- phenixbb - phenix-online.org

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 21 Oct '10

21 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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real space refinement or fix rotamers
by helene.krueger＠staff.uni-marburg.de 14 Oct '10

14 Oct '10

Hi, I want to fit bad fitting residues into electron density of my 2.0 A dataset. To do so should I use the "real space" option or the "fix bad sidechain rotamers" option? or both? Thanks Helene -- Helene Köster Philipps-Universität Marburg Institute of Pharmaceutical Chemistry AG Klebe Marbacher Weg 6 35032 Marburg, Germany Phone: +49-6421-28-25908 Mail: helene.krueger(a)staff.uni-marburg.de www.agklebe.de

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How to eliminate or decrease negative electron density at ligand position
by J J 13 Oct '10

13 Oct '10

Hello everyone, I have fine electron density 2Fo-Fc around a small ligand (~20 atoms) binding to my protein (at 1sigma level, all of the ligand atoms are surround by electron density, resolution=3 angstrom). However, I also see some negative electron density Fo-Fc surrounding some of the ligand atoms. My question is should I care about these negative electron density? If I should, what should I do in order to decrease or eliminate these negative electron density? I have tried occupancy refinement. It does help to decrease the negative density. However, it also makes 2Fo-Fc weaker. Another method I tried is to use tls refinement only for the ligand. It also helped to decrease the negative electron density. But since the data resolution is only 3 angstrom, I do not know if I am even allowed to do tls refinement? Thank you all in advance. Jason University of Pittsburgh

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Average B-factors when using TLS
by Phil Jeffrey 13 Oct '10

13 Oct '10

I'm having a discussion with a colleague here about what we expect to see on a model with and without TLS being used. I had the expectation that if you'd compared both models the Biso values reported in the ATOM line for the same atom w/ and w/o TLS would be somewhat comparable. Not the same, because the ADP model is different, but similar. However in the case of the TLS-refined model the average B-factors are systematically higher over the whole structure (86 A^2 vs 69A^2 for one polypeptide chain). Is this reasonable ? Expected ? Phil Jeffrey Princeton

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Re: [phenixbb] When to freeze crystal?
by miket＠chem.ucla.edu 13 Oct '10

13 Oct '10

Just last week I had crystals on Friday, then by Monday they dissolved back into the drop. I don't really understand how or why this happens, but it does. After experiencing this and complaining about it, I heard several other similar stories from around the department. Lesson learned: if you think you have a decent crystal, freeze it. Having said this, I've also heard of good data being collected from a crystal that was over a year old. Like Bert said, I think that occasionally a crystal survives or even improves over time, but those cases are much more rare than cases where the crystal deteriorates. Do how many crystals do you have? You might try freezing some and saving the others in the drop, then you can see for yourself. Good luck, Mike ----- Original Message ----- From: "Nathaniel Echols" <nechols(a)lbl.gov> To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> Sent: Wednesday, October 13, 2010 8:44:42 AM GMT -08:00 US/Canada Pacific Subject: Re: [phenixbb] When to freeze crystal? On Wed, Oct 13, 2010 at 4:16 PM, J J <phenix.upitt(a)gmail.com> wrote: > Hi everyone, > Sorry to ask a question that is not really related to phenix. I hope someone > here will be able to help me out. > I have a few crystals at hand right now, but I will not be able to look at > them for at least another month or so due to beamline schedule. Do you think > I should freeze them now or wait till I have my beamtime, or it is crystal > dependent? Thanks in advance. (Bert meant to send this to the list, but since he's using the wrong email address, it went to the list admin instead:) From: "Van Den Berg, Bert" <Lambertus.VandenBerg(a)umassmed.edu> To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> Date: Wed, 13 Oct 2010 11:27:32 -0400 Subject: Re: [phenixbb] When to freeze crystal? It is crystal dependent, but if they are big enough I would freeze them now. I have seen many crystal forms deteriorate over time and wouldn’t take the risk of that happening. It can happen though that old crystals get better (presumably due to slow dehydration of the drop), but I think these cases are fairly rare. Bert _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles miket(a)chem.ucla.edu

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When to freeze crystal?
by J J 13 Oct '10

13 Oct '10

Hi everyone, Sorry to ask a question that is not really related to phenix. I hope someone here will be able to help me out. I have a few crystals at hand right now, but I will not be able to look at them for at least another month or so due to beamline schedule. Do you think I should freeze them now or wait till I have my beamtime, or it is crystal dependent? Thanks in advance. Jason University of Pittsburgh

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Merging low resolution mtz file with high resolution sca file with phenix_reflection_file_editor
by Pei-Chun Lin 13 Oct '10

13 Oct '10

Hi, If I merge my low resolution mtz file with the high resolution sca file with phenix.reflection_file_editor GUI, is it the same as : Merge in hires data phenix.autobuild data=solve_2.mtz hires_file=w1.sca seq_file=seq.dat in Phenix Autobuild? PC

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secondary structure restraints question
by Peter Grey 12 Oct '10

12 Oct '10

Dear Phenix community, I have a very large model with many chains (due to NCS and complexity of model) where chain-id is not unique (e.g. there are several chain A) but segid is. All atom selections (for rigid body refinement, ncs restraints, tls etc...) are defined by segid. When I look at the output of phenix.secondary_structure_restraints I see that these restraints are defined by chain-id and residue number. Does this mean I must have unique chain-id names to correctly apply these secondary structure restraints or am I missing something ? Thank you for your time, Peter

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