November 2009 - phenixbb - phenix-online.org

Can PHENIX write the peak list to a PDB file?
by Joe Krahn 04 Dec '10

04 Dec '10

PHENIX has an option to find positive and negative peaks, but only lists them in the log file along with the residue they are closest to. Is it possible to write out the actual peak coordinates, such as to a PDB file? Thanks, Joe Krahn

5 7

Bad ligand parameters
by Joe Krahn 21 Oct '10

21 Oct '10

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

9 13

Re: [phenixbb] phenix.automr ensemble/component question
by Thomas C. Terwilliger 24 Jul '10

24 Jul '10

Hi Scott, Your first command looks good to me. It is saying that the composition of the crystal is 2 copies of each chain: component_1.component_copies=2 component_2.component_copies=2 and you want to search for 2 copies of each of your search models: ensemble_1.copies_to_find=2 ensemble_2.copies_to_find=2 All the best, Tom T > 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 > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb >

2 2

Using LigandFit to identify unknown density
by Katya Heldwein 28 Jan '10

28 Jan '10

Hi, I'd like to run LigandFit to identify a small molecule accounting for an unknown density. How do I do that, preferably, in a command-line mode? 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

5 8

Re: [phenixbb] sigma cutoff
by Kay Diederichs 01 Dec '09

01 Dec '09

> > > Hi, > > According to the Phenix manual, phenix.refine uses no sigma cutoff by > default. Since I haven't changed this manually, why do I see in my pdb > file MIN(FOBS/SIGMA_FOBS) 1.340? > > Thanks for help, > Karolina > > This one I can answer because I asked myself the same question recently. The answer is that Phenix does not impose any sigma cutoff, but rather your data are such that the minimum value of Fobs/Sigma_Fobs is 1.34 . You can verify this for yourself by going through your reflection file, line by line, and calculating Fobs/Sigma_Fobs for each reflection. You will find that all your reflections have a Fobs/Sigma_Fobs larger or equal to 1.34 . So it has nothing to with phenix; phenix just reports a property of your data. An easier way than doing it "manually" is using CCP4 sftools for calculating a new column "ratio", writing out the resulting MTZ file, and looking at this with mtzdmp. HTH, Kay -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: Kay.Diederichs(a)uni-konstanz.de Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universitaet Konstanz, Box M647, D-78457 Konstanz

2 1

Re: [phenixbb] Confused by the output from Phenix autobuild jobs
by Thomas C. Terwilliger 30 Nov '09

30 Nov '09

Hi Serah, You are right that the coefficients that you want for a difference map are not present in the overall_best_refine_map_coeffs.mtz file. The coefficients in that file (labelled FP PHIM) are the same as 2FOFCWT PH2FOFCWT from the refinement output, but there are no difference map coefficients. I will change this. In the meantime, I would do this after the end of autobuild: phenix.refine AutoBuild_run_1_/overall_best.pdb \ AutoBuild_run_1_/exptl_fobs_phases_freeR_flags.mtz and then you will have your map coefficients. >> I'm still wondering about the overall_best_*.* outputs - are these the >> really final output, or do we go for cycle_best_3.* series? The overall_best_xxx files are copied from the cycle_best_xxx files which are copied from the original files, all of which are in the TEMP0/ subdirectory. Thanks for pointing out that the difference coefficients are not present in the autobuild map file. I will fix the output to have the original refinement map file available. All the best, Tom T

1 1

alternate conformation
by subhash bihani 26 Nov '09

26 Nov '09

Hi, I am refining a structure with ligand in alternate conformations. I tried giving them A and B, it worked. but I feel that this doesnot make interactions between alternate conformations absolutely zero. Is there any command in phenix similar to Igroup statement in CNS which can be used for such cases. Regards subhash -- Subhash Bihani Scientific Officer Solid State Physics Division Bhabha Atomic Research Centre Trombay, Mumbai-85 Ph. 25594688 (o) alternate email: subhashbihani(a)yahoo.co.in

5 10

R-free rules
by Bryan W. Lepore 25 Nov '09

25 Nov '09

in the phenix.reflection_file_editor gui not sure i understand this: [x] Extend existing R-free array(s) ... [R-free flags generation] <--+ | | | | +-if this is checked, then do NOT check "Generate R-free flags" in here ... because "extend" is not the same as "generate", right? ... and thanks for the help before. -bryan

12 35

Age Concern edition of the Computing Commission and Teaching Commission newsletter
by Ralf W. Grosse-Kunstleve 25 Nov '09

25 Nov '09

Posted on behalf of Lachlan Cranswick: The Computing Commission and Teaching Commission has produced a joint November 2009 newsletter on the theme of "Age Concern", which deals with issue concerning "the slow march towards retirement of the major generation of crystallographic programmers", as further explained by David Watkin within the newsletter. http://www.iucr.org/resources/commissions/crystallographic-computing/newsle… or via http://www.iucr.org/resources/commissions/crystallographic-teaching/newslet… --------------------------- This issue's articles include : - the latest background and information from the UK based EPSRC funded Age Concern Project. - history and science within the Caltech based CRYRM single crystal suite; DIMS - Direct methods In Multidimensional Space software; Crunch 1.5 Direct Methods Software; the Glasgow based GX single crystal suite; the Italian based CAOS structure refinement software; Ton Spek's Platon; and a list of programs archived at Armel Le Bail's Crystallography Source Code Museum. - experience in conversion of large crystallographic Fortran-77 to C++; as well as the place of the Quick and Dirty Crystallographic Computer Program - Historical group photographs from some of the Crystallographic Computing and Teaching School of the 1970's. - Archived manuals and source code from the above mentioned software. - Teaching material of Isabella L. Karle, as she presented at the 1978 Erice School on Direct Methods for Solving Crystal Structures - A reprint of the The Analytical Theory of Point Systems (1923) by J. D. Bernal (1901-1971) Further Computing Commission newsletters are intended on theme of Age Concern : capturing the history and the crystallographic science behind past and present Small Molecule, Powder Diffraction, Protein and other crystallographic software. Submissions on this topic are welcome and encouraged. - Lachlan Cranswick ( lachlan.cranswick(a)nrc.gc.ca )

1 0

Confused by the output from Phenix autobuild jobs
by Serah Wangari 24 Nov '09

24 Nov '09

Dear Phenix users, I have run a number of Autobuild jobs using the Phenix GUI and in all cases, I'm not sure what output I should proceed with to the next step. - The first job was for rebuilding a loop section in the model (rebuild-in-place) - As far as I can remember, there was no mtz generated from this job, I had to generate map coefficients with the overall_best pdb and an old mtz using another refinement program. Did I miss something during the job input step, so that no mtz was generated, or how would I proceed in such a case? - The next job involved rebuilding the whole model (rebuild-in-place) - in this case, I took the overall_best pdb, but when I tried to open the overall_best_refine_map_coeffs.mtz in coot, I got this error that coot failed to find F/Phi columns in the mtz file. Then I checked in the TEMPO directory, and I managed to open a random mtz from one of the refinement cycles with coot, but I wasn't confident building into that, so again I had to generate map coefficients using overall_best pdb and an old mtz in another program. - The other job was rebuilding (rebuild-in-place) another model with composite maps generation - Here, in addition to the 12 mtz and pdb files from the 12 omit regions, I got resolve_composite_map.mtz I should assume as the only final output; and no final pdb. Again, this mtz file doesn't have the F/Phi columns as I got the same error as above in coot. I'm not sure how to proceed with this mtz...... I would really appreciate if someone could point me to the right direction or at least direct me to some literature where the output from Phenix autobuild jobs is explained - as I haven't come across such info yet. Thank you in advance, Serah --

3 2