- phenixbb - phenix-online.org

omit maps without density modification?
by NATHAN THOMSEN 18 Mar '09

18 Mar '09

Hi, Is there is a way to calculate simple omit maps and sa-omit maps in phenix without using density modification? The density modification seems to be flattening the weaker regions of my map - when compared to omit maps from cns for instance. Thanks! Nathan

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AutoBuild error: csh word too long
by Zheng Zhou 16 Mar '09

16 Mar '09

Hi, All I am new to phenix. I met the following error when I run autobuild. I also found the following link from Dr. Lang asking the similar question. But I didn't find a clear solution. Thanks for your help. http://www.phenix-online.org/pipermail/phenixbb/2008-June/001087.html Starting job 1... ******************************************************************************** Failed to carry out AutoBuild_build_cycle: child process stderr output: command: 'csh /home/zz/AutoBuild_run_1_/TEMP0/RUN_FILE_1' Word too long. ******************************************************************************** Zheng

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Covalent ligands
by cdas＠purdue.edu 15 Mar '09

15 Mar '09

Greetings everyone: I have been dealing with a structure of a protein that has a Cys residue covalently modified with a peptide fluromethyl ketone. Can someone tell me how to include this ligand in phenix.refine? In the past, I have used CNS for this purpose. I created a topology and parameter file (using ProDrug server) and modified a patch in the refine script in CNS to establish a covalent connection between an atom in the ligand and gamma sulfur of the protein in question. Thanks. Chitta

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Beamtime proposal deadline for ALS GU time
by Peter Zwart 13 Mar '09

13 Mar '09

The deadline for the may/June cycle of general user time for PX in the ALS is coming up soon (This Sunday). The Berkeley Center for Structural Biology (BCSB) has recently completed a number of upgrades: Sector 8: Recent improvements include: * A high-accuracy microdiffractometer on BL 8.2.1 allows for centering and viewing of very small crystals; * Robot automounters on BL8.2.1 and 8.2.2 are now fully commissioned and the beamlines can be used remotely; * A new large format (315mm active surface area) CCD detector on BL 8.2.1 facilitates data collection on large unit cell crystals. Sector 5: Recent improvements include: * Beamlines (5.0.1 and 5.0.3) now generate 1.5x1011 photons per second at 0.97 Angstrom. This wavelength is slightly above the Se K edge making them ideal for performing Se SAD experiments. * Beamline 5.0.2 (the tunable beamline) generates a peak flux of 8x1011 photons per second, and the energy range of 5.0.2 has been extended to 17 keV, enabling the routine use of shorter wavelengths and anomalously scattering elements such as bromine. * All sector 5 beamlines can be run remotely. The automated sample mounter holds six pucks (96 sample in total). On weekdays, staff is available 22 hours (out of 24) for puck changes and assistance. Please visit http://bcsb.lbl.gov/ for more details about the Center and its beamlines. If you'd like to apply for May/June beamtime at the Advanced Light Source, please submit a General User proposal by March 15, 2009. To find out more, click on: http://www-als.lbl.gov/als/quickguide/independinvest.html We invite you to submit a proposal at: http://alsusweb.lbl.gov/4DCGI/WEB_GetForm/PXProposalEntry.shtml/Initialize. If you have any questions or would like to request open beamtime, please e-mail BCSBBeamtime(a)lbl.gov. [Please note that executed user agreements must be received by LBNL prior to beamtime. Proprietary fees, if applicable, must be received by LBNL at least five working days prior to scheduled beamtime.] -- ----------------------------------------------------------------- P.H. Zwart Beamline Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org CCTBX: http://cctbx.sf.net -----------------------------------------------------------------

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Re: [phenixbb] phenix.multi_crystal_average with twinned data
by Thomas C. Terwilliger 12 Mar '09

12 Mar '09

Hi Peter and Mary, For the cross-crystal averaging procedure, no refinement is done, so no problem about using detwinned data in phenix.refine. in this case. If detwinned data is supplied then it will be used for density modification. That is probably the best procedure at present. (Note that when running autobuild, you can input a specific "input_refinement_file" for refinement (raw data) and separately specify an input_map_file with a map and a data file with (optionally) detwinned data.) All the best, Tom T Hi, Detwinning is possible with xtriage or phenix.refine (on way or the other). Integrating this into density modification might be hard, especially when the twin fraction is high. What is your twin fraction? Tom, Is it possible to use a different set of amplitudes for density modification then for refinement? You wouldn't want to refine against detwinned data. Cheers Peter 2009/3/11 Thomas C. Terwilliger <terwilliger(a)lanl.gov>: > Hi Mary, > > I have not tried the phenix multi-crystal averaging procedure with > twinned > data, but here are some suggestions of how to proceed. > > 1. This routine does not do any refinement, only density modification. > The density modification step does not know about twinning, so it will > be > necessary (if your data are significantly twinned) to supply structure > factor files with detwinned data. I will check with Peter Zwart on > producing detwinned data in phenix; it may be necessary to do that with > other tools as normally phenix.refine uses the original data and does > the > calculations internally. > > 2. The models you supply are used to (a) identify NCS symmetry and > cross-crystal symmetry. Therefore it should not really matter if these > models are incomplete, and therefore the approach you are using should > work for improving the region where you have no model. The region where > NCS is applied is defined as a region centered near the center-of-mass > of > the supplied model over which the NCS correlation is high. > > > I hope that helps! > All the best, > Tom T > > > I started running this function and then realized that I probably need > to > do something to take the perfect twinning into account. I'm not sure of > the best way to do this. I believe the map coefficients output by a run > phenix.refine should be detwinned as I give a twin law when running > phenix.refine. Should I detwin the mtz containing the data and then use > those files for the multi crystal averaging? Is there a way to output > detwinned data mtz files in phenix or do I need to use another program? > > Also, I have two ncs copies in the ASU. There's a region of density in > both ncs copies that I'm trying to improve the maps for with the multi > crystal averaging. I don't have anything built in the region yet. Is > there a way to use the NCS and multi crystal averaging at the same time > without any pdb coordinates in that region? > > Even with my goof up about the twinning, the eff script I created > appeared to run without problems. > > Thanks, > > Mary X. Fitzgerald > Postdoctoral Associate > Arnold Lab > _______________________________________________ > 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 > -- ----------------------------------------------------------------- P.H. Zwart Beamline Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org CCTBX: http://cctbx.sf.net -----------------------------------------------------------------

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Re: [phenixbb] phenix.multi_crystal_average with twinned data
by Thomas C. Terwilliger 12 Mar '09

12 Mar '09

Hi Mary, I have not tried the phenix multi-crystal averaging procedure with twinned data, but here are some suggestions of how to proceed. 1. This routine does not do any refinement, only density modification. The density modification step does not know about twinning, so it will be necessary (if your data are significantly twinned) to supply structure factor files with detwinned data. I will check with Peter Zwart on producing detwinned data in phenix; it may be necessary to do that with other tools as normally phenix.refine uses the original data and does the calculations internally. 2. The models you supply are used to (a) identify NCS symmetry and cross-crystal symmetry. Therefore it should not really matter if these models are incomplete, and therefore the approach you are using should work for improving the region where you have no model. The region where NCS is applied is defined as a region centered near the center-of-mass of the supplied model over which the NCS correlation is high. I hope that helps! All the best, Tom T I started running this function and then realized that I probably need to do something to take the perfect twinning into account. I'm not sure of the best way to do this. I believe the map coefficients output by a run phenix.refine should be detwinned as I give a twin law when running phenix.refine. Should I detwin the mtz containing the data and then use those files for the multi crystal averaging? Is there a way to output detwinned data mtz files in phenix or do I need to use another program? Also, I have two ncs copies in the ASU. There's a region of density in both ncs copies that I'm trying to improve the maps for with the multi crystal averaging. I don't have anything built in the region yet. Is there a way to use the NCS and multi crystal averaging at the same time without any pdb coordinates in that region? Even with my goof up about the twinning, the eff script I created appeared to run without problems. Thanks, 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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phenix.multi_crystal_average with twinned data
by Mary Fitzgerald 12 Mar '09

12 Mar '09

I started running this function and then realized that I probably need to do something to take the perfect twinning into account. I'm not sure of the best way to do this. I believe the map coefficients output by a run phenix.refine should be detwinned as I give a twin law when running phenix.refine. Should I detwin the mtz containing the data and then use those files for the multi crystal averaging? Is there a way to output detwinned data mtz files in phenix or do I need to use another program? Also, I have two ncs copies in the ASU. There's a region of density in both ncs copies that I'm trying to improve the maps for with the multi crystal averaging. I don't have anything built in the region yet. Is there a way to use the NCS and multi crystal averaging at the same time without any pdb coordinates in that region? Even with my goof up about the twinning, the eff script I created appeared to run without problems. Thanks, Mary X. Fitzgerald Postdoctoral Associate Arnold Lab

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March 15, 2009 deadline- User proposal submission for Collaborative Crystallography at BCSB
by Banumathi Sankaran 11 Mar '09

11 Mar '09

Dear Users, Deadline for May/June 2009 proposals will be March 15, 2009. Through the Collaborative Crystallography Pilot Program (CC) at the Advanced Light Source, scientists can send protein crystals to Berkeley Center for Structural Biology (BCSB) staff researchers for data collection and analysis. The CC Pilot 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. Thumbnail Description: ====================== The Collaborative Crystallography program will be piloted on beamlines 5.0.1 and 5.0.2 for one year; if successful it will be implemented on a permanent basis. CC proposals will go through the regular 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 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 submit a proposal, go to: http://www-als.lbl.gov/als/quickguide/independinvest.html Click on "protein crystallography" to begin proposal. For question 3 select "Collaborative PX 501/502." For question 9, please describe a specific research project with a clear end point. In order to request CC time for May/June 2009 allocation period, proposals must be submitted by March 15, 2009. The deadline for CC proposals for the time period July/August 2009 will be May 15, 2009. Regards, Banumathi Sankaran

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ADP group definitions
by Roeland Boer 10 Mar '09

10 Mar '09

Dear all, I have a question regarding the definition of the ADP groups. I'm refining a structure using a different isotropic B for each domain, while applying TLS for some mobile domains (I'm also using NCS restraints for all equivalent domains). In the refinement log file, however, the isotropic B of the domains refined with TLS, as reported in the "TLS refinement" section, is equal to the B of the starting model in all refinement macro cycles. It seems, therefore, that the isoB for the TLS groups in not refined, although I've included these domains in the .adp.group definitions (the log file actually confirms that there are 7 adp groups). Is it possible to refine TLS and isotropic B's on the same part of a model? I include the input file below. Thanks for any suggestions, Roeland Boer. refinement.input.xray_data.labels=F refinement.refine.strategy=tls+individual_sites+group_adp refinement.refine.adp.tls="chain A and resid 4:132" refinement.refine.adp.tls="chain B and resid 4:132" refinement.refine.adp.tls="chain C and resid 4:132" refinement.refine.adp.tls="chain X and resid 4:132" refinement.refine.adp.tls="chain Y and resid 4:132" refinement.refine.adp.tls="chain Z and resid 4:132" refinement.refine.adp.one_adp_group_per_residue=False refinement.refine.adp.group="resid 133:203" refinement.refine.adp.group="chain A and resid 4:132" refinement.refine.adp.group="chain B and resid 4:132" refinement.refine.adp.group="chain C and resid 4:132" refinement.refine.adp.group="chain X and resid 4:132" refinement.refine.adp.group="chain Y and resid 4:132" refinement.refine.adp.group="chain Z and resid 4:132" refinement.main.number_of_macro_cycles=4 refinement.input.xray_data.low_resolution=20.0 refinement.input.xray_data.high_resolution=3.4 refinement.main.ncs = True refinement.ncs.find_automatically = False refinement.ncs.restraint_group { reference = chain A and resid 133:203 selection = chain B and resid 133:203 selection = chain C and resid 133:203 selection = chain X and resid 133:203 selection = chain Y and resid 133:203 selection = chain Z and resid 133:203 } refinement.ncs.restraint_group { reference = chain B and resid 4:132 selection = chain A and resid 4:132 selection = chain C and resid 4:132 selection = chain X and resid 4:132 selection = chain Y and resid 4:132 selection = chain Z and resid 4:132 } refinement.output.prefix=test

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RuntimeError: Not enough memory for cubicles:
by Gino Cingolani 10 Mar '09

10 Mar '09

Dear Phenix community, I am still having problems to refine a large unit cell (~13,500 residues/asymmetric unit). The refinement goes well but at the very last cycle, immediately prior to outputting the refined model, phenix stops with the following error message: $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ ========== residual map mFobs-DFmodel: highest peaks and deepst holes ========= ----------peaks---------- Traceback (most recent call last): File "/usr/local/phenix-1.4-3/phenix/phenix/command_line/refine.py", line 9, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/command_line.py", line 89, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/driver.py", line 1098, in run call_back_after_monitor_collect = call_back_after_monitor_collect) File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/strategies.py", line 710, in refinement_machine fmodels=fmodels, model=model, log=log) File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/strategies.py", line 738, in highest_peaks_and_deepest_holes_in_residual_map log = log) File "/usr/local/phenix-1.4-3/mmtbx/find_peaks.py", line 212, in show_highest_peaks_and_deepest_holes log = log) File "/usr/local/phenix-1.4-3/mmtbx/find_peaks.py", line 117, in __init__ map = fft_map_data).all(max_clusters = max_number_of_peaks) File "/usr/local/phenix-1.4-3/cctbx/maptbx/__init__.py", line 196, in peak_search max_clusters=parameters.max_clusters()) File "/usr/local/phenix-1.4-3/cctbx/maptbx/__init__.py", line 303, in __init__ general_positions_only=self._general_positions_only) File "/usr/local/phenix-1.4-3/cctbx/crystal/__init__.py", line 479, in site_cluster_analysis cubicle_epsilon=cubicle_epsilon) RuntimeError: Not enough memory for cubicles: This may be due to unreasonable parameters: cubicle_edge=0.7 space_span=(293.298,92.903,214.527) n_cubicles=(419,133,307) max_number_of_bytes=1724676096 Traceback (most recent call last): File "/usr/local/phenix-1.4-3/phenix/phenix/command_line/refine.py", line 9, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/command_line.py", line 89, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/driver.py", line 1098, in run call_back_after_monitor_collect = call_back_after_monitor_collect) File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/strategies.py", line 710, in refinement_machine fmodels=fmodels, model=model, log=log) File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/strategies.py", line 738, in highest_peaks_and_deepest_holes_in_residual_map log = log) File "/usr/local/phenix-1.4-3/mmtbx/find_peaks.py", line 212, in show_highest_peaks_and_deepest_holes log = log) File "/usr/local/phenix-1.4-3/mmtbx/find_peaks.py", line 117, in __init__ map = fft_map_data).all(max_clusters = max_number_of_peaks) File "/usr/local/phenix-1.4-3/cctbx/maptbx/__init__.py", line 196, in peak_search max_clusters=parameters.max_clusters()) File "/usr/local/phenix-1.4-3/cctbx/maptbx/__init__.py", line 303, in __init__ general_positions_only=self._general_positions_only) File "/usr/local/phenix-1.4-3/cctbx/crystal/__init__.py", line 479, in site_cluster_analysis cubicle_epsilon=cubicle_epsilon) RuntimeError: Not enough memory for cubicles: This may be due to unreasonable parameters: cubicle_edge=0.7 space_span=(293.298,92.903,214.527) n_cubicles=(419,133,307) max_number_of_bytes=1724676096 $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ Following the various suggestions received after my previous email (~2 weeks ago), I have tried the following: --> Using phenix 1.4-3, which gave exactly the same problem as phenix 1.3 --> Using MACRO_CYCLE=0 before refinement to see if phenix can write out such a large asymmetric unit, and that works. Phenix does write out the model at a starting Rfree ~35.5%. --> Removing ordered_solvent=true Right now the refinement scheme I am using is as follows: phenix.refine XX.mtz model.pdb simulated_annealing=true elbow.XX_pdb.cif strategy=individual_sites+group_adp+tls tls_group_selections.params main.number_of_macro_cycles=5 main.ncs=true refinement.ncs.excessive_distance_limit=None refinement.pdb_interpretation.clash_guard.nonbonded_distance_threshold=No Once again, the refinement proceeds smoothly for 2-3 days; the Rfree drops nearly 3 points, and right at the very end, the programs stops without outputting a refined model. Does anybody have any idea what's going on? Thanks, Gino *********************************************************** Gino Cingolani, Ph.D. Assistant Professor Dept. of Biochemistry and Molecular Biology SUNY Upstate Medical University 750 E. Adams Street, Syracuse, NY, 13210 Tel. (315) 464 8744 Fax. (315) 464 8750 Email: cingolag(a)upstate.edu *********************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e conoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120)

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installation : cctbx or cci apps
by Bryan W. Lepore 09 Mar '09

09 Mar '09

i hope this is a "yes" or "no" question : i just got the latest phenix and the latest cci_apps running together. is the latest cctbx necessary? -bryan

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Restraints on water molecules
by Engin Ozkan 09 Mar '09

09 Mar '09

Are restraints on water molecules overwritten on successive cycles of refinement where ordered solvent is on? I seem to lose my distance restraints between specific waters and metal, unless I name my water molecules something else (and supply phenix with a cif for that name which is identical to water inside). The distance restraints also seem to be in effect for all cycles if ordered_solvent is off. I am also trying to make sure water numbers don't change during solvent picking/deleting. Engin

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PDF slides: introduction to refinement, phenix.refine and why automation is important (PHENIX)
by Pavel Afonine 09 Mar '09

09 Mar '09

Dear PHENIX community: I would like to draw your attention to these two PDF files with the slides that I recently made for a PHENIX workshop (workshop on Neutron crystallography, March 5-6, Japan). The first file (69 of very dense slides) makes a general introduction to crystallographic structure refinement (certainly biased towards how things are done in phenix.refine), plus some introduction to phenix.refine functionality. The second PDF file talks about PHENIX and "quick validation" with the strong accent of why automation is important. In general, I don't like and normally don't do such advertisements, but in this case I believe I can make an exception since I spent too much "of my software development" time on making these slides and they might be instructive for (new) PHENIX users. The links are (the first two!): http://www.phenix-online.org/presentations/neutron_japan_2009/ Thanks, Pavel. PS> Two slides in the first file are borrowed from Sasha Urzhumtsev, and 2-3 slides are borrowed from Paul Adams (second file).

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Re: [phenixbb] phenixbb Digest, Vol 40, Issue 7
by Pascal Egea 09 Mar '09

09 Mar '09

Pavel and Paul, this is really awesome.Thanks a lot. Pascal Egea UCSF Department of Biochemistry and Biophysics Laboratory of Robert Stroud On Sun, Mar 8, 2009 at 1:00 PM, <phenixbb-request(a)phenix-online.org> wrote: > Send phenixbb mailing list submissions to > phenixbb(a)phenix-online.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.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. PDF slides: introduction to refinement, phenix.refine and why > automation is important (PHENIX) (Pavel Afonine) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 07 Mar 2009 23:41:35 -0800 > From: Pavel Afonine <PAfonine(a)lbl.gov> > Subject: [phenixbb] PDF slides: introduction to refinement, > phenix.refine and why automation is important (PHENIX) > To: phenixbb(a)phenix-online.org > Message-ID: <49B376AF.1020803(a)lbl.gov> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Dear PHENIX community: > > I would like to draw your attention to these two PDF files with the > slides that I recently made for a PHENIX workshop (workshop on Neutron > crystallography, March 5-6, Japan). > > The first file (69 of very dense slides) makes a general introduction to > crystallographic structure refinement (certainly biased towards how > things are done in phenix.refine), plus some introduction to > phenix.refine functionality. > > The second PDF file talks about PHENIX and "quick validation" with the > strong accent of why automation is important. > > In general, I don't like and normally don't do such advertisements, but > in this case I believe I can make an exception since I spent too much > "of my software development" time on making these slides and they might > be instructive for (new) PHENIX users. > > The links are (the first two!): > > http://www.phenix-online.org/presentations/neutron_japan_2009/ > > Thanks, > Pavel. > > PS> Two slides in the first file are borrowed from Sasha Urzhumtsev, and > 2-3 slides are borrowed from Paul Adams (second file). > > > > > ------------------------------ > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb > > > End of phenixbb Digest, Vol 40, Issue 7 > *************************************** >

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Re: [phenixbb] refinement using a multiprocessor machine or on a cluster
by Pavel Afonine 07 Mar '09

07 Mar '09

Hi Gino, phenix.refine does not use any advantage of multiple available CPUs. Sorry. Pavel. On 3/4/09 11:26 AM, Gino Cingolani wrote: > Dear Phenix community, > > I was wondering if it is possible to run a refinement job on multiple > processor. The refinement of my 13,000 asymmetric unit takes about 2 > days. It could be greatly speeded up by taking advantage of the 4 CPUs > in my PC. The phenix manual suggest to use > nproc=3 > to run using a multiprocessor machine or on a cluster. > But this applies only to LigandFit and AutoBuild Wizards. > What about simple refinement? > > Thanks in advance, > > Gino > >

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fwd: TLS without isotropic adp refinement
by Nathaniel Echols 07 Mar '09

07 Mar '09

(I think the server must have a lag time between adding a new email address and accepting posts from it. . .) > From: Roeland Boer <rbocri(a)ibmb.csic.es> > Date: March 5, 2009 5:29:19 AM PST > To: phenixbb(a)phenix-online.org > Subject: TLS without isotropic adp refinement > > Dear all, > > I'm trying to refine a structure using TLS on some of the domains > without refining the isotropic B factors of the atoms of the full > structure. I haven't been able to do this: the isotropic B factors > seem to be refined per residue when I include TLS. If I don't use > TLS, the B factors are not refined. I've looked around in the > archives and browsed the manual without luck. Any suggestions would > be highly appreciated. I include the parameter file I've used. Quoting Pavel (since he's teaching a workshop): "phenix.refine always writes out the total B-factors and not split them. The total B-factor in phenix.refine is defined as: Utotal = Utls + Ulocal + Ucryst." So the atomic B-factors in your structure are not being refined individually, but they change anyway because the contribution of the TLS refinement is included. -Nat > > Kind regards, > Roeland Boer. > > > ++++++++++++++ Parameters ++++++++++++++++ > > refinement.main.number_of_macro_cycles=4 > refinement.main.ncs = True > refinement.input.xray_data { > labels=F > low_resolution=20.0 > high_resolution=3.6 > } > refinement.refine { > strategy=tls+individual_sites > adp { > tls="chain A and (resid 4:132 or resid 301)" > tls="chain B and (resid 4:132 or resid 301)" > tls="chain C and (resid 4:132 or resid 301)" > tls="chain X and (resid 4:132 or resid 301)" > tls="chain Y and (resid 4:132 or resid 301)" > tls="chain Z and (resid 4:132 or resid 301)" > } > } > refinement.ncs { > find_automatically = False > restraint_group { > reference = chain A and resid 133:203 > selection = chain B and resid 133:203 > selection = chain C and resid 133:203 > selection = chain X and resid 133:203 > selection = chain Y and resid 133:203 > selection = chain Z and resid 133:203 > } > restraint_group { > reference = chain B and (resid 4:132 or resid 301) > selection = chain A and (resid 4:132 or resid 301) > selection = chain C and (resid 4:132 or resid 301) > selection = chain X and (resid 4:132 or resid 301) > selection = chain Y and (resid 4:132 or resid 301) > selection = chain Z and (resid 4:132 or resid 301) > } > } > refinement.output.prefix=3.6-tlsnter-indsite-inputb-autowght-ncs > -------------------- Parameters -------------------------- > > ------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 NEchols(a)lbl.gov

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Re: [phenixbb] fwd: kicked maps
by Pavel Afonine 07 Mar '09

07 Mar '09

Hi Maia, I think it's easier to try out and have an answer right away rather than speculate. Why don't you just try and see if it helps? I can't tell in advance if it will help or not. Again, a "average kick map" (AKM) is computed as following: we create a large ensemble of structures (~500 structures) that are all randomly shaken. The shake amount (rmsd distortion introduced to coordinates) varies from 0 to 1.0A. Then for each structure the map is computed (mFo-DFc or 2mFo-DFc or any other requested by the user). And finally, all maps are averaged out to produce one "averaged kick map". Obviously, just from general considerations, such map is supposed to have less or no bias, less noise and enhanced signal, and potentially can clear up some initially bad densities. I would also try an "omit AKM", where you remove some model parts in questions and compute mFo-DF and 2mFo-DFc AK maps. Please use the latests CCI Apps for this since we recently fixed a number of problems with this. Pavel. >> Hi Pavel, I have a problem with long linkers between domains in a >> protein structure that is a biological hexamer. >> I don't have much density for the linkers. Should "kicked maps" help >> me to see the density? The resolution of the X-ray data is 2.3A. >> >> Maia >

1 0

default bondlengths - metal
by Engin Ozkan 07 Mar '09

07 Mar '09

Hi, all, Recently following the phenixbb, I was made aware of phenix.metal_coordination. So I just gave it a try for a structure of mine with sodium in it. Specifically, I decided to turn the use-default-bondlengths option on. The result was surprising, because the output file thinks that sodum to oxygen distances are supposed to be 1.9 Angstroms. Work done by Marjorie Harding and others have shown that this distance should be about 2.4 (Acta Cryst. D62 (2006), 678-682; for a summary of their numbers, http://tanna.bch.ed.ac.uk/newtargs_06.html). I wonder why phenix.metal_coordination chose 1.9 A as the default Na-O distance, or is the default option a different type of bond distance, I am not sure. Any clarification from the authors would be appreciated. Below is part of the output, showing the distance: refinement.geometry_restraints.edits { bond { action = *add atom_selection_1 = name NA and chain N and resname NA and resseq 1 atom_selection_2 = name O and chain A and resname PHE and resseq 76 distance_ideal = 1.920420 sigma = 0.01 } } Engin

5 7

fwd: phenix.autobuild- multiple models.
by Nathaniel Echols 05 Mar '09

05 Mar '09

> (The server bounced this message for some reason.) > From: Michael Karl Uhl <michael.uhl(a)uni-graz.at> > Date: March 3, 2009 11:55:16 PM PST > To: phenixbb(a)phenix-online.org > Subject: phenix.autobuild- multiple models > Reply-To: michael.uhl(a)a-b.at > > > Hello, > > I have not registered for this list until now, but have a very > urgent question concerning phenix.autobuild and multiple models as > input. Is there a possibility to merge models generated by different > phenix.autobuild runs. I have several overall_best-structure and > want to merge them into one single overall_best structure. I have > found the keyword "merge_models= True" but it does not really work > (Sorry, unknown file or keyword: merge_models=True). How should I > make the input in this case? > > > Thanks a lot, > > > Michael Uhl. > > ------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 NEchols(a)lbl.gov

2 1

Re: [phenixbb] Please help with neutron composite SA-omit
by Pavel Afonine 03 Mar '09

03 Mar '09

Hi Anna, a "kick map" is computed as following: we create a large ensemble of structures (~500 structures) that are all randomly shaken. The shake amount (rmsd distortion introduced to coordinates) varies from 0 to 1.0A. Then for each structure the map is computed (mFo-DFc or 2mFo-DFc or any other requested by the user). And finally, all maps are averaged out to produce one "averaged kick map". Obviously, such map is supposed to have less or no bias, less noise, and potentially can clear up some initially bad densities. The is currently no paper published about this method; we are preparing the manuscript. There are scattered references and uses of AK maps, mostly by Dusan Turk (he originally implemented it in his program MAIN). Documentation is not yet updated, this is true. Sorry. In phenix.refine GUI you can just check the corresponding box to compute a kick map (under map menu). In command line version you need to supply a parameter file that will define such map: refinement.electron_density_maps { map { mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT likelihood_weighted = True obs_factor = 2 calc_factor = 1 kicked = True fill_missing_f_obs_with_weighted_f_model = True } map { mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT likelihood_weighted = True obs_factor = 1 calc_factor = 1 kicked = True fill_missing_f_obs_with_weighted_f_model = True } } I was recently trying this with neutron maps and the maps are significantly better (computed with AK approach). Please use the latest version of CCI Apps for this. Let me know if you have any questions or problems. Pavel. On 2/24/09 7:58 AM, Anna Gardberg wrote: > Hi, Pavel. > > I'm not trying to bring up features, exactly, but rather trying to get > an unbiased, quantitative measure of the the deuterium atoms' nuclear > density. The idea is to compare the visibility of hydrogen or > deuterium atoms with x-ray and neutron diffraction, correlating this > parameter (perhaps in the form of OMIT density) to others. > > I have only briefly toyed with kick-maps, but the lack of > documentation (http://phenix-online.org/documentation/refinement.htm > doesn't say much about how best to use them) made it frustrating. Can > you recommend an article about kick maps? Or some suggestions on how > to best use this feature, please? > > > -Anna > > On Mon, Feb 23, 2009 at 11:46 PM, Pavel Afonine <PAfonine(a)lbl.gov> wrote: > >> Hi Anna, >> >> you can ask phenix.refine produce "kick maps" that are supposed to be less >> biased, contain less noise and, if you are lucky, might bring some more >> features (that were buried in noise before). >> >> Let me know if you have any questions. >> >> Pavel. >> >> >> On 2/23/09 11:40 AM, Anna Gardberg wrote: >> >>> Hello. >>> >>> I am attempting to create an SA-omit composite map with neutron >>> scatterers. >>> >>> Unfortunately, >>> >>> phenix.autobuild data= "neutron.mtz" model="neutron_004.pdb" >>> composite_omit_type=sa_omit scattering_table=neutron >>> >>> results in an error: >>> >>> "Sorry, unknown file or keyword: scattering_table=neutron >>> Possibilities... (use 'phenix.autobuild --help all' to get full help): >>> general.resolve_pattern_command_list=neutron >>> density_modification.use_resolve_pattern=neutron >>> decision_making.semi_acceptable_r=neutron >>> decision_making.acceptable_r=neutron >>> multiple_models.multiple_models_starting_resolution=neutron >>> " >>> >>> Can someone here help, please? >>> >>> (For what it's worth: I'd use nCNS, but while CNS 1.21 (precompiled >>> binaries) works on my computer, CNS 1.1 version seems to compile, it >>> will not run. When I apply the nCNS patch to CNS 1.1, again it seems >>> to compile, but will not run. ) >>> >>> Regards, >>> Anna Gardberg >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org >>> http://www.phenix-online.org/mailman/listinfo/phenixbb >>> >>>

2 2

AutoBuild after resolve
by Mo Wong 01 Mar '09

01 Mar '09

Hi all, Can someone tell me where in the AutoBuild GUI I can set "phases_from_resolve"? I've looked for it in the "set variable" section, but it's not listed. Thanks!

2 3

rfree flag fractions
by Yusuf Akhter 28 Feb '09

28 Feb '09

Hi Everybody! I am using phenix version 1.3b for refining a structure at 3 A resolution and total number of total reflections are 12680. I have seen a provision in phenix to change the default maximal number of test flags to be generated and the fraction with this command line xray_data.r_free_flags.fraction=0.05 xray_data.r_free_flags.max_free=500 My queries are 1)when should somebody use this utility ?? 2)what is minimum number of Rfree flags one should use on this resolution and this total number of reflections?? Any kind of suggestions will be appreciated. Cheers! Yusuf

2 1

RuntimeError: Not enough memory for cubicles:
by Gino Cingolani 27 Feb '09

27 Feb '09

Hi, I'm refining a huge structure with ~13,000 residues in the asymmetric unit. I started a massive job with the following inputs: phenix.refine data.mtz model.pdb ordered_solvent=true strategy=individual_sites+group_adp+tls tls_group_selections.params main.ncs=true main.number_of_macro_cycles=10 After >24 h the Rfree had dropped from 45% to 33%, but at the very end, just before outputting the refined pdb model, Phenix died with the following error message: ############################################################ Hello all========== residual map mFobs-DFmodel: highest peaks and deepst holes ========= ----------peaks---------- Traceback (most recent call last): File "/usr/local/phenix-1.3-final/phenix/phenix/command_line/refine.py", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.3-final/phenix/phenix/refinement/command_line.py", line 89, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/usr/local/phenix-1.3-final/phenix/phenix/refinement/driver.py", line 1081, in run call_back_after_monitor_collect = call_back_after_monitor_collect) File "/usr/local/phenix-1.3-final/phenix/phenix/refinement/strategies.py", line 724, in refinement_machine fmodels=fmodels, model=model, log=log) File "/usr/local/phenix-1.3-final/phenix/phenix/refinement/strategies.py", line 752, in highest_peaks_and_deepest_holes_in_residual_map log = log) File "/usr/local/phenix-1.3-final/mmtbx/mmtbx/find_peaks.py", line 210, in show_highest_peaks_and_deepest_holes log = log) File "/usr/local/phenix-1.3-final/mmtbx/mmtbx/find_peaks.py", line 117, in __init__ map = fft_map_data).all(max_clusters = max_number_of_peaks) File "/usr/local/phenix-1.3-final/cctbx/cctbx/maptbx/__init__.py", line 196, in peak_search max_clusters=parameters.max_clusters()) File "/usr/local/phenix-1.3-final/cctbx/cctbx/maptbx/__init__.py", line 303, in __init__ general_positions_only=self._general_positions_only) File "/usr/local/phenix-1.3-final/cctbx/cctbx/crystal/__init__.py", line 477, in site_cluster_analysis cubicle_epsilon=cubicle_epsilon) RuntimeError: Not enough memory for cubicles: This may be due to unreasonable parameters: cubicle_edge=0.7 space_span=(293.298,92.903,214.527) n_cubicles=(419,133,307) max_number_of_bytes=1724676096 ###################################################### Any suggestion on what to do? As invididual refinement modules (e.g. regular rigid body refinemnet, SA, energy minimization, TLS, etc) run OK, is the problem coming from the "ordered_solvent=true" command? Thanks in advance! Gino Cingolani, Ph.D. *********************************************************** Gino Cingolani, Ph.D. Assistant Professor Dept. of Biochemistry and Molecular Biology SUNY Upstate Medical University 750 E. Adams Street, Syracuse, NY, 13210 Tel. (315) 464 8744 Fax. (315) 464 8750 Email: cingolag(a)upstate.edu *********************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e conoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120)

4 4

Failed to carry out AutoBuild_parallel_omit
by Jhon Thomas 26 Feb '09

26 Feb '09

Hello all There is a problem with running phenix.autobuild. Failed to carry out AutoBuild_parallel_omit: child process stderr output: command: 'csh /home/thomas/phenix_omitmap/AutoBuild_run_1_/TEMP0/RUN_FILE_1' Badly placed ()'s. What could be solution. Thanks Thomas

2 1

resolve.phenix and helices_strands_only
by Mo Wong 26 Feb '09

26 Feb '09

Hi all, I'm sure I've done this before, but could some please let me know/remind me what the correct syntax is for including "helices_strands_only=True" in a resolve script like the one below? phenix.resolve<<EOD hklin solve.mtz labin FP=FP SIGFP=SIGFP PHIB=PHIB FOM=FOM HLA=HLA HLB=HLB HLC=HLC HLD=HLD solvent_content 0.43 database 5 EOD Thanks!

2 2

Select atoms by B-factors?
by Oliver Clarke 25 Feb '09

25 Feb '09

Hi, I'm currently refining a structure at 1.6A. Substantial portions of the structure are very well ordered, with B-factors < 15. I'd like to refine these well ordered regions using anisotropic thermal parameters, while keeping everything else isotropic. However, in doing so, the atom selections tend to become quite convoluted. Is there any way to select all atoms which initially have an isotropic B less than a certain cuttoff value? That way one could (after isotropic B-factor refinement) select the most ordered regions of the structure for anisotropic refinement. Cheers, Oliver Clarke

2 1

links and REMARK 3 record in the final PDB
by Pascal Egea 24 Feb '09

24 Feb '09

Dear All, I apologize if this question has already been answered. I am refining a structure of a glycosylated-enzyme and I understood the way to define all the links (N-glycosylation to the ASN and beta-glycosidic bonds between the NAG units) and refinement is complete and everything is good. All the links I included in my cif_link definition file where taken into account and dealt with by Phenix (the .def and .geo files are fine). Is it normal however that in the resulting refined PDB file, no such links are written by PHENIX under the REMARK 3 record ? Same thing for the 5 disulfide bonds present in the protein. Thanks in advance for the clarification. Pascal Egea University of California San Francisco Department of Biochemistry and Biophysics Laboratory of Robert Stroud

3 2

Please help with neutron composite SA-omit
by Anna Gardberg 24 Feb '09

24 Feb '09

Hello. I am attempting to create an SA-omit composite map with neutron scatterers. Unfortunately, phenix.autobuild data= "neutron.mtz" model="neutron_004.pdb" composite_omit_type=sa_omit scattering_table=neutron results in an error: "Sorry, unknown file or keyword: scattering_table=neutron Possibilities... (use 'phenix.autobuild --help all' to get full help): general.resolve_pattern_command_list=neutron density_modification.use_resolve_pattern=neutron decision_making.semi_acceptable_r=neutron decision_making.acceptable_r=neutron multiple_models.multiple_models_starting_resolution=neutron " Can someone here help, please? (For what it's worth: I'd use nCNS, but while CNS 1.21 (precompiled binaries) works on my computer, CNS 1.1 version seems to compile, it will not run. When I apply the nCNS patch to CNS 1.1, again it seems to compile, but will not run. ) Regards, Anna Gardberg

2 1

Re: [phenixbb] Please help with neutron composite SA-omit
by Thomas C. Terwilliger 24 Feb '09

24 Feb '09

Hi again Anna, Can you possibly try this syntax for the "refine.eff" file: refinement{ main {scattering_table=neutron} } and then say phenix.autobuild <your usual parameters> refine_eff_file=refine.eff That should do it! All the best, -Tom T > Hello. > > I am attempting to create an SA-omit composite map with neutron > scatterers. > > Unfortunately, > > phenix.autobuild data= "neutron.mtz" model="neutron_004.pdb" > composite_omit_type=sa_omit scattering_table=neutron > > results in an error: > > "Sorry, unknown file or keyword: scattering_table=neutron > Possibilities... (use 'phenix.autobuild --help all' to get full help): > general.resolve_pattern_command_list=neutron > density_modification.use_resolve_pattern=neutron > decision_making.semi_acceptable_r=neutron > decision_making.acceptable_r=neutron > multiple_models.multiple_models_starting_resolution=neutron > " > > Can someone here help, please? > > (For what it's worth: I'd use nCNS, but while CNS 1.21 (precompiled binaries) works on my computer, CNS 1.1 version seems to compile, it will not run. When I apply the nCNS patch to CNS 1.1, again it seems to compile, but will not run. ) > > Regards, > Anna Gardberg > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb >

1 0

Re: [phenixbb] Please help with neutron composite SA-omit
by Thomas C. Terwilliger 24 Feb '09

24 Feb '09

Hi Anna, Try putting your cmmand "scattering_table=neutron" in a "refine.eff" file and then run phenix.autobuild including the keyword refine_eff_file=refine.eff (note that you may need to specify the scope of scattering_table just as if you were using the command directly for phenix.refine) That is the way you can put any phenix.refine parameters into autobuild. Let me know if that doesn't do it! -Tom T > Hello. > > I am attempting to create an SA-omit composite map with neutron > scatterers. > > Unfortunately, > > phenix.autobuild data= "neutron.mtz" model="neutron_004.pdb" > composite_omit_type=sa_omit scattering_table=neutron > > results in an error: > > "Sorry, unknown file or keyword: scattering_table=neutron > Possibilities... (use 'phenix.autobuild --help all' to get full help): > general.resolve_pattern_command_list=neutron > density_modification.use_resolve_pattern=neutron > decision_making.semi_acceptable_r=neutron > decision_making.acceptable_r=neutron > multiple_models.multiple_models_starting_resolution=neutron > " > > Can someone here help, please? > > (For what it's worth: I'd use nCNS, but while CNS 1.21 (precompiled > binaries) works on my computer, CNS 1.1 version seems to compile, it > will not run. When I apply the nCNS patch to CNS 1.1, again it seems > to compile, but will not run. ) > > Regards, > Anna Gardberg > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb >

2 1

DTT at special position
by Nikos Pinotsis 24 Feb '09

24 Feb '09

Dear all, even though I checked the documentation and previous threads I didn't find something relative to my problem: I have an elongated e-density that looks like DTT and appears to be located on a special position (there is actually an axis betwenn C2 and C3 atoms of DTT). Refining with phenix.refine using either 0.5 or 1.0 occupancy, I am getting the DTT molecule outside the density (and the symmetry related DTT from the other side and still in the middle the strong difference density. thanks in advance for any suggestions-solutions Nikos -- --------------------------------- Dr. Nikos Pinotsis Section of Structural Biology Institute of Cancer Research Chester Beatty Laboratories 237 Fulham Road London SW3 6JB, UK Tel: +44 20 7153 5453 / 5447 --------------------------------- The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.

2 1

ADP refinement
by Katya Heldwein 21 Feb '09

21 Feb '09

Hi, I would like to use TLS refinement for protein (I have selected TLS groups) and individual isotropic refinement for water. How can I specify this in phenix.refine? Thanks, Katya -- Ekaterina Heldwein, Ph.D. Assistant Professor Department of Molecular Biology and Microbiology Tufts University School of Medicine 136 Harrison Ave Boston, MA 02111 phone: 617-636-0858 fax: 617-636-0337 e-mail: katya.heldwein(a)tufts.edu

2 1

Strange negative density when refining at low resolution
by Andrew Purkiss-Trew 21 Feb '09

21 Feb '09

Dear Phenixers I've been helping a colleague with a dataset at ~3.8 Angstroms (phases and map from AutoSharp using SAD phasing). At the moment he has an incomplete polyALA model consisting of two chains related by NCS and a few extra sections. Refinement seems to proceed OK using phenix.refine version 1.4-3, but the resultant maps have blobs of negative density in the core of the protein. I am assuming that these are a side-effect of the bulk-solvent correction part of the refinement which is confusing the region where the protein sidechains would be as solvent. There are no corresponding negative peaks on the surface of protein, but some positive peaks where larger sidechains may be. Is this interpretation likely to be correct and if so, which parameter should be altered in the Bulk Solvent section of the input to allow for a bigger mask around the protein. I see that it isn't recommended to change the parameters, but the refinement.mask.solvent_radius=1.0 looks like an obvious candidate. If necessary, I can get an image made showing the maps. Thanks Andrew Purkiss-Trew This communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a charity registered under number 1089464 and a company limited by guarantee registered in England & Wales under number 4325234. Our registered address is 61 Lincoln's Inn Fields, London WC2A 3PX. Our central telephone number is 020 7242 0200. This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so.

2 1

2 Wonderings: adding H atoms and overcoming overfitting problem
by Young-Jin Cho 20 Feb '09

20 Feb '09

Hi, my current wonderings are as below: First, how can I add H atoms into nucleotide ligands in pdb file? I did 'phenix.reduce model.pdb > model_h.pdb', but as I see it didn't add H's of sugar (1', 2', 3' 4' and 5'). Once I had this kind of problem before, I was suggested to use phenix.ready_set command but seemingly this does not work any longer with last version that I am using now. Also, is it possible to add H into phosphate group? The second very general question is about getting over overfitting problem. My phenix runs gave me too much difference between R and Rfree about .7 w/o adding H atoms. I assume it came from water molecules because it(huge gap) just starts to happen after 1_bss stage. If anybody can suggest a good way to get over this problem, you will save my tremendous times and useless efforts. Big thanks in advance, Young-Jin

3 4

optimizing target weights in phenix
by Yusuf Akhter 20 Feb '09

20 Feb '09

*Hi Everybody, I am using phenix-1.3b. When i tried to use "Optimizing target weights" utility by typing following command line * *phenix.refine data.hkl model.pdb optimize_wxc=true optimize_wxu=true I got following error. * Traceback (most recent call last): File "/public/xtal/phenix/phenix-1.3b/phenix-1.3b/phenix/phenix/command_line/refine.py", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/public/xtal/phenix/phenix-1.3b/phenix-1.3b/phenix/phenix/refinement/command_line.py", line 78, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/public/xtal/phenix/phenix-1.3b/phenix-1.3b/phenix/phenix/refinement/driver.py", line 1308, in run log = log) File "/public/xtal/phenix/phenix-1.3b/phenix-1.3b/phenix/phenix/refinement/strategies.py", line 642, in refinement_machine log = log) File "/public/xtal/phenix/phenix-1.3b/phenix-1.3b/phenix/phenix/refinement/weight_xray_chem.py", line 327, in __init__ self.wxc_optimization() File "/public/xtal/phenix/phenix-1.3b/phenix-1.3b/phenix/phenix/refinement/weight_xray_chem.py", line 450, in wxc_optimization rw, rf, b, a, a_xc = self.wx_opt_helper(w = wxc_scale_0 * wxc, sites=True) File "/public/xtal/phenix/phenix-1.3b/phenix-1.3b/phenix/phenix/refinement/weight_xray_chem.py", line 387, in wx_opt_helper verbose = 0) TypeError: __init__() takes at least 5 non-keyword arguments (3 given) *May anybody tell me please how can i fix these errors?? Thanks in advance. yusuf *

3 3

maintenance release of CCI Apps
by Pavel Afonine 18 Feb '09

18 Feb '09

PHENIX users: A maintenance release of CCI Apps is available: http://www.phenix-online.org/download/ See "Changes" section for the list of problems fixed: http://www.phenix-online.org/download/cci_apps/ Pavel.

1 0

phenix.refine GUI freezes when using Coot or Pymol
by Derek Logan 18 Feb '09

18 Feb '09

Hi, I've been using the phenix.refine GUI for a few days now and find it a very valuable addition. However I notice that when I choose to display the results of refinement in Pymol or Coot, it freezes the GUI until I exit the chosen graphics program. Is this a bug or a feature? If nothing else, it makes it hard to analyse the MolProbity results in Coot. I'm using Mac OS X 10.5.6. Thanks Derek __________________________________________________________________ Derek Logan tel: +46 46 222 1443 Associate Professor fax: +46 46 222 4692 Molecular Biophysics mob: +46 76 8585 707 Centre for Molecular Protein Science Lund University, Box 124, 221 00 Lund, Sweden

2 1

Re: [phenixbb] individual plus group adp's
by Pavel Afonine 18 Feb '09

18 Feb '09

Hi Emmanuel, why don't you just do combined TLS + individual ADP refinement, which is the best option in most of cases? Anyway, here is the answer to your question. If you are running phenix.refine from the command line, the following command phenix.refine model.pdb data.hkl params.txt where the file "params.txt" contains these lines refinement.refine { strategy = *individual_sites rigid_body *individual_adp *group_adp tls \ *occupancies group_anomalous adp { individual { isotropic = chain A or chain B } group_adp_refinement_mode = one_adp_group_per_residue \ two_adp_groups_per_residue *group_selection group = chain C } } will refine: - individual coordinates for all atoms; - individual isotropic B-factors for all atoms in chain A and B; - group B-factor for chain C (one B-factors per whole chain C); - occupancies for all atoms in alternative conformations (if any present in your structure). Also should be able to do this using phenix.refine GUI. Please let me know if you have any questions! Pavel. On 2/17/2009 7:47 AM, Manolis Saridakis wrote: > Dear Colleagues, > I have a question that I guess has a simple answer which however I haven't been able to > find in the manual. I am using phenix.refine version 1.4. > > My model has 3 chains + solvent and I would like to refine individual adp's for > everything except one of the chains, for which I would like to keep a group adp > refinement option. > > My attempts have failed so far: depending on what exactly I do (which I guess there is > no point detailing here), I am either refining my other chains as groups too (i.e. the > same number is added to all adp's of the chain) or nothing stays grouped. However, in > the manual it does say if I am not mistaken that one can do what I want (but there is > no example of that situation). > > Many thanks for your help! > > Best wishes, > > Emmanuel Saridakis > >

1 0

LINK records, sugars, and a question in two parts
by Engin Ozkan 15 Feb '09

15 Feb '09

Hi everyone, I was wondering if phenix.refine does or does not write out LINK records in the output pdb. Also, are carbohydrate groups written out as ATOM or HETATMs? The reason I am asking is that I was trying to use a sugar group geometry/naming validation tool called pdbcare (at glycosciences.de), and the program is failing to read out the sugar groups from the pdb. One reason I can see is that the sugars are written out with ATOM cards, while the program possibly expects HETATM, and the other is that this program might be looking for LINK cards (These pdb files were written put by phenix 1.3rc6, so maybe if I rerefined them with 1.4.3, I might get a different result). By the way, I can get these files to be read properly by pdb2linucs at the same webpage (after telling it to use both ATOM and HETATM, and telling it to calculate linkages itself). If there is anyone out there who has used the pdbcare successfully on phenix.refine pdb files, please let me know. It would also be great to add carbohydrate validation tools to the army of great modules in phenix (such as phenix.xtriage and phenix.ramalyze). Engin

2 1

phenix.automr ensemble/component question
by Scott Classen 14 Feb '09

14 Feb '09

Hi Phenixers, I'm a bit confused about the proper syntax for my phenix.automr job. This is probably a simple concept, but I'm running on 3 hours of sleep as my kid was up all night, and my synapses aren't working so good. I expect 2 copies of my protein per AU My protein is composed of two domains I have a single PDB search model for each domain is either of these commands correct? phenix.automr data=mydata.sca \ ensemble_1.coords=domain1.pdb \ ensemble_1.identity=95 \ ensemble_1.copies_to_find=2 \ component_1.mass=40579 \ component_1.component_copies=2 \ ensemble_2.coords=domain2.pdb \ ensemble_2.identity=95 \ ensemble_2.copies_to_find=2 \ component_2.mass=13410 \ component_2.component_copies=2 or phenix.automr data=mydata.sca \ ensemble_1.coords=domain1.pdb \ ensemble_1.identity=95 \ ensemble_1.copies_to_find=1 \ component_1.mass=40579 \ component_1.component_copies=2 \ ensemble_2.coords=domain2.pdb \ ensemble_2.identity=95 \ ensemble_2.copies_to_find=1 \ component_2.mass=13410 \ component_2.component_copies=2 essentially I'm not really using an ensemble of search models, I only have a single PDB for each domain. So should ensemble_1.copies_to_find and ensemble_2.copies_to_find be set to 1 or 2? 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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Error
by Knapp, Mark 12 Feb '09

12 Feb '09

This occurs when running phenix.refine_gui with twin mode turned on. A Python error was detected. This is almost certainly a bug; please send an email containing this message to phenixbb(a)phenix-online.org so we can fix it. Thanks! TypeError : float argument required, not NoneType Traceback: Traceback (most recent call last): File "/protos/package/strucbio/phenix-1.4-3/phenix/wxGUI2/Refine.py", line 269, in OnUpdate self.notebook.run_tab.OnStatsUpdate(event) File "/protos/package/strucbio/phenix-1.4-3/phenix/wxGUI2/RefineNotebook.py", line 277, in OnStatsUpdate self.xyzerr_val.SetLabel("%.2f" % f_info.ml_coordinate_error) TypeError: float argument required, not NoneType Mark Knapp Structural Chemistry NIBR 4560 Horton Street M/S 4.4 Emeryville, CA 94608 510-923-6926

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wx._core.PyDeadObjectError?
by TC Hu 12 Feb '09

12 Feb '09

Dear all, I got the "wx._core.PyDeadObjectError" when using Phenix 1.4-3 GUI under OS X 10.5.6 for a SAD run. The program stuck at the blue window after the first step of AutoSol. Attached is the log file. Could anyone help me find out what is wrong? Thanks very much in advance! Cheers, Tiancen Hu Shanghai Institute of Materia Medica Chinese Academy of Sciences " PHENIX distribution located in /usr/local/phenix-1.4-3/phenix Project Details Project Name: phenix2 Date Stamp : Thu Feb 12 01:08:25 2009 Machine : htcdemacbook-pro.local Directory : /Users/htc/xtal/subjects/cd147se/phenix2 PDS Server Details User : htc Machine : 192.168.1.3 Directory : /Users/htc/xtal/subjects/cd147se/phenix2 Port : 47702 PID : 4863 WIZARD: AutoSol ************************************************************ PHENIX AutoSol Thu Feb 12 01:19:23 2009 ************************************************************ PHENIX VERSION: 1.4 of 08-12-2008 PHENIX RELEASE_TAG : 3 PHENIX MTYPE : mac-intel-osx PHENIX MVERSION : osx-10.5.6 LOCAL INIT: Readdatabase: True SetUpInputs: True AutoSol Thu Feb 12 01:19:23 2009 Gathering defaults from ['AutoBuild', 'ImportRawData', 'LigandFit', 'AutoMR'] WORKDIR: /Users/htc/xtal/subjects/cd147se/phenix2 Checking for KnownWizards: ['AutoSol', 'AutoBuild', 'ImportRawData'] Running start first time through Setting default value of 2.5 for resolution Setting default value of 0.5 for solvent_fraction Setting default value of 200 for residues Guessing sequence file is cd147_21a.seq application method: AutoSol_start Getting inputs on first pass... SUMMARY Input files dataset #1 amom360_p41212_31A.sca Traceback (most recent call last): File "/usr/local/phenix-1.4-3/phenix/wxGUI/wxtask.py", line 522, in OnGoButton try: self.parent.OnGo() File "/usr/local/phenix-1.4-3/phenix/wxGUI/Dialogs.py", line 470, in OnGo gp.RunStrategy() File "/usr/local/phenix-1.4-3/phenix/wxGUI/BMPTaskCanvas.py", line 1170, in RunStrategy self.RunRemotely() File "/usr/local/phenix-1.4-3/phenix/wxGUI/BMPTaskCanvas.py", line 1380, in RunRemotely remote = frame.RemoteHostName, File "/usr/local/phenix-1.4-3/phenix/phenix/pds_server/StrategyUtils.py", line 124, in RunStrategy LastStrategy File "/usr/local/phenix-1.4-3/phenix/phenix/server/PhenixClient.py", line 87, in StartProcessMaster return self._remote_call('StartProcessMaster',arg,kw) File "/usr/local/phenix-1.4-3/phenix/phenix/server/PhenixClient.py", line 466, in _remote_call raise result AssertionError: No user for ssh to machine 192.168.1.3 Traceback (most recent call last): File "/usr/local/phenix-1.4-3/phenix/wxGUI/wxtask.py", line 892, in OnTableKillFocus self.OnTableTextEnter(event) File "/usr/local/phenix-1.4-3/phenix/wxGUI/wxtask.py", line 861, in OnTableTextEnter (grid, cbox, ctrl, t_param, ir, ic) = self.get_event_table(event) File "/usr/local/phenix-1.4-3/phenix/wxGUI/wxtask.py", line 1204, in get_event_table (ctrl, group_list, key_list, winszr) = self.get_ctrl_context(evtwin) File "/usr/local/phenix-1.4-3/phenix/wxGUI/wxtask.py", line 1173, in get_ctrl_context result = self.RootWinSzr.FindInParentSizer(ctrl) File "/usr/local/phenix-1.4-3/phenix/wxGUI/wxtask.py", line 159, in FindInParentSizer result = child.FindInParentSizer(window, child_groups, child_keys) File "/usr/local/phenix-1.4-3/phenix/wxGUI/wxtask.py", line 143, in FindInParentSizer if (child.GetId() == SearchWinId): File "/usr/local/phenix-1.4-3/build/mac-intel-osx/base/Python.framework/Versions/2.6/lib/python2.6/site-packages/wx-2.8-mac-ansi/wx/_core.py", line 14522, in __getattr__ raise PyDeadObjectError(self.attrStr % self._name) wx._core.PyDeadObjectError: The C++ part of the Panel object has been deleted, attribute access no longer allowed. "

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Constrained occ refinement -- sum not equal 1
by Schubert, Carsten [PRDUS] 11 Feb '09

11 Feb '09

Hi, I am trying to sort out some issues with the constrained occupancy refinement in phenix 1.4.3. The structure I am working on is fairly high resolution ~1.4A and it looks as if a couple of the alternative conformations would benefit from occupancy refinement, no hydrogens are present yet. I defined the constrained groups like this: occupancies { individual = None remove_selection = None constrained_group { selection = chain A and resid 66 and altid A selection = chain A and resid 66 and altid B } .... I expected that the sum of occupancies would be restrained to 1, which they should according to the manual, but the refinement gives me occupancies of 0.7 for altid A and 0.34 for altid B, starting values were both 0.5. Similar discrepancies were also present in other groups, like 0.5 A, 0.37 B etc. The latter is the largest deviation from 1 I have seen in thus far. The alternate conformations were generated in coot, by splitting at the CA position. Is this a rounding error I just have to contend with or is there some other parameter I need to tweak? Cheers, Carsten

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phenix.ready_set and SS bond
by dziuba＠amu.edu.pl 09 Feb '09

09 Feb '09

Hi, Is it possible to prevent phenix.ready_set (or actually phenix.reduce) from . adding hydrogen atoms to Cys SG atoms if they are involved in disulphide bonds? Karolina

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phenix.superpose_pdbs_1.4
by David Garboczi 08 Feb '09

08 Feb '09

The default unit cell and symmetry for the "fitted" model (the one that was moved) is the unit cell and symmetry of the "fixed" pdb. As I am superimposing the same model from several space groups to study the differences in packing, I need the "fitted" pdb to keep its own unit cell and symmetry. How might I do this? When is the current default of altering the unit cell and symmetry of the moving model useful? thanks, Dave --

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TLS in phenix.refine_gui
by Miles Pufall 04 Feb '09

04 Feb '09

Hi Guys - Is there a way to load the TLS groups, generated so kindly by TLSMD in old phenix format, into the new gui? It would save a lot of typing. Thanks! Miles Miles Pufall Postdoctoral Scholar Yamamoto Lab UC San Francisco Cellular and Molecular Pharmacology Mail Stop 2280 600 16th Street, Genentech Hall S-574 San Francisco, California 94158-2517 (415)476-4480

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modification of nonbonded geo restraints between symmetry mates
by Alejandro Buschiazzo 04 Feb '09

04 Feb '09

Dear PHENIX users, I wonder what is the 'correct' way of (re)defining geometric restraints among atoms. Here's what I need to do : I have several cations that are chelated by protein residues; some of them involve residues from the same monomer, yet others involve atoms from both the ASU monomer as well as crystal neighbors (i.e. symmetry mates). I see that in the .geo file, these parameters are taken into account as nonbonded simple and nonbonded asu respectively ... how can I change the ideal distances to get proper Zn+2 coordination bonds for both kind of partners? Thank you in advance for your help! -- Alejandro Buschiazzo, PhD Research Scientist Laboratory of Protein Crystallography Pasteur Institute of Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +5982 5220910 int. 120 Fax: +5982 5224185

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map coeffs?
by Walter Novak 04 Feb '09

04 Feb '09

Hi all, I am doing joint X-ray neutron refinement, and in the 1.4-3 version I now get twice the number of choices of map coefficients when opening the mtz. Half now have "no_fill" with them. I am assuming that the difference between maps has something to do with missing Fobs, is that right? Which maps should I be looking at then? Thanks, Wally Walter R.P. Novak, Ph.D. Postdoctoral Fellow Rosenstiel Basic Medical Research Center Brandeis University 415 South St. MS 029 Waltham, MA 02454-9110 Phone: (781) 736-4944 Fax: (781) 736-2405

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TLS + anisotropic ADP mixed refinement
by Scott Classen 03 Feb '09

03 Feb '09

I am trying to perform refinement on a model with three chains (two protein and one DNA... plus water, Cl, and a few other solventy things). The B factors for chain A are generally better than for the other two and I am thinking that the resolution (1.8Å) warrants attempting anisotropic individual adp refinement for at least chain A, and then using TLS for the other two. So my strategy is: *individual_sites *individual_adp *tls *occupancies adp.individual.isotropic = "not Chain A" adp.individual.anisotropic = "Chain A" adp.tls = "Chain B" adp.tls = "Chain D" Previously the model had only been refined with individual isotropic adp (no TLS). The starting model has an r_work=0.2079 and r_free=0.2427. With this new aniso/TLS strategy in the first macrocycle when it gets to the initial TLS refinement it completely blows up with r_work and r_free both going up to 60% have I specified my refinement with bad syntax? or is this even possible with phenix.refine? I can submit more of the log file if you're interested. 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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can phenix.refine calculate r_work and r_free without doing refinement?
by Scott Classen 03 Feb '09

03 Feb '09

Hi all, I was wondering if phenix can calculate r_work and r_free without refinement, sort of like the model_stats from CNS. 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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