March 2011 - phenixbb - phenix-online.org

Low rmsd values
by Teemu Haikarainen 23 Mar '11

23 Mar '11

Hi all, I am getting quite low rmsd values for my structure. I am finishing the refinement and I have rmsd of 0.003 Å for bonds and 0.67 for angles, with R/Rfree of 0.148/0.176. The resolution is 2.0 Å. I am refining with riding hydrogens and using the automatic weight optimization. I have also tried to change the weights manually, but the more eye-pleasing rmsd values always result in worse Rfree. Is there any reason to worry about the low rmsd values and should I always use the optimized weights in refinement? I am using the latest version of Phenix. Regards, Teemu -- Teemu Haikarainen (M.Sc.) Turku Centre for Biotechnology Tykistokatu 6 BioCity, Turku FIN-20521, Finland

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Re: [phenixbb] Autobuild parent process aborted--running combine_models in Autobuild
by Thomas C. Terwilliger 22 Mar '11

22 Mar '11

Hi Mark, The answer depends on whether this is a "rebuild_in_place=True" run or not. (I think you are using rebuild_in_place=true, but I'll give both answers): Assuming "rebuild_in_place=True": You can combine models with autobuild, providing all models have exactly the same set of atoms (aside from any solvent) by editing this script (basically you run a dummy autobuild run to create a directory and database entries, then you copy your files there, then you run autobuild and tell it to carry on and do the combine step): #!/bin/csh -f if (-d PDS || -d AutoBuild_run_1_) then echo "Please run in a directory without PDS or AutoBuild_run_1_" exit 1 endif echo "Setting up combine models with a dummy run. NOTE: multiple_models_group_number must be correct" phenix.autobuild fobs.mtz multiple_models=true seq_file=seq.dat combine_only=true multiple_models_group_number=2 multiple_models_number=1>& dummy_autobuild.log echo "Copying files to AutoBuild_run_1_/MULTIPLE_MODELS" mkdir AutoBuild_run_1_/MULTIPLE_MODELS cp coords1.pdb AutoBuild_run_1_/MULTIPLE_MODELS/initial_model.pdb_1_1 cp coords2.pdb AutoBuild_run_1_/MULTIPLE_MODELS/initial_model.pdb_1_2 cp map_coeffs_1.mtz AutoBuild_run_1_/MULTIPLE_MODELS/initial_model.mtz_1_1 cp map_coeffs_2.mtz AutoBuild_run_1_/MULTIPLE_MODELS/initial_model.mtz_1_2 ls AutoBuild_run_1_/MULTIPLE_MODELS/ echo "Running autobuild to combine files in AutoBuild_run_1_/MULTIPLE_MODELS" phenix.autobuild combine_only=true seq_file=seq.dat carry_on=true run=1 > autobuild_combine.log # END OF COMBINE_MODELS SCRIPT Assuming "rebuild_in_place=False": In this case you can provide autobuild with a list of files with consider_main_chain_list="file1.pdb file2.pdb" , or simply dump all the models into a singe pdb file and use model=all_models.pdb, and run autobuild one more time. Let me know if that doesn't do it! -Tom On Mar 22, 2011, at 3:00 PM, Mark A Saper wrote: I ran AutoBuild from command line and it submitted 5 jobs with qsub. Apparently I aborted the parent process. So I have the 5 jobs running, apparently producing 5 different models (I specified nproc = 5 as suggested in the documentation). Can I rerun AutoBuild and have it combine the 5 models already calculated? Mark _________________________________ Mark A. Saper, Ph.D. saper(a)umich.edu phone (734) 764-3353 fax (734) 764-3323 _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss

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Autobuild parent process aborted
by Mark A Saper 22 Mar '11

22 Mar '11

I ran AutoBuild from command line and it submitted 5 jobs with qsub. Apparently I aborted the parent process. So I have the 5 jobs running, apparently producing 5 different models (I specified nproc = 5 as suggested in the documentation). Can I rerun AutoBuild and have it combine the 5 models already calculated? Mark _________________________________ Mark A. Saper, Ph.D. saper(a)umich.edu phone (734) 764-3353 fax (734) 764-3323

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Another question about twinned maps
by Mary Ho 22 Mar '11

22 Mar '11

Pavel- Another related question... Does the option for Fill Missing F(Obs) with F(Calc) work for twinned maps? If I turn it on, I don't get an error but the maps don't seem any different. Just wondering, Thanks, Mary On Mon, Mar 21, 2011 at 11:44 AM, Pavel Afonine <pafonine(a)lbl.gov> wrote: > Hi Mary, > > I'm not sure map sharpening is done in case of twinning (otherwise it is an > option that you can turn on/off either in phenix.refine or in more specific > tool for maps calculation called phenix.maps). I will check this later today > and reply. > > Pavel. > > > > On 3/21/11 8:08 AM, Mary Ho wrote: > >> I'm using phenix-1.7-650. When phenix.refine generates the detwinned maps >> with apply B-factor sharpening on and no value inputed, is the value the >> program uses for sharpening output anywhere? >> >> Thanks, >> >> Mary X. Ho >> Postdoctoral Associate >> Arnold Lab >> Rutgers >> > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb >

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refinement for ligands with alternative conformation
by zhengyi＠msu.edu 22 Mar '11

22 Mar '11

Hello, I am working on the refinement of a structure about 2.8A, which the substrate ligand has an odd conformation. A blob of negative difference density about 4.8 sigma between the one portion of the ligand and the other. If I break down the ligand into two parts, the negative density disappears, however, one part of the ligands does not fit well. We suspect a mixture of conformations. Any suggestions would be appreciated on how to setup refinement for ligands with alternative conformation. Many thanks, Yi Zheng Department of Biochemistry Michigan State University

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Re: [phenixbb] "FOM" or HL coeffs from model?
by Dyda 21 Mar '11

21 Mar '11

Phoebe, >How can I get phenix to spit out not just PhiModel but an estimated FOM or fake HL coefficients (without experimental phases - just based on how badly my model agrees with FOBS)? And I'd like the weights in their own personal mtz column(s), not just precombined in a "weighte d phi" column.< can sigmaa do that for you from Fcalc (vector) and Fo (magnitude)? Fred [32m******************************************************************************* Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular Biology Fax: 301-496-0201 DHHS/NIH/NIDDK e-mail:[email protected] Bldg. 5. Room 303 Bethesda, MD 20892-0560 URGENT message e-mail: 2022476710(a)mms.att.net Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred *******************************************************************************[m

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B factor sharpening in twinned maps
by Mary Ho 21 Mar '11

21 Mar '11

I'm using phenix-1.7-650. When phenix.refine generates the detwinned maps with apply B-factor sharpening on and no value inputed, is the value the program uses for sharpening output anywhere? Thanks, Mary X. Ho Postdoctoral Associate Arnold Lab Rutgers

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changing the project directory
by Charisse Crenshaw 19 Mar '11

19 Mar '11

Hello, I have recently started a project whose folder was located on my desktop. I would like to move that folder off of my desktop as I've heard that having a messy desktop slows down one's computer. I moved the project directory somewhere else, and this resulted in Phenix not being able to find the project (understandably). So I moved it back to its original location and Phenix could then open the project. So, in an X11 shell, I copied the project folder to the new desired location, then changed the output directory in the Phenix main window to that new path. But when I clicked on the project again, the output directory that is indicated changes back to the original path. Now I am looking through the preferences etc for a way to change the path of the project directory within Phenix and I cannot. Can anyone tell me if this is possible and if so, how do I do it? Thanks, Charisse The Salk Institute for Biological Studies

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Refinement Strategy vs. R gap
by Yuri 17 Mar '11

17 Mar '11

Pavel, It seemed like I had to close the GUI window and reopen it for the default (automatic aniso/iso) to take effect. I ran a TLS with 5 groups and ended up with better statistics. Rwork 0.18 Rfree 0.239 -- Yuri Pompeu

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Refinement Strategy vs. R gap
by Yuri 16 Mar '11

16 Mar '11

Hello phenixers, I am refining a liganded structure at 2.1 and I am pretty far into my modeling. Rfree = .265 rwork= .20 My asu has 399 residues one prosthetic group (3178 atoms) and 236 HOH. I just want to do one last refinement round before submission and I am not sure about the strategy I should select as I am running into the following: I- If I refine individuals sites and real space (XYZ) and individual ADP with aniso/iso selection automatic my Rfree goes up slightly and Rwork drops to about .196. I also select optimize x-ray/ADp weight I should say. II- When I choose no XYZ refinement with anisotropic ADP for protein chain only with weight optimization Rwork plummets to 0.15 and Rfree also drops to 0.25. But my gap is now .10 !! I checked my log file and it looks like in default automatic individual ADP phenix.refine is picking all the residues to be anisotropic even though I would not try that at 2.1 A. Could someone point me in the right direction, there is probably something I am overlooking. Thank you -- Yuri Pompeu

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