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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 13 Oct '08

13 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 06 Oct '08

06 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 06 Oct '08

06 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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wxc_scale automatically doubled during the refinement
by yentingl＠gate.sinica.edu.tw 06 Oct '08

06 Oct '08

Dear phenix users, I've observed that in phenix 1.3 final if I specify wxc_scale the value is automatically doubled in every successive macrocycle. For example if I set wxc_scale=0.9 at the beginning, it becomes 1.8, 3.6, 7.2, 14.4 ... at macrocycle 2, 3, 4, 5 ... Is this normal? This was not found in phenix 1.3 rc4 on the same machine. Thanks! Yen-Ting

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library values for H in phenix.refine and MOLPROBITY
by Pavel Afonine 06 Oct '08

06 Oct '08

Hi Jianghai, > Another thing about riding H atoms. As I said before, the bond > distance between riding H and its attached atoms is different from > phenix library (ccp4 mono library) to the library MOLPROBITY uses. I > think the distance from MOLPROBITY is longer. The result is that the > structure refined by phenix.refine has a not so good clash score. Is > there a way to keep the distance from phenix.reduce in phenix.refine? Yes, I remember you mentioned this in the past (may be even several times). And this is true: the distances in Mon.Lib. and internal library in Molprobity might be different. Theoretically, longer distances are more correct since they reflect the actual nuclear position (that one can observe in neutron diffraction experiment), while the X-rays show hydrogens shifted along the bond towards the atom they are bonded to. This is why some programs (like SHELX) use shortened distances for X-H bonds and some uses those obtained from neutron scattering. Overall, I agree that the dictionaries must be made consistent within the package - this is something to fix on PHENIX end. Pavel.

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TLS refinement
by HUA YUAN 05 Oct '08

05 Oct '08

Dear Phenix community members, I have a molecular replacement solution refined agains a twinned 2.7 angstrom data to Rfree as 33%, with TLS and twin-law and others as default. The map looks good and shows extra map for my flavin ligand. Then I manually rebuild the model, fixing some obvious off-map residues and put a flavin molecule into the model. After this, I used the *def file from previous run to do another round of refinement. This time the Rfree increased to 36%. I realized that it has something to do with the TLS, isotropic and aniostropic B factor. However, I don't know exactly what's the reason and what to do at this stage. Any comments or suggestions? Should I do TLS refinement at the last step? Thanks and Best Wishes for all, Hua

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AssertionError in refinement
by Raja Dey 05 Oct '08

05 Oct '08

Dear PhenixBB Members, I am getting the following error while I am running the refinement given below: It stopped after a while. I enclosed the last part of the log file. phenix.refine gat.mtz gat-tlsmd.pdb simulated_annealing=true strategy=rigid_body+individual_sites+group_adp+individual_adp+tls tls.params output.prefix=final_1 --overwrite ================================ ADP refinement =============================== ----------TLS refinement---------- |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2491 r_free = 0.3251 target = 3.621992 convergence test = off | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 15)----------------| | r_work = 0.2437 r_free = 0.3120 target = 3.588460 convergence test = off | |-----------------------------------------------------------------------------| |-Information about rigid groups----------------------------------------------| | Total number of atoms = 1591 Number of rigid groups = 3 | | group: start point: end point: | | x B atom residue <> x B atom residue | | 1: -3.758 92.66 N MET 259 <> 10.389 94.12 CD2 LEU 300 | | 2: 14.264 58.92 N ILE 301 <> 1.800 100.80 O THR 315 | | 3: 1.098 66.36 N SER 316 <> -10.129 70.49 CE MET 368 | |-----------------------------------------------------------------------------| Traceback (most recent call last): File "/usr/local/phenix-1.3b-rc6/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-1.3b-rc6/phenix/phenix/refinement/command_line.py", line 82, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/usr/local/phenix-1.3b-rc6/phenix/phenix/refinement/driver.py", line 1143, in run call_back_after_monitor_collect = call_back_after_monitor_collect) File "/usr/local/phenix-1.3b-rc6/phenix/phenix/refinement/strategies.py", line 549, in refinement_machine h_params = h_params) File "/usr/local/phenix-1.3b-rc6/mmtbx/mmtbx/refinement/adp_refinement.py", line 153, in __init__ tools.split_u(fmodels.fmodel_xray().xray_structure, tls_selections, offset) File "/usr/local/phenix-1.3b-rc6/mmtbx/mmtbx/tls/tools.py", line 498, in split_u assert (u_iso < 0.0).count(True) == 0 AssertionError While I can successfully run similar refinement on another project. I have another question. Inclusion of individual_adp in strategy increases R and R(free) in one case(2.8 A data), while decreases in another case (3.6 A data). Both are at the final stage of refinement. Is there any explanation? Looking forward to hearing from you... Thanking you in advance... Raja

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sfcheck & Phenix
by john kryst 04 Oct '08

04 Oct '08

Hi all, I have a little problem... R and R-free from phenix.refine are 22.9 and 30.6 respectively.... when i validated in the rcsb server... sfcheck gave me a R and Rfree of 30.8 and 37.8. I am aware that sfcheck never reproduces the result. but i am worried that the difference is quite large... indeed i have used TLS NCS and bulk solvent correction... Did i do anything wrong... please help me Thanks for your help regards John

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