to define the disulfides manually one by one, with the ideal distances and sigmas you want to use. Use a log file from a previous phenix.refine run to obtain the list of all disulfides. Ralf

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disulfide bonds in phenix.refine
by Allister.Crow＠uea.ac.uk 18 Jan '08

18 Jan '08

Hello all, I am currently trying to refine a structure (with phenix.refine) that contains a number of disulfide bonds. Many of these disulfides appear to be partly broken such that the default restraints given to these disulfides by phenix.refine cause the cysteine sulfur atoms to be placed too close to one another. This results in difference density in the fo-fc map. I want to try to model these partially broken states a bit more accurately, either by modelling two alternative conformations (i.e. one cysteine pair in a disulfide and the other pair as free thiols) or by allowing the disulfide bond distance to stretch. Currently refinement drives the S-S bond length close to dictionary values regardless of how far apart I model the cysteines in my input pdb file and whether the density implies a bridge or not. My two questions are: 1) How do I specifically prevent a disulfide bond from being defined between two sulfurs that are close together (I tried manipulating the "disulfide_distance_cutoff" variable but this doesn't seem to stop a disulfide being formed). 2) How can I soften the restraint on the disulfide bond length for specific cysteine residues. Thanks for your time. Dr. Allister Crow

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Continue from an AutoBuild job abruptly killed
by Miguel Ortiz-Lombardía 17 Jan '08

17 Jan '08

Dear all, We had a problem with a machine running AutoBuild, which resulting in the computer going down and the AutoBuild job consequently killed. I've tried to find out if there is a way to continue the job (it had been running for four days and still had a few hours to go I guess: a pretty big unit cell) but I failed. I would appreciate if someone could point to the relevant pages in the manual/tutorials or give me advice about how to do such a thing. If that's possible, of course. We're using the latest phenix (1.3b-rc6) and cci apps. Thank you! Miguel -- http://www.pangea.org/mol/spip.php?rubrique2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Je suis de la mauvaise herbe, Braves gens, braves gens, Je pousse en liberté Dans les jardins mal fréquentés! Georges Brassens

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MSE gap
by Troy E Messick 16 Jan '08

16 Jan '08

Hello, I seem to be having a problem with phenix.refine and the seleno-methionine residue (resname MSE). It seems that I have a gap in the peptide bond between the C atoms and the N atom of the subsequent residue. Is there something I could add to the restraints_edits.params file to get it to click together? What is the distance_ideal and sigma for a peptide bond? Thanks for your help, Troy

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phenix.find_ncs and DANO
by Bryan W. Lepore 15 Jan '08

15 Jan '08

in principle, phenix.find_ncs should be fine with FP=DANO, right? and - do i understand correctly that phenix only correlates the map with the .pdb sites, and does not rotate the map about itself (like in getax, i think)? -bryan p.s: i can run phenix.find_ncs with FP=DANO, but seems that resolve wants it to be FP as usual.

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autosol : input_ncs_file
by Bryan W. Lepore 15 Jan '08

15 Jan '08

using PHENIX VERSION: 1.3b of 20-11-2007. does phenix.autosol use "input_ncs_file"? the documentation implies that phenix.autosol will take `input_ncs_file` (at the 'find_ncs' entry, "input_ncs_file" is mentioned but no where else), yet, i get a 'Sorry, unknown file or keyword:' message with no such command line option listed. -bryan

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strategy of refinement for a structure phased by bromide soaking
by Pascal EGEA 10 Jan '08

10 Jan '08

Dear All, I have a 1.8A resolution data set of a protein collected on a crystal soaked in KBr and I am solving using Phenix. I used AutoSol and gave a rough estimate of f_prime and f_double_prime for the Br scatterer as a starting point. It worked great and Phenix found 31 Bromide ions (only one is fully occupied) and the resulting map is remarkably clear. Automatic building has done a great job and I was able to build most of the 4 monomers present in the AU. However I am confused and have a couple of questions. 1-As Phenix started it generated a fobs_experimental_phases_free_Rflag.mtz file. I have been using this file and no longer my data.hkl file for further refinement. I would like to know why the best_solution after the automatic building run does not contain any of the Bromide ions. It has water molecules but no Bromide ions? What is the reason for that? 2-I have been refining against the mtz file I mentioned but without any of these Bromide ions and although the refinement is converging , I suspect I have been doing something bad and wrong. Should I start my refinement again from the first best pdb after automatic building and include right away the bromide ions with simultaneous f_prime, f_double_prime and occupancy refinement for the anomalous scatterers? As it stands now the Rfree is 22.9 and the Rfac is 19.7. The map looks fine except for the solvent, some of this atoms are obviously bromide and there is extra density in the Fo-Fc around some "solvent" atoms. Thanks a lot in advance for your suggestions. Pascal Egea University of California San Francisco Department of Biochemistry and Biophysics

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iotbx.shelx.from_ins
by Foelker, Andrew 10 Jan '08

10 Jan '08

Hello Perhaps one of you could assist me with this question. In the from_ins.py file, there is a function by the name of from_ins. I am passing a .RES file to this function, but am not passing any of the other optional arguments to it. When line 51 in the file is reached, an exception is thrown. Here is the line of code that blows up: b = record.tempFactor + record_next.tempFactor The exception correctly states that the record_next object has no attribute named 'tempFactor'. Perhaps I am doing something incorrectly, or perhaps there is a bug in the from_ins function itself. If any of you can offer some insight into this problem I would greatly appreciate it. Thank you. ------------------------------------------------------------------------ -------- Andrew J. Foelker Software Engineer Bruker AXS Inc. 5465 E. Cheryl Parkway Madison, WI 53711 Tel: +1 608-276-3812 andrew.foelker(a)bruker-axs.com www.bruker-axs.com <http://www.bruker-axs.com/> ------------------------------------------------------------------------ ----------

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Reading Rfree Flags from Refmac
by James Fraser 08 Jan '08

08 Jan '08

Hello, Someone in our lab has started a refinement run in REFMAC and wants to continue it in Phenix.refine. Is there an easy way to get phenix to recognize the r-free flag from REFMAC (freeR=0)? Thanks, jf -- James Fraser jamesfraser(a)berkeley.edu Alber Lab 356 Stanley Hall, QB3 UC Berkeley Berkeley, CA 94720 http://ucxray.berkeley.edu/~jfraser/

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Failure when calculating a composite omit map
by Dale Tronrud 07 Jan '08

07 Jan '08

Hi all, I'm trying to calculate a composite omit map so that I can get a clear view of a troublesome region in my structure. I have two copies of everything in the asu so I created some dummy atoms to mask the region in the A chain and called those atoms chain Y and another collection to mask the region in the C chain and created a Z chain for them. I put these atoms in a file name Mask.pdb I attempted to calculate the composite omit map starting from my MR solution but that fails because Autobuild doesn't like being given the Fourier coefficients produced by Phaser. To work around this problem I decided to ask it to create the omit map based on the results of my AutoBuild followed the MR. My script is: phenix.autobuild model=AutoBuild_run_12_/overall_best.pdb data=1M50-2.mtz \ input_refinement_labels="FP SIGFP None None None None None None FreeR_flag" \ seq_file=../fmo-ct.pir \ resolution=2.2 dmax=20 refinement_resolution=2.2 \ cif_def_file_list=/usr/users/dale/geometry/chromophores/bcl_tnt.cif \ input_lig_file_list=AutoMR_run_4_/MR.1-Bchl-a.pdb \ composite_omit_type=iterative_build_omit omit_region_specification=omit_around_pdb omit_box_pdb=Mask.pdb\ omit_res_start_list="1 1" omit_res_end_list="39 30" omit_chain_list="Y Z" \ rebuild_in_place=Yes Mask.pdb is attached. Resolve is unable to create a mask. The log file, omit_box_id.log is also attached. Resolve creates a temp file named TMP.pdb which I would expect to contain the contents of my Mask.pdb. It only contains the first set of dummy atoms; chain Y. Then when Resolve reads this file it appears not to find even those atoms. I know Tom is out of reach for quite a while. Is there someone else who could help me over this hurdle? Dale Tronrud

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