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Nov 15, 2010 deadline- User proposal submission for Collaborative Crystallography at BCSB
by Banumathi Sankaran 08 Nov '10

08 Nov '10

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

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Fixing a ligand by a symmetry axis
by Simon Kolstoe 04 Nov '10

04 Nov '10

Dear Phenix bb, I have a palindromic ligand bound to my protein that crosses a symmetry axis. Although the head-group that is in close contact with the protein refines beautifully (in phenix..refine version 1.6.4 run from the command line on a mac), the atom closest to the symmetry axis get knocked away from the equivalent atom that it binds to on the other side of the symmetry axis. Is there any way of stopping phenix.refine from refining the atoms closest to the symmetry axis, or should I just manually position the wayward atom in the appropriate orientation prior to my structure deposition? Thanks, Simon

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More trained monkeys please (request for improvements to auto-NCS)
by Kendall Nettles 03 Nov '10

03 Nov '10

Dear PHENIX developers, I am writing to ask about the automated NCS selection procedure. I have a structure with 2 homodimers in the ASU, and there are significant differences in the two monomers that make up teach dimer. When I run automr/autobuild I am very pleased with the result overall, but it does not choose the best NCS groups- it groups all chains to the A chain, instead of one dimer to the other. The result is a helix that is obviously out of place (see attached image). I wonder if this could be fixed by implementing a throw away round of refinement, in order to identify optimal NCS groups? Though it looks like there are only a few areas of significant difference, the structures end up better by grouping one dimer against the other, rather than just the regions that are obviously different. This brings me to my second question. Might it be worthwhile to implement an NCS optimization procedure, which would compare different NCS groups, similarly to the optimize solvents, weights, etc? Kendall Nettles[cid:[email protected].]

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Does phenix have any utility to do the 2mFo-DFc composite omit map calculations?
by zhangh1＠umbc.edu 03 Nov '10

03 Nov '10

Hi, Does phenix have any utility to do the 2mFo-DFc composite omit map calculations (similar to OMIT in CCP4)? Thanks in advance! Hailiang

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phenix.model_vs_data : resolution cutoff from .pdb
by Bryan Lepore 02 Nov '10

02 Nov '10

[ phenix dev-568 ] TIL using phenix.model_vs_data, if the "REMARK 3" records in .pdb are adjusted e.g. to set a resolution limit, e.g REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : [change to whatever high resolution limit] REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.511 phenix.model_vs_data will pick this up and compute the R-factors for that range. Thanks Pavel -bryan

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Riding H
by Jianghai Zhu 02 Nov '10

02 Nov '10

Hi all, If I use the riding H atoms come out of phenix.refine in molprobity, it gives me a decent clash score. But if I strip the H atoms and let molprobity to add H atoms, I get a much worse clash score. I saw the manual of phenix recommends the first method. So what is the cause of the difference here? I know long time ago that phenix and molprobity used different bond length to add the riding H atoms. I don't know what the situation is now. Does phenix.refine refine the riding H atom positions? Thanks. -- Jianghai

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cancel that ...
by Phoebe Rice 01 Nov '10

01 Nov '10

Despite the error messages, it really did make restraints that seem to work. I just didn't realize they'd be in a hidden directory. Can I put in a request for no hidden defaults? They make me feel like a trained monkey. thanks, Phoebe

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error in making links
by Phoebe Rice 01 Nov '10

01 Nov '10

Hi BB, I wanted to run phenix on a structure from the database with covalent serine-DNA links, 1zr4. The "ready-set" feature to prepare restraints from the pdb link records sounded lovely, but fails with the message "Error interpreting command line argument parament definition: "1ZR4.link.edits" RuntimeError: Unexpected end of input" This happens with either version 1.6.4-486 or a nightly build installed a few weeks ago (phenix 551; installed on 10/7/2010.) Am I asking to much to get nice Ser-DNA links without sweating blood to read the fine print? thanks, Phoebe ===================================== Phoebe A. Rice Dept. of Biochemistry & Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alph… http://www.rsc.org/shop/books/2008/9780854042722.asp

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refine : "merged" in .def
by Bryan Lepore 29 Oct '10

29 Oct '10

[ dev-564 on GNU/Linux ] why does phenix - apparently - keep putting the label "merged" in output .def's, when neither the input .def or .mtz has this label - and what generally is the significance? the .mtz has separate Bijvoets, and I's. e.g: input .def: (concise) labels = "I(+),SIGI(+),I(-),SIGI(-)" label = "R-free-flags" output .def: labels = "I(+),SIGI(+),I(-),SIGI(-),merged" label = "R-free-flags" i re-checked the .mtz lacks "merged" (not shown). -bryan

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Autobuild error - bash/dash/sh
by Stephen Graham 29 Oct '10

29 Oct '10

Hi there, Apologies if this has been reported before, but the autobuild job I tried to run last night failed after a short while... The job was started from the command line using: phenix.autobuild data=../mydata_free.mtz seq_file=../protein.fasta map_file=../ccp4i/protein_phaser.1_parrot2.mtz input_map_labels='parrot.F_phi.F parrot.F_phi.phi None' And it got to the point where it was trying to submit the three jobs before it died as follows: Splitting work into 3 jobs and running with 1 processors using sh background=False in /home/stepheng/Projects/my_protein/autobuild/AutoBuild_run_3_/TEMP0 Starting job 1...Log will be: /home/stepheng/Projects/my_protein/autobuild/AutoBuild_run_3_/TEMP0/RUN_FILE_1.log *************ERROR ENDING ******************* ******************************************************************************** Failed to carry out AutoBuild_build_cycle: child process stderr output: command: 'sh /home/stepheng/Projects/my_protein/autobuild/AutoBuild_run_3_/TEMP0/RUN_FILE_1' /home/stepheng/Projects/my_protein/autobuild/AutoBuild_run_3_/TEMP0/RUN_FILE_1.sh: 5: Syntax error: Bad fd number ******************************************************************************** *************ERROR ENDING ******************* I think the problem might be that the RUN_FILE_1.sh script seems to use a bash command/redirection that is not implemented in plain old 'sh' spec, and thus not supported by dash (the lean version of sh that ships with ubuntu)? If I change the #! line of RUN_FILE_1.sh to call /bin/bash rather than /bin/sh the script seems to run to completion... Is there any easy way to change the script template to use /bin/bash or remove the offending command? I'm running phenix dev-550 on an x86 ubuntu 10.10 machine. Thanks, Stephen P.S. The reason I'm trying to run autobuild from the command line rather from the GUI is that the GUI seems to crash every time I give autobuild a sequence file in either the FASTA or PIR format. Is there another format I should be using? -- Dr Stephen Graham 1851 Research Fellow Cambridge Institute for Medical Research Wellcome Trust/MRC Building Addenbrooke's Hospital, Hills Road Cambridge, CB2 0XY, UK Phone: +44 1223 762 638

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Twin Law question
by Young-Jin Cho 28 Oct '10

28 Oct '10

Dear Phenix users, Thanks in advance to answer my question. As my recent data did not give me perfect statistics, I was wondering what the problem was (one of things is ice ring though). When I ran Xtriage with my struggling current data set and looked like I got twinned data. I reran PHASER as was suggested and confirmed that current space group is right. My question is now how I can handle this problem. First, as was recommended I input twin_law, however not all the cases (I have a couple of data sets) were working. One favorite(!) error message was as following: "Map type 'Fc' not supported for twinned structures. Allowed types: Fo-Fc, Fobs-Fobs-Fmodel, 2mFo-DFc, 2mFobs-DFmodel, mFo-DFc, mFobs-DFmodel, gradient, m_gradient." I got this from both GUI and shell environment. . 1. Now from now on, whenever I want to phenix.refine, should I include twin_law command such as 'twin_law=-h,l,k'? 2. In this case, what do I expect to see such as lowering Rfree or else? If it doesn't help lowering Rfree, what to do next? 3. Do I have to report I did with twinlaw option in case of preparing a paper or presentation? I mean I also heard that if one got twinned data, they re-collected data. How much can I convince my refinement is OK with twined data? Additionally, I checked other data, and applied twin_law but the result R/Rfree were exactly same as the one I refined without twin_law option, it this normal case? With many thanks in advance, Young-Jin Cho

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maximum allowable B-factor value
by Christian Roth 27 Oct '10

27 Oct '10

Dear all, I did a refinement run with a built in ligand. Within the ligand the B-factor jumps between two connected atoms from 60 up ~110, which is i think a bit too much. Is there a way to restrain the B-factors that they could not jump so much. I would accept negative difference density for the atom. Maybe the ligand is a bit degraded. Best regards Christian @Pavel Tanks for your suggestions with occupancy refinement and B-factors. -- Christian Roth Institut für Bioanalytische Chemie Biotechnologisch-Biomedizinisches Zentrum Fakultät für Chemie und Mineralogie Universität Leipzig Deutscher Platz 5 04103 Leipzig Telefon: +49 (0)341 97 31316 Fax: +49 (0)341 97 31319

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Re: [phenixbb] Sigma-A vs Resolution plot
by Bryan Lepore 25 Oct '10

25 Oct '10

On Thu, Oct 21, 2010 at 12:04 PM, Pavel Afonine <pafonine(a)lbl.gov> wrote: > the plot "Sigma-A vs Resolution" will be available in the next PHENIX > nightly build: Looks nice - I greatly appreciate this - thanks Pavel, Nat, anyone else I forgot. -Bryan

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nightly builds
by Bryan Lepore 22 Oct '10

22 Oct '10

is it me, or was there just a dev-562? ------------------------------------------------------------------------------- PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography Version: dev Release tag: 562 Platform: intel-linux-2.6 linux User: ------------------------------------------------------------------------------- but latest is : dev-555 2010-10-10 successful cctbx, cci_apps, phaser, phenix, misc docs; changelog

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R-free problem with phenix.refine
by Vinson LIANG 22 Oct '10

22 Oct '10

Dear all, Recently I deposited a structure to PDB. However, I was told >> The R value of SF check are different from your reported value. >> >> R work in SF check = 0.2859 >> your reported R work = 0.1474 >> Also there are no R free flags in your sending files, but you reported R >> free value in your all deposition. So, I rerun my deposited file with phenix.refine, and it gave a R-work=0.1475, R-free=0.1742. However, when I tried to run the same file with refmac5, error came with "Free R label has not been set". I guess phenix.refine gives Rree-R label that other program could not recognize. Could anyone please help me to solve this problem? Thank you very much in advance. I don't know why structure refined with phenix.refine has such problem. I wish this problem will disappear in the future, since I so like phenix.refine. Best, Vinson,Liang

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refine : peculiar TLS tensors
by Bryan Lepore 22 Oct '10

22 Oct '10

[ phenix 1.6.4-486 ] [ ALSO : tlsanl, refmac, etc. from ccp4 6.1.3 ] [ molscript/povscript ] the one-liner : i have some TLS tensors that sometimes do not compare at all well with refmac/anisoanl tensors. sometimes, the principal axes of a TLS tensor refines *very* far away from the center of mass(=center of reaction), or the axes from tlsanl are exceptionally small as if not scaled properly. the eigenvalues are really small too. see [*] for troubleshooting and strategy used. i suspect i am missing something. i also understand this might not be a phenix question. -bryan [*] i compared another .def that gave sensible TLS results with a different dataset/model, and my {} are all good AFAIK. anisoanl/refmac/parvati results are reasonable. the phenix refinement appears well behaved. these are all using tlsextract to get the eigenvalues/origins, and molscript to check the axes/centers of mass. input B factors are Beq unless i made an error. the tls group selections can vary - however, simple groups also can give these results. in general, using strategy (excerpt) : refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp *tls *occupancies *group_anomalous sites { individual = None torsion_angles = None rigid_body = None } adp { individual { isotropic = None anisotropic = None } group_adp_refinement_mode = *one_adp_group_per_residue \ two_adp_groups_per_residue group_selection group = None tls = "chain A and (resid 1:41 or resid 42:159 or resid 195:237 or resid 263:420)" tls = "chain A and resid 160:194" tls = "chain A and resid 245:252" } [...cut off ... ] example output of an ill-behaved S tensor from tlsanl : SCREW ROTATION AXIS ABSOLUTE POSITION (A) PITCH (A) X Y Z 1 70.667 154.197 308.627 -144.435 2 977.334 819.588******** 6222.947 3 640.7191431.084 471.341 269.382

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maps : sigma-a
by Lepore, Bryan 21 Oct '10

21 Oct '10

how might one start to go about getting phenix to automatically write out the value of sigma_A vs. resolution? e.g. when making maps, to get that nice table in Randy Read's SIGMAA program output of ln(sigma_A) vs. resolution. -bryan

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Bad ligand parameters
by Joe Krahn 21 Oct '10

21 Oct '10

I found that residue TRS has different dihedral target angles for the three hydroxyl oxygens, which are actually all equivalent. They have a periodicity of 1, but should have a periodicity of 3. What is the best way to handle such discrepancies? Most ligand parameters are probably auto-generated based on a reference structure, and there is probably a lot of conformation bias. In this case, it seems that parameterization should have been able to detect symmetry. It would be nice if parameters could include information about whether a human has done any validation. Actually, a ligand Wiki might be nice, where people can easily put comments, even if they are not sure about how to improve the parameters. Joe Krahn

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refine : a priori TLS tensor eigenvalues
by Bryan Lepore 21 Oct '10

21 Oct '10

[ phenix 1.6.4-486 ] i gather that phenix.refine will not take a priori refined TLS tensor eigenvalues - either from input or from the pdb header. is this right? -bryan

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Joint X-ray/Neutron Refinement
by Louis Lazar 21 Oct '10

21 Oct '10

Hello, Sorry for reposting, I am trying to get a better response with a more detailed subject line. I am seeing an internal error while trying to conduct joint x-ray/neutron refinement, and any help with the issue below would be greatly appreciated. Thank you very much in advance: ================================ ADP refinement=============================== Traceback (most recent call last): File "/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/phenix/phenix/refinement/command_line.py", line 89, in run call_back_handler=call_back_handler) File "/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/phenix/phenix/refinement/driver.py", line 1182, in run call_back_handler = call_back_handler) File "/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/phenix/phenix/refinement/strategies.py", line 735, in refinement_machine h_params = h_params) File "/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/cctbx_project/mmtbx/refinement/adp_refinement.py", line 192, in __init__ all_params = all_params) File "/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/cctbx_project/mmtbx/refinement/adp_refinement.py", line 216, in refine_adp model.set_refine_individual_adp() File "/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/cctbx_project/mmtbx/model.py", line 1035, in set_refine_individual_adp iselection = selection_iso.iselection()) RuntimeError: cctbx InternalError: /net/anaconda/scratch1/phenix/phenix-1.6.4-486/cctbx_project/cctbx/xray/scatterer_flags.h(417): CCTBX_ASSERT(f.use_u_iso()) failure. This error occurs during the 2nd macro cycle of refinement using this general command: phenix.refine model.pdb data_xray.hkl neutron_data.file_name=data_neutron.hkl input.xray_data.labels=FOBSx input.neutron_data.labels=FOBSn Thanks again. Regards, Louis

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Stretched Maps
by Joel Weadge 21 Oct '10

21 Oct '10

Hi all,I have just finished doing molecular replacement and an initial round of refinement (with simulated annealing) on a number of different datasets. They have all be straightforward since most of them are either point mutants and/or co-crystal structures. However, two of the structures are giving me some trouble. The data appears to be of good quality and resolution (2.25 and 2.55Å). The MR proceeds as normal with good scores and then in the subsequent round of refinement the maps (2Fo-Fc and Fo-Fc) look strange. The density is stretched or flattened in one direction. Can anyone help me with what I may be overlooking?Thanks in advanceJW

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occupancy refinement of a metal ion
by Christian Roth 20 Oct '10

20 Oct '10

Dear all, if I understood the manual correctly I could refine the occupancy and set the B-Factor to a constant value, or vice versa. Is there a possibility that phenix refine the B-Factor automatically to the value of the coordinating residues and adjust than the occupancy to a good value? I seems to be that the metal site is not fully occupied. I guess I have to set the B-value manually to the value of the surrounding residues and do than a refinement, right? Best regards Christian

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fix rotamers question
by Peter Grey 20 Oct '10

20 Oct '10

Dear Phenix community, I would like to have some additional information regarding fix_rotamers. In particular : - How Phenix chooses which rotamers need to be fixed ? - Does Phenix really re-calculate the three maps after correcting each rotamer ? For very large structures this is very time-consuming and one can settle for calculating a new map every 10-20 residues. Perhaps this could be a user-controlled parameter ? -Can you please explain how fix_rotamers works together with ncs restraints ? Thank you in advance for shedding light on this, Peter

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about low resolution refinement
by crystallogrphy 18 Oct '10

18 Oct '10

Hi, I am refining a low resolution data. According to sigma vs. resolution, my resolution is 4.7A. Because there are four identical molecular per asymetric unit, I can use positional refinement. There are about 65% alpha-helices in the structure, so I want to use secondary structure restrain. Does phenix has this restrain in the refinement? I am using Phenix-1.4 version.

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Question
by Louis Lazar 18 Oct '10

18 Oct '10

Hello, I am seeing an internal error while trying to conduct joint x-ray/neutron refinement, and any help with the issue below would be greatly appreciated. Thank you very much in advance: ================================ ADP refinement =============================== Traceback (most recent call last): File "/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/phenix/phenix/refinement/command_line.py", line 89, in run call_back_handler=call_back_handler) File "/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/phenix/phenix/refinement/driver.py", line 1182, in run call_back_handler = call_back_handler) File "/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/phenix/phenix/refinement/strategies.py", line 735, in refinement_machine h_params = h_params) File "/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/cctbx_project/mmtbx/refinement/adp_refinement.py", line 192, in __init__ all_params = all_params) File "/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/cctbx_project/mmtbx/refinement/adp_refinement.py", line 216, in refine_adp model.set_refine_individual_adp() File "/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/cctbx_project/mmtbx/model.py", line 1035, in set_refine_individual_adp iselection = selection_iso.iselection()) RuntimeError: cctbx InternalError: /net/anaconda/scratch1/phenix/phenix-1.6.4-486/cctbx_project/cctbx/xray/scatterer_flags.h(417): CCTBX_ASSERT(f.use_u_iso()) failure. This error occurs during the 2nd macro cycle of refinement using this general command: phenix.refine model.pdb data_xray.hkl neutron_data.file_name=data_neutron.hkl input.xray_data.labels=FOBSx input.neutron_data.labels=FOBSn Thanks again. Regards, Louis

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