- phenixbb - phenix-online.org

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 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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chainid and segid?
by deborah.palestrant＠novartis.com 23 Sep '08

23 Sep '08

Hi Phenix Community- A very basic question.. Is there an option to have a "segid" automatically generated? (For example, in CNS generate.inp, it was possible to "convert chainid to segid if chainid is non-blank"). Unless I strip out the segid completely, I am running into problems when I add residues using Coot (which adds chainid, but not segid) and then follow up with refinement in Phenix. Thanks for your input, Deb Deborah Palestrant, PhD Novartis Institutes for BioMedical Research CPC, Protein Structure Unit USCA, 600-6C343 Novartis Institutes for BioMedical Research, Inc. 250 Massachusetts Avenue Cambridge, MA 02139 USA Phone: +1 617 8713565 Email : deborah.palestrant(a)novartis.com _________________________ CONFIDENTIALITY NOTICE The information contained in this e-mail message is intended only for the exclusive use of the individual or entity named above and may contain information that is privileged, confidential or exempt from disclosure under applicable law. If the reader of this message is not the intended recipient, or the employee or agent responsible for delivery of the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately by e-mail and delete the material from any computer. Thank you.

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Simon Holton ist außer Haus.
by simon.holton＠bayerhealthcare.com 23 Sep '08

23 Sep '08

Ich werde ab 23.09.2008 nicht im Büro sein. Ich kehre zurück am 24.09.2008. Ich werde Ihre Nachricht nach meiner Rückkehr beantworten.

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memory error
by Anastasia A Aksyuk 22 Sep '08

22 Sep '08

Hello everyone! I have the following error when using phenix-1.3-final: /========================== Target weights: x-ray data ========================= Traceback (most recent call last): File "/usr/local/rossmann/phenix/phenix-1.3-final/phenix/phenix/command_line/refine.py", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/rossmann.master/phenix/phenix-1.3-final/phenix/phenix/refinement/command_line.py", line 89, in run File "/usr/local/rossmann.master/phenix/phenix-1.3-final/phenix/phenix/refinement/driver.py", line 1081, in run File "/usr/local/rossmann.master/phenix/phenix-1.3-final/phenix/phenix/refinement/strategies.py", line 472, in refinement_machine File "/usr/local/rossmann.master/phenix/phenix-1.3-final/phenix/phenix/refinement/weight_xray_chem.py", line 264, in __init__ File "/usr/local/rossmann.master/phenix/phenix-1.3-final/phenix/phenix/refinement/weight_xray_chem.py", line 307, in xyz_weights File "/usr/local/rossmann.master/phenix/phenix-1.3-final/phenix/phenix/refinement/weight_xray_chem.py", line 196, in __init__ File "/usr/local/rossmann/phenix/phenix-1.3-final/mmtbx/mmtbx/__init__.py", line 72, in update_xray_structure force_update_f_mask = force_update_f_mask) File "/usr/local/rossmann/phenix/phenix-1.3-final/mmtbx/mmtbx/f_model.py", line 675, in update_xray_structure force_update = force_update_f_mask) File "/usr/local/rossmann/phenix/phenix-1.3-final/mmtbx/mmtbx/masks.py", line 207, in f_mask return self.compute_f_mask() File "/usr/local/rossmann/phenix/phenix-1.3-final/mmtbx/mmtbx/masks.py", line 222, in compute_f_mask miller_set = self.miller_array) File "/usr/local/rossmann/phenix/phenix-1.3-final/mmtbx/mmtbx/masks.py", line 138, in structure_factors flex.grid(fft_manager.m_real()).set_focus(fft_manager.n_real())) MemoryError /I am running with defaults, i.e. the following command: phenix.refine se.water2.noano_001-2acetate-noH-coot-0.pdb cr2remote.cr3.1.8-2_scaleit1.mtz ray_data.r_free_flags.test_flag_value=1 output.prefix=se.noano2.acetate refinement.input.xray_data.labels="F_peak(+),SIGF_peak(+),F_peak(-),SIGF_peak(-),merged" I would greatly appreciate your help to resolve this issue and I can provide any additional information needed. Thank you, Anastasia

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phenix 1.3-rc4 vs. phenix 1.3-final
by Jianghai Zhu 19 Sep '08

19 Sep '08

Hi, I have done a couple of refinements using either phenix.refine 1.3-rc4 or phenix.refine 1.3-final. And phenix.refine 1.3-rc4 always gave me a lower Rfree, about 1% lower than phenix.refine 1.3-final, which actually is pretty big. What has changed between this two versions? -- Jianghai

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Deborah Palestrant is out of the office.
by deborah.palestrant＠novartis.com 16 Sep '08

16 Sep '08

I will be out of the office starting 09/16/2008 and will not return until 09/18/2008. I will be checking email and will respond to your message at my earliest convenience.

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Anomalous difference map file
by Andrzej Lyskowski 16 Sep '08

16 Sep '08

Hi, Is it possible to write an anomalous difference map file and not just the coefficients in the mtz file? Would it be possible to get a short instructions for the operations... Regards, Andrzej Lyskwoski -- Andrzej LYSKOWSKI, Ph.D. (andrzej[.]lyskowski[(a)]helsinki[.]fi) Institute of Biotechnology - Structural Biology & Biophysics P. O. Box 65 - Viikinkaari 1 - Floor/Room: 4/4316 Mail: FIN-00014 University of HELSINKI, FINLAND Delivery: FIN-00710 University of HELSINKI, FINLAND TEL.: 358 9 191 58921 FAX : 358 9 191 59940

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phenix autobuild question
by Alex Berndt 16 Sep '08

16 Sep '08

Dear phenix community, I started an AutoBuild run using the phenix GUI (ver 1.3 rc4) on a linux cluster. It worked okay and all the refinement looked pretty decent. However, after quite a while I obtained the following error message (see below). Would anyone please tell me what to do to prevent this error and get phenix get its job finished? Also, I don't understand why phenix AutoBuild creates 5 (or whatever number) AutoBuild_run_x in the AutoBuild-run_1/TEMP0 directory and not two dirs up in the tree. In other words in my /someplace/home/someuser/ work/someproject/phenix2/AutoBuild_run_1_/TEMP0 directory are more AutoBuild_run_x_ directories (with x=1 to 5). It is a bit confusing to me. A final question: I realised that the phenix.refine drastically increases the number of outliers. I know that thare is a weighting term someplace ... but what was it again? Many thanks in advance, Alex warnings Failed to carry out AutoBuild_multiple_models: Sorry, subprocess failed...message is: ******************************************************************************** phenix.autobuild \ write_run_directory_to_file=/someplace/home/someuser/work/someproject/ phenix2/AutoBuild_run_1_/TEMP0/INFO_FILE_1 Reading effective parameters from /someplace/home/someuser/work/ someproject/phenix2/AutoBuild_run_1_/TEMP0/PARAMS_1.eff Sending output to AutoBuild_run_1_/AutoBuild_run_1_1.log ******************************************************************************** Failed to carry out AutoBuild_build_cycle: failure ******************************************************************************** ******************************************************************************** work_pdb_file "AutoBuild_run_1_/edited_pdb.pdb" working_directory "/someplace/home/someuser/work/someproject/phenix2" worst_percent_res_rebuild 2.0 --------------------------------------------------- Alex Berndt MRC-Laboratory of Molecular Biology Hills Road Cambridge, CB2 0QH U.K. phone: +44 (0)1223 402113 ---------------------------------------------------

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BEAM TIME AVAILABLE FOR MACROMOLECULAR CRYSTALOGRAPHY
by Cyndi Salbego 15 Sep '08

15 Sep '08

BEAM TIME AVAILABLE FOR MACROMOLECULAR CRYSTALLOGRAPHY AT THE TWO ID BEAMLINES OF NE-CAT AT APS. Beamline 24ID-C: Variable energy between 6-18keV, ADSC Q315 Detector, MAD Capable. Beamline 24ID-E: Equipped with MD2 microdiffractometer, delivering beam as small as 5 microns. Single energy (12662eV), ADSC Q315 Detector. Contact csalbego(a)anl.gov for further details. See http://necat.chem.cornell.edu for information on our beamlines and a calendar of available days.

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link in a double conformation residue
by mvliberato＠ursa.ifsc.usp.br 12 Sep '08

12 Sep '08

Dear all, I'm refining a protein structure with a cysteine covalently bonded with a fatty acid. However, this cysteine has a double conformation. I try to make a link with "cif_link.params", but I don't know how to describe the double conformation. How can I make this link between the fatty acid oxigen and the sulfur of the cysteine in one of the conformations? Any help would be much appreciated! Thanks Marcelo Marcelo Vizoná Liberato, Ms Physics Institute of São Carlos - USP São Carlos, Brazil ---------------------------------------------------------------- WEBMAIL - IFSC - Instituto de FÃsica de SÃ£o Carlos

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Odd twinning issue (or maybe all twinning issues are odd by default)
by Francis E Reyes 11 Sep '08

11 Sep '08

All I had a structure that seemed perfectly twinned in P41 21 2, completely built to the observable density (no peaks in 2Fo-Fc map over 2sigma) and refined to 33/35 (R/Rfree). I indexed, scaled, and merged the original unmerged data to P41, molecular replaced using the above model. Three rounds of rigid body refinement of the MR solution with group adp's dropped R/Rfree to 28/30 (while generating new free R flags based on the P41 data). The resolution was to 2.5 so I skipped the NCS. Now I try to do a second round of refinement with this time individual_sites and individual_adps with no change to the input model. The final R/Rfree's are now in the 50's? Am I missing something (fundamental) ? 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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difficulties with autoMR
by Feldman III, George Franklin 10 Sep '08

10 Sep '08

I am trying to run phenix.automr on what I believe is perhaps a perfectly twinned data set, at 3A resolution. It is in space group 146 and according to the matthews has 3 molecules in the asu. This is a mutant of an orriginally published structure in which only one residue has been mutated (but crystallizes in a different space group). When I give the autoMR the following input: phenix.automr coords="MR.1.pdb" data=dtscale.ref resolution=0 component_type=protein identity="95" mass=13900 build=False copies=3 seq.dat I get an LLG of 37 and the run goes quite quickly. The speed of the run itself leads me to believe that I have a correct solution regardless of the slightly low LLG, but when I open the .pdb output file there is only one molecule in the asu. Am I doing something incorrectly? Why is there only one molecule instead of 3 in the asu, and how can I go about getting the other two to appear? I did let the program go ahead run autobuild, this resulted in a structure with an r_work:.5448 and r_free:.6005. I am relatively new to crystallography, but these values seem rather high to be a good starting point for refinement. I would appreciate any advice that might help me move on with my structure. Attached is the log file from phenix.xtriage in case it may be of any help. Thank you, in advance, for all of your help and advice. Best Regards, George F. Feldman

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Re: [phenixbb] cci_apps on irix
by Ralf W. Grosse-Kunstleve 07 Sep '08

07 Sep '08

On 22 Aug 2008 o.h.weiergraeber(a)fz-juelich.de wrote: > I am just compiling the latest cci_apps package for the IRIX > platform. I know this is unsupported, but since the package is very > self-contained, I would not expect major problems with the command-line > packages (who needs a gui, anyway ;)) > I'm just running into two issues with the boost package which are > obviously a matter of syntax: Our IRIX machine is up again, and - to my surprise - the current CCI Apps compiled without errors. The IRIX binary bundle is available again at the usual place: http://www.phenix-online.org/download/cci_apps/ Ralf

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selection usage
by Mark Collins 05 Sep '08

05 Sep '08

Hi All, The current phenix 1.3 release automatically selects alternate conformations when refine *occupancy is selected. How do I select a loop region (in low density) to refine the loop occupancy without messing up the auto selection? Thanks in advance, Mark

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Deborah Palestrant is out of the office.
by deborah.palestrant＠novartis.com 04 Sep '08

04 Sep '08

I will be out of the office starting 09/04/2008 and will not return until 09/08/2008.

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