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define angle between groups of atom 'planes' for refinement restraint?
by Francis E Reyes 10 Nov '11

10 Nov '11

Hi all I was wondering if there was language in the monomer restraint libraries (.cif) or a custom phenix.refine geometry restraint a that defines an angle between two planes, where each plane is a group of coplanar atoms. Thanks! F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

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nproc for autobuild
by Michael Thompson 09 Nov '11

09 Nov '11

Hello, I apologize if this question seems very basic, but I am new to phenix.autobuild. I would like to set up a series of phenix.autobuild runs on our cluster, and would like to maximize the speed. I am trying to make single rebuilt models using the command below: phenix.autobuild data=data.mtz model=coords.pdb map_file=map_coeffs.mtz multiple_models_number=1 n_cycle_rebuild_max=5 ncycle_refine=5 s_annealing=true refine_with_ncs=True place_waters=True nproc=?? run_command=/home/qsub.sh The AutoBuild documentation says "if you are using rebuild_in_place=False, then use nproc=4" and "if you are using rebuild_in_place=True, then use nproc=5. (Any more will not make any difference)." My interpretation of the documentation is that for the above AutoBuild run with multiple_models_number=1, I should set nproc=5 (or 4?). Is this correct? Also, if I were to change the command so that multiple_models_number=10, should I then use nproc=50 (i.e. 5 processors per model), or is it still the case that setting nproc>5 doesn't make a difference? Thanks in advance for your help! Mike -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles miket(a)chem.ucla.edu

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phenix.phaser output .param file
by G Y 08 Nov '11

08 Nov '11

Dear Experts, I run my script for phenix.phaser in bash shell and one of the output file is filename.param (please note there is no "s" at the end of param) There are only two lines inside this file: # [no title set] TNCS IGNORE ON I do not really know what this file doing for. And, if I run the phaser from GUI, I will not find any .param file. What is this file doing for? Is it some kind of redundant information which is not useful at all? What should I edit in input params.eff file to avoid this output file? I would appreciate to any help from you. Thanks. Best, G

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Constrained group refinement
by Christian Roth 08 Nov '11

08 Nov '11

Dear all, I defined the following contrained groups which should a ligand in two alternative forms and an ion at the same position refine to an summed occupancy of 1. constrained_group { selection = chain Z and resname 2CL and altloc A selection = chain Z and resname 2CL and altloc B selection = chain r and resname Cl } constrained_group { selection = chain c and resname 2CL and altloc A selection = chain c and resname 2CL and altloc B selection = chain m and resname Cl } constrained_group { selection = chain N and resseq 69 and altloc A selection = chain N and resseq 69 and altloc B selection = chain o and resname 2Cl } } At the end I get an error because of the very small nonbonded interactions. it seems that my definition are not correct, but I am at the moment unsure why. Could someone point me to the mistake. Thanks in advace for your help Best Regards Christian

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Constrained group refinement Addendum
by Christian Roth 08 Nov '11

08 Nov '11

Do the ions have to be altlocC for the group definition? Best Regards Christian

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Cross Validation Reflection Set question
by Yuri 07 Nov '11

07 Nov '11

Thanks for the replies. >I just tried doing this, and it looks like the R-free flags will cover >the full resolution range, at least with the current code. By current code, you mean 1.7.2-869 and newer, right? >Is this really necessary in this case (refine against lower res data, >then continue with the whole data set I think I have a backbone shift in this structure (relative to native protein used for MR) so I wanted to do it this way befor trying to go all the way down to 2A. One last question does phnix do NCS averaging to improve maps? -- Yuri Pompeu

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Re: [phenixbb] AutoBuild runtime
by Nathaniel Echols 07 Nov '11

07 Nov '11

On Mon, Nov 7, 2011 at 9:14 AM, Shya Biswas <shyabiswas(a)gmail.com> wrote: > Thanks for the suggestions. Unfortunately my MR solution is not good enough > to get a good map. Autobuild does give me a solution when i put in my > sequence but the map does not look good. I was wondering if the final model > that Autobuild gives has undergone density modification. Strictly speaking, it's the map that undergoes density modification - but yes, this will be done unless you explicitly disable it. -Nat

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Cross Validation Reflection Set question
by Yuri 07 Nov '11

07 Nov '11

Dear All, Here is the situation, I have data to 2 A. I refined the model to 3 A first with S.A. Now I want to use higher res data for the rest of refinement. My Rfree created in the first round when I only used data to 3A. Was Rfree set created using all the data or just up to 3A shell? or do I have to extend into higher res shells? one caviot is I had twin law h,-k,-h-l enabled when they were created. Thanks, -- Yuri Pompeu

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Re: [phenixbb] AutoBuild runtime
by Nathaniel Echols 05 Nov '11

05 Nov '11

On Sat, Nov 5, 2011 at 12:02 PM, Shya Biswas <shyabiswas(a)gmail.com> wrote: > I was running autobuild using my protein sequence and the best MR model that > I got out of phaser, however it is taking really long to finish the job. Is > there a way to reduce the time period? Several options: - turn on quick mode (quick=True, or equivalent button in GUI) - use multiple processors if you have them (nproc=X, or equivalent control in GUI) - cut back resolution: if you have really good and/or high-resolution data*, you may be able to get nearly as good a model with fewer reflections, and it will be much faster (mostly due to refinement time, I think). However, this can also significantly degrade your model if the data aren't that great. - instead of AutoBuild, use phenix.phase_and_build (also in the GUI), which is basically the building procedure from AutoSol. It will usually not produce as complete a model (or R-factors as low) as AutoBuild, but it's much faster. -Nat (* the p9-sad tutorial is a good example of this - when we run workshops, we usually tell attendees to set the resolution limit for AutoSol to 3.0 instead of using all data to 1.7. The resulting model is nearly complete, and it finishes in less than half the time. Of course these data are unusually good...)

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Call for submissions to Computational Crystallography Newsletter (corrected)
by Nigel Moriarty 05 Nov '11

05 Nov '11

Calling for articles and short communications of interest tostructural biologists. The deadline for publication in the January2012 issue is 1st Dec, 2011. The Computational Crystallography Newsletter (CCN) is an electronicnewsletter for structural biologists, and is published online every 6months. Feature articles, meeting announcements and reports can besubmitted to me at any time for consideration. Submission of text byemail or word-processing files using the CCN templates is requested.Past newsletters and the template are available atwww.phenix-online.org/newsletter. Cheers Nigel -- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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