- phenixbb - phenix-online.org

Can Phenix do MR with medium/low res EM models?
by Gino Cingolani 19 Mar '09

19 Mar '09

Hi Phenix community, I was wondering if Phenix can handle MR starting from medium/low res EM models. I have a very large oligomeric protein (2.4MDa) with lots of NCS and >450 Se-Mets. In principle, I could use low res MR phases from the "replaced" model to locate Se-sites and then NCS-averaging to locate more sites and improve my phases. Any suggestions how to get Phenix to use an EM model? Has anybody done it successfully using Phenix? Thanks in advance, 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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Re: [phenixbb] Can Phenix do MR with medium/low res EM models?
by Thomas C. Terwilliger 19 Mar '09

19 Mar '09

Hi Gino, I have never tried any problem of this size...but here is a way to proceed using Randy's "input_partpdb_file" option for Phaser that is now available in the autosol wizard. Take your EM model with all its NCS copies, and give it to AutoSol with the keywords: input_partpdb_file=MR.pdb partpdb_rms= 3.0 The partpdb_rms should be the estimated RMSD between the MR model and the true model. You will have as good an idea about this as anyone... You also would supply the usual information to autosol: phenix.autosol sad-data.sca seq.dat 450 Se f_prime=-8 f_double_prime=4.5 \ build=False input_partpdb_file=MR.pdb\ partpdb_rms=3.0 \ resolution=6.0 You might cut the resolution to a pretty low value like 6 A as above. If you get a lot of good sites refined by phaser, then you may be on the right track. This autosol run will output phaser_1.mtz and also resolve_1.mtz that you can use as a starting point for further density modification and model-building as appropriate. Given the size of this problem, I would anticipate lots of challenges, and we will be happy to help as you carry on with it. You might try running everything at really low resolution (20A) at first just to get things to run... All the best, Tom T Hi Phenix community, I was wondering if Phenix can handle MR starting from medium/low res EM models. I have a very large oligomeric protein (2.4MDa) with lots of NCS and >450 Se-Mets. In principle, I could use low res MR phases from the "replaced" model to locate Se-sites and then NCS-averaging to locate more sites and improve my phases. Any suggestions how to get Phenix to use an EM model? Has anybody done it successfully using Phenix? Thanks in advance, 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) _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://www.phenix-online.org/mailman/listinfo/phenixbb

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omit maps without density modification?
by NATHAN THOMSEN 17 Mar '09

17 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 14 Mar '09

14 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 12 Mar '09

12 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 11 Mar '09

11 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 11 Mar '09

11 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 11 Mar '09

11 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 10 Mar '09

10 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 09 Mar '09

09 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 09 Mar '09

09 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 08 Mar '09

08 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 >

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default bondlengths - metal
by Engin Ozkan 06 Mar '09

06 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

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fwd: phenix.autobuild- multiple models.
by Nathaniel Echols 04 Mar '09

04 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

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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 >>> >>>

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AutoBuild after resolve
by Mo Wong 28 Feb '09

28 Feb '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!

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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

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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)

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