October 2008 - phenixbb - phenix-online.org

high temperature factor refinement
by allbette＠gmail.com 17 Oct '08

17 Oct '08

Hi All, I just refined a structure at 2.95A and getting a good R-work and R-free(0.236 and 0.274). When I checked the PDB, I found many residues have high temperature factor over 100. How can I use Phenix or CNS fix those high temperature factor for further refinment? Thank you Jason

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Re: [phenixbb] sa_omit-map -- it's fine
by Thomas C. Terwilliger 17 Oct '08

17 Oct '08

Hi again Pavel and Vladimir, The omit maps are fine. I'm sorry for the false alarm; I had run a tiny test structure with too few omit boxes so that the omitted regions were way too much of the structure and it looked really bad. Using more omit regions fixed the problem. A regular structure (nsf-d2 from the PHENIX structure library) gets a fine sa-omit map with the defaults. A further-improved map can be obtained with a higher-than-default value of "n_box_target=32" (default=12, note that you don't necessarily get exactly the number you ask for as it has to be something that the asymmetric unit can be divided into.) All the best, Tom T Hi Pavel and Vladimir, After all this discussion...I think there is something wrong with the composite omit maps in the current version. They do not finish correctly...I will check this out. If you instead just omit around the atoms in a pdb file with "omit_box_pdb=target.pdb" that seems fine however. I'm sorry for the problem. All the best, Tom T > Hi Tom, > > don't we need to add "maps_only=True" as well (as Manual suggests in section "Just make maps; don't do any building."; > http://www.phenix-online.org/documentation/autobuild.htm) ? > > I'm asking because the original question was specific about it: compute map and "nothing extra". > > Thanks, > Pavel. > > On 10/13/2008 2:17 PM, Thomas C. Terwilliger wrote: >> Hi Vladimir, >> You can do this with: >> >> phenix.autobuild data=data.mtz model=coords.pdb >> composite_omit_type=sa_omit nproc=4 >> >> All the best, >> Tom T >> >> >> >>> After phenix.refine stage I would like to get just the sa_omit map for the >>> whole assymetric unit (nothing extra). How can I do it? >>> Regards. >>> Vladimir >>> >>> >>> >>> _______________________________________________ >>> 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 >> >

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sa_omit-map
by pletnev＠hwi.buffalo.edu 17 Oct '08

17 Oct '08

After phenix.refine stage I would like to get just the sa_omit map for the whole assymetric unit (nothing extra). How can I do it? Regards. Vladimir

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Reporting phasing statistics.
by Francis E Reyes 16 Oct '08

16 Oct '08

So normally when I run autosol, my primary indicator of 'goodness' would be the SKEW, but in reporting to papers, it seems that the MIR statistics involve Rcullis, phasing power, and FOM. I can find FOM from solve_x.prt and resolve_x.log but where are the others? Thanks FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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? about optimize weights
by gerwald jogl 16 Oct '08

16 Oct '08

Hi All, I just started using phenix.refine and it's working quite well so far. I ran the optimize weight strategy at the end of a test refinement and it lowered the Rfree as intended. Unfortunately, when I ran the next refine job based on the output .def file, it seems that the 'best weights' found in the previous run were not conserved as the geometry and R factors got a lot worse. Where can I find the weights determined by the optimize run and how can I fix those for further refinement? Thanks, Gerwald

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helix deformed during refinement in phenix
by Raja Dey 14 Oct '08

14 Oct '08

Dear All, I am using phenix to refine a long helix of about 120 residues in a complex structure, but in course of refinement the helix becoming distorted from helical geometry. As a result when I am displaying the refined structure in pymol as cartoon one long helix showed 3/4 discontinuous helices in a single chain. Is there any way to constrain or restrain the helix during refinement, so that refinement process can maintain the helical geometry? Any suggestion is well appreciated. With regards... Raja Raja Dey, Ph.D. Research Associate Molecular and Computational Biology University of Southern California

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detwin data
by HUA YUAN 14 Oct '08

14 Oct '08

Dear Phenix community, I've used the phenix.refine with its detwin function. Is there any way to have a detwinned data output so that I can use it for other things. I tried use CCP4 detwin with the same twin law and twin fraction obtained from Phenix. However, this didn't work. Another question is whether I can use "some" phase information, say from DM into Phenix? I tried to include the PHIDM but Phenix complained about it saying "wrong array". Any suggestions or comments are hightly appreciated! Thanks, Hua

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Re: [phenixbb] Files generated in Autobuild from simulated annealing runs
by Tom Terwilliger 07 Oct '08

07 Oct '08

Hi Rebecca, I'm sorry this didn't get answered on the phenix_bb! I somehow missed it too. When you run an omit map with model=mymodel.pdb omit_box_pdb=mymodel.pdb omit_res_start_list=500 omit_res_end_list=500 the autobuild wizard edits mymodel.pdb, setting the occupancies of all atoms that are within a box enclosing the atoms in residue 500 of mymodel.pdb (plus a 2 A border) to zero. Then it runs the cycles of autobuild you specify (in this case just a SA step), and produces a density-modified map (resolve_composite_map.mtz) using the resulting model to generate phase information (and keeping the occupancies of these atoms at zero). If mydata.mtz contains phase information, that is used as well. The output map is in resolve_composite_map.mtz and a pseudo-map showing where the OMIT region(s) is(are) located is in omit_region.mtz The file overall_best_denmod_map_coeff.mtz is actually not really relevant or useful when you are doing OMIT maps because it is just one of the intermediate files that are produced. In this particular example it will be identical to resolve_composite_map.mtz but if you do other types of OMIT maps it won't be the same. I changed the output of the autobuild wizard recently, so you might want to upgrade to the 1.3-final version. The end of the log file in this case should say: -------------------------------------------------- Summary of model-building for run 1 Tue Oct 7 08:17:30 2008 Files are in the directory: /net/chevy/raid1/terwill/misc/test/ AutoBuild_run_1_/ Starting mtz file: /net/chevy/raid1/terwill/misc/test/perfect.mtz Sequence file: /net/chevy/raid1/terwill/misc/test/seq.dat Composite omit map is in : /net/chevy/raid1/terwill/misc/test/ AutoBuild_run_1_/OMIT/resolve_composite_map.mtz Boundaries of omit regions are in : /net/chevy/raid1/terwill/misc/test/ AutoBuild_run_1_/OMIT/omit_region.mtz -------------------------------------------------- Which I hope is clearer than earlier output in which the overall_best_denmod_map_coeff.mtz file is mentioned but is irrelevant. I hope that helps! All the best, Tom T On Oct 7, 2008, at 7:19 AM, Page, Rebecca wrote: > Hi Tom, > I posted the question on the phenix bb and, when I got no response, > shot an email over to Frank von Delft, an old friend, to see if he > knew answer. > > He didn’t, but recommended I email you directly and to “ask him to > post the answer on the general bb :)”. He also mentioned he hadn’t > seen the post on the phenix bb and I would be interested to know if > you did not see it either (I received it). > > At any rate, here it goes: > > > I am newcomer to phenix and have a rookie question about the > generated > > files using the phenix.autobuild command. I generated an sa-omit map > > of my model, omitting the coordinates for a bound ligand (ligand is > > residue > > 500): > > > > phenix.autobuild data=mydata.mtz model=mymodel.pdb > > omit_box_pdb=mymodel.pdb omit_res_start_list=500 > omit_res_end_list=500 > > omit_chain_list=A composite_omit_type=sa_omit > > > > The output omit map (resolve_composite_map.mtz) looks great. > > > > > > My question is: > > What, exactly, is the "overall_best_denmod_map_coeff.mtz" in this > case > > and how is it related, if at all, to the > "resolve_composite_map.mtz"? > > > Thanks for your help, > Rebecca > > Rebecca Page > Brown University >

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Files generated in Autobuild from simulated annealing runs
by Page, Rebecca 07 Oct '08

07 Oct '08

Dear Phenix users: I am newcomer to phenix and have a rookie question about the generated files using the phenix.autobuild command. I generated an sa-omit map of my model, omitting the coordinates for a bound ligand (ligand is residue 500): phenix.autobuild data=mydata.mtz model=mymodel.pdb omit_box_pdb=mymodel.pdb omit_res_start_list=500 omit_res_end_list=500 omit_chain_list=A composite_omit_type=sa_omit The output omit map (resolve_composite_map.mtz) looks great. My question is: What, exactly, is the "overall_best_denmod_map_coeff.mtz" in this case and how is it related, if at all, to the "resolve_composite_map.mtz"? Thanks in advance, Rebecca

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phenix.refine v.1.3 vs 1.24
by Leo Sazanov 07 Oct '08

07 Oct '08

When refining the same (large) molecule in several different crystal forms at about 3.1 A resolution, I noticed that in two cases when experimental phase information is available, in phenix.refine-1.3 I get worse Ramachandran compared to phenix.refine-1.24 - about 2% less residues in most favored regions. In one case when there is no experimental phase information, there is no difference between two phenix versions. What could be the reason for that? These comparisons where done for cases when final RMSDs and R-factors are similar (and all RMSDs calculated in v.1.3), so automatic weights adjustment in v.1.3 should not have played much role. Adding to other people's comments, it would be useful to be able to switch this adjustment off, as sometimes one wants full control over final RMSDs, etc. Thanks! -- Dr. Leonid A. Sazanov Research group leader Medical Research Council Dunn Human Nutrition Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-dunn.cam.ac.uk Tel: +44-1223-252910 Fax: +44-1223-252915

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