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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 04 Oct '08

04 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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mmCIF format
by Simon Kolstoe 30 Sep '08

30 Sep '08

Is there a simple way of creating an mmCIF formatted structure factor file for pdb deposition from the outputs of a phenix.refine run? Thanks, Simon

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Deborah Palestrant is out of the office.
by deborah.palestrant＠novartis.com 30 Sep '08

30 Sep '08

I will be out of the office starting 09/30/2008 and will not return until 10/02/2008.

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error
by Jianghai Zhu 25 Sep '08

25 Sep '08

Hi, I got the following error from phenix.refine version 1.3-rc4. iotbx.reflection_file_utils.Sorry_Not_a_suitable_array: Not a suitable array of experimental phases: refineme nt.input.experimental_phases.labels=HLAM,HLBM,HLCM,HLDM What is the problem? -- Jianghai

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Post-doctoral position available with Phaser team
by Randy J. Read 24 Sep '08

24 Sep '08

We are looking to expand the team developing our program Phaser, for use within both the CCP4 and Phenix packages. Our goals include expanding the functionality to new phasing experiments (in addition to the options for molecular replacement and SAD that exist in the current version), and enhancing the automation of Phaser runs. The ideal applicant would be someone with experience solving macromolecular crystal structures and programming in both C++ and Python. However, if you only have experience in one of those areas, but a strong desire to expand your skills, then you might be the right person. If you're interested, please look at the formal advertisement (http://www.admin.cam.ac.uk/offices/hr/jobs/vacancies.cgi?job=4017), and submit an application as described there. I'm also happy to answer any informal enquiries. The position is funded by a grant from the Wellcome Trust, which extends to May 2013. Please note that the closing date for applications is 2 October 2008. Regards, Randy Read

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