October 2010 - phenixbb - phenix-online.org

scattering factors
by Goragot Wisedchaisri 21 Jun '11

21 Jun '11

Hi, I am new to Phenix but I have used Solve/Resolve in the past. I am currently using Phenix 1.6.2 and I have electron diffraction data to ~2A from a 300kV electron microscope that I would like to use Autobuild and phenix.refine to iteratively rebuild and refine my partial structure. I have a file containing electron scattering factors for 300kV EM that has been used successfully for refinement with CNS before for electron diffraction data. How can I tell Phenix to use electron scattering factors during refinement? I think currently Phenix has 4 choices for X-ray and neutron scattering factors but not for electron scattering. Is there a good way to implement electron scattering factors into phenix library? Any suggestions are welcome. George Wisedchaisri

5 12

Geometry problem with sugars refined in phenix
by Tirumala Kumar Chowdary 03 Mar '11

03 Mar '11

Hi, I have refined a structure with NAGs linked to ASNs at 3 places in my structure. I used the right link definitions and the NAG definitions are from Phenix library. Phenix refined all the sugars right and made the right links between the NAGs. However, while submitting, PDB found problem with the geometry of NAGs linked to the ASN at two places. This is the issue -the atoms around C1 atom of the sugar molecule NAG A #810 and NAG A #1670 are on a plane and the C1 atom center is far off to be tetrahedral. Please, verify the chirality of C1 and provide the correct coordinates if necessary.- Any ideas on how to fix the geometry of these sugars will be of great help. Regularization and real space refine in Coot is not working or I don't know how to do it. I am looking for alternative ways to fix this problem. Thank You Tirumal

3 2

Problem with Autobuild
by Claudia Scotti 12 Jan '11

12 Jan '11

Dear List, Sorry fo r the easy question, but I have a problem with Autobuild. I'm trying to rebuild a scFv, composed of two domains linked by a linker. I've managed to find an MR solution with a polyalanine model deprived of the loops, which is my starting model for rebuilding. I've given Autobuild three input files: the mtz, the model coordinates and the sequence of the scFv, asking to model only the beta strands and helices. Problem is that in the final model Autobuild seems to guess incorrectly the density of two beta-strands, inserting the linker there instead of the expected side chains. Any suggestions on how to correct this? Shall I manually rebuild this part to avoid problems? Or is it crucial to prevent errors, for example, that the model and the sequence are numbered so that they are in register? Thanks in advance, Claudia Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673 _________________________________________________________________ Hotmail: Trusted email with powerful SPAM protection. https://signup.live.com/signup.aspx?id=60969

4 5

Problem with Molprobity analysis in phenix 1.6.4
by Mark A Saper 23 Dec '10

23 Dec '10

I am running phenix 1.6.4-486 with GUI and obtained high clash scores in the Molprobity calculations done by phenix.refine. I think I know why after doing some experiments with the current Molprobity running at http://molprobity.biochem.duke.edu/. If I take my well-refined structure as output by phenix (.pdb) and use it directly on the Molprobity web site, the clash score is much lower: 2.75 for 39 total bumps. Many of these involve residues or waters with high B factors. If I first remove all hydrogens from the phenix-refined .pdb file with a text editor, and upload it to the Molprobity web site, then add hydrogens, and then calculate clash score, the score is now 8.69 or 123 bumps for 14150 atoms. This is *identical* to what phenix calculates. Therefore, why doesn't phenix feed the refined coordinates directly into the Molprobity (probe) calculations? Has this change been made in one of the nightly builds? Thanks, Mark Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry University of Michigan Biophysics, 3040 Chemistry Building 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. saper(a)umich.edu phone (734) 764-3353 fax (734) 764-3323 http://www.biochem.med.umich.edu/?q=saper http://www.strucbio.umich.edu/

6 7

Can PHENIX write the peak list to a PDB file?
by Joe Krahn 04 Dec '10

04 Dec '10

PHENIX has an option to find positive and negative peaks, but only lists them in the log file along with the residue they are closest to. Is it possible to write out the actual peak coordinates, such as to a PDB file? Thanks, Joe Krahn

5 7

Riding H
by Jianghai Zhu 01 Nov '10

01 Nov '10

Hi all, If I use the riding H atoms come out of phenix.refine in molprobity, it gives me a decent clash score. But if I strip the H atoms and let molprobity to add H atoms, I get a much worse clash score. I saw the manual of phenix recommends the first method. So what is the cause of the difference here? I know long time ago that phenix and molprobity used different bond length to add the riding H atoms. I don't know what the situation is now. Does phenix.refine refine the riding H atom positions? Thanks. -- Jianghai

4 7

refine : "merged" in .def
by Bryan Lepore 29 Oct '10

29 Oct '10

[ dev-564 on GNU/Linux ] why does phenix - apparently - keep putting the label "merged" in output .def's, when neither the input .def or .mtz has this label - and what generally is the significance? the .mtz has separate Bijvoets, and I's. e.g: input .def: (concise) labels = "I(+),SIGI(+),I(-),SIGI(-)" label = "R-free-flags" output .def: labels = "I(+),SIGI(+),I(-),SIGI(-),merged" label = "R-free-flags" i re-checked the .mtz lacks "merged" (not shown). -bryan

3 3

Autobuild error - bash/dash/sh
by Stephen Graham 29 Oct '10

29 Oct '10

Hi there, Apologies if this has been reported before, but the autobuild job I tried to run last night failed after a short while... The job was started from the command line using: phenix.autobuild data=../mydata_free.mtz seq_file=../protein.fasta map_file=../ccp4i/protein_phaser.1_parrot2.mtz input_map_labels='parrot.F_phi.F parrot.F_phi.phi None' And it got to the point where it was trying to submit the three jobs before it died as follows: Splitting work into 3 jobs and running with 1 processors using sh background=False in /home/stepheng/Projects/my_protein/autobuild/AutoBuild_run_3_/TEMP0 Starting job 1...Log will be: /home/stepheng/Projects/my_protein/autobuild/AutoBuild_run_3_/TEMP0/RUN_FILE_1.log *************ERROR ENDING ******************* ******************************************************************************** Failed to carry out AutoBuild_build_cycle: child process stderr output: command: 'sh /home/stepheng/Projects/my_protein/autobuild/AutoBuild_run_3_/TEMP0/RUN_FILE_1' /home/stepheng/Projects/my_protein/autobuild/AutoBuild_run_3_/TEMP0/RUN_FILE_1.sh: 5: Syntax error: Bad fd number ******************************************************************************** *************ERROR ENDING ******************* I think the problem might be that the RUN_FILE_1.sh script seems to use a bash command/redirection that is not implemented in plain old 'sh' spec, and thus not supported by dash (the lean version of sh that ships with ubuntu)? If I change the #! line of RUN_FILE_1.sh to call /bin/bash rather than /bin/sh the script seems to run to completion... Is there any easy way to change the script template to use /bin/bash or remove the offending command? I'm running phenix dev-550 on an x86 ubuntu 10.10 machine. Thanks, Stephen P.S. The reason I'm trying to run autobuild from the command line rather from the GUI is that the GUI seems to crash every time I give autobuild a sequence file in either the FASTA or PIR format. Is there another format I should be using? -- Dr Stephen Graham 1851 Research Fellow Cambridge Institute for Medical Research Wellcome Trust/MRC Building Addenbrooke's Hospital, Hills Road Cambridge, CB2 0XY, UK Phone: +44 1223 762 638

4 5

Twin Law question
by Young-Jin Cho 28 Oct '10

28 Oct '10

Dear Phenix users, Thanks in advance to answer my question. As my recent data did not give me perfect statistics, I was wondering what the problem was (one of things is ice ring though). When I ran Xtriage with my struggling current data set and looked like I got twinned data. I reran PHASER as was suggested and confirmed that current space group is right. My question is now how I can handle this problem. First, as was recommended I input twin_law, however not all the cases (I have a couple of data sets) were working. One favorite(!) error message was as following: "Map type 'Fc' not supported for twinned structures. Allowed types: Fo-Fc, Fobs-Fobs-Fmodel, 2mFo-DFc, 2mFobs-DFmodel, mFo-DFc, mFobs-DFmodel, gradient, m_gradient." I got this from both GUI and shell environment. . 1. Now from now on, whenever I want to phenix.refine, should I include twin_law command such as 'twin_law=-h,l,k'? 2. In this case, what do I expect to see such as lowering Rfree or else? If it doesn't help lowering Rfree, what to do next? 3. Do I have to report I did with twinlaw option in case of preparing a paper or presentation? I mean I also heard that if one got twinned data, they re-collected data. How much can I convince my refinement is OK with twined data? Additionally, I checked other data, and applied twin_law but the result R/Rfree were exactly same as the one I refined without twin_law option, it this normal case? With many thanks in advance, Young-Jin Cho

3 2

maximum allowable B-factor value
by Christian Roth 27 Oct '10

27 Oct '10

Dear all, I did a refinement run with a built in ligand. Within the ligand the B-factor jumps between two connected atoms from 60 up ~110, which is i think a bit too much. Is there a way to restrain the B-factors that they could not jump so much. I would accept negative difference density for the atom. Maybe the ligand is a bit degraded. Best regards Christian @Pavel Tanks for your suggestions with occupancy refinement and B-factors. -- Christian Roth Institut für Bioanalytische Chemie Biotechnologisch-Biomedizinisches Zentrum Fakultät für Chemie und Mineralogie Universität Leipzig Deutscher Platz 5 04103 Leipzig Telefon: +49 (0)341 97 31316 Fax: +49 (0)341 97 31319

2 3