November 2008 - phenixbb - phenix-online.org

Difference Fouriers using AutoSol
by Mo Wong 14 Nov '08

14 Nov '08

Hi, I'm a new Phenix user, so please forgive me if I ask an obvious question... I have pretty good SIRAS phases from one derivative, and calculating difference maps for 2 other derivatives show decent peaks above 5 sigma in both these maps. I've tried to follow the MIR example, but no sites are found in the two other derivatives (I thought Phenix calculates difference Fouriers for other derivatives as soon as it finds sites in one of the datasets - but it doesn't appear to in my case). Anyway, the following is my effeort at trying to use the SIRAS phases of the good derivative and the 5sigma peaks in the 2 other derivatives to phase a better map. Please could someone advise me if this script won't do what I'd like it to (i.e., calulate difference Fouriers for derviatives 2 and 3, refine the HA sites that I've included, and calculate phases): cell 100.000 100.000 100.000 90.000 90.000 90.000 # cell params resolution 5.5 # Resolution solvent_fraction 0.47 input_seq_file seq.dat ##### READ IN DERIV 1 SIRAS PHASES ###### input_phase_file solve_4.mtz input_phase_labels FP SIGFP PHIB FOM HLA HLB HLC HLD ############### DERIV 2 ################# input_file_list nat.sca hg.sca # Native and deriv 2 nat_der_list Native Hg # identify files by ha type inano_list noinano inano # say if ano diffs to be used f_prime -2.1 f_double_prime 9.5 n_ha_list 0 6 # number of heavy-atoms sites_file hg-sites.xyz run_list start # read in datafiles for dataset run_list read_another_dataset # about to start a new dataset here ############### DERIV 3 ################# input_file_list nat.sca xe.sca # Native and deriv 3 nat_der_list Native Xe # identify files by ha type inano_list noinano inano # say if ano diffs to be used f_prime -0.1 f_double_prime 3.5 n_ha_list 0 11 # number of heavy-atoms sites_file xe-sites.xyz ########################################## Many thanks!

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General user proposal deadline November 15
by Peter Zwart 14 Nov '08

14 Nov '08

Dear All, The deadline for general user proposals for PX beamtime at the ALS is comming up soon! At the BCSB, we have 5 beamlines for which you can apply for beamtime. At the Berkeley Center for Structural Biology (BCSB) we have recently completed a number of upgrades: Sector 8: Recent improvements include: * A high-accuracy microdiffractometer on BL 8.2.1, allowing for centering and viewing of very small crystals * Robotic automounters which can increase the screening throughput at the beamlines, and allows for the implementation of remote data collection. * A new large format (315mm active surface area) CCD detector on BL 8.2.1, facilitating data collection on large unit cell crystals Sector 5: Beamlines (5.0.1 and 5.0.3) now generate 1.5x10^11 photons per second at 0.97 Angstrom. This wavelength is slightly above the Se K edge making them ideal for performing Se SAD experiments. Beamline 5.0.2 (the tunable beamline) generates a peak flux of 8x10^11 photons per second, and the energy range of 5.0.2 has been extended to 17 keV, enabling the routine use of shorter wavelengths and anomalously scattering elements such as bromine. Remote data collection for general users on sector 5 is currently being tested for a limited number of users. Please contact beamline staff for details. Please visit http://bcsb.lbl.gov/ for more details about the Center and its beamlines. If you'd like to apply for next round of beamtime (Jan-Feb) at the Advanced Light Source, please submit a General User proposal by November 15, 2008. To find out more, click on: http://www-als.lbl.gov/als/quickguide/independinvest.html We invite you to submit a proposal at: http://alsusweb.lbl.gov/4DCGI/WEB_GetForm/PXProposalEntry.shtml If you have any questions or would like to request open beamtime, please e-mail BCSBBeamtime(a)lbl.gov. (Please note that executed user agreements must be received by LBNL prior to beamtime. Proprietary fees, if applicable, must be received by LBNL at least five working days prior to scheduled beamtime.) ----------------------------------------------------------------- P.H. Zwart Beamline Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org CCTBX: http://cctbx.sf.net -----------------------------------------------------------------

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Autosol: cell keyword
by Page, Rebecca 13 Nov '08

13 Nov '08

Hi phenixers: Is there a way to use the Autosol Wizard with unmerged data from Scalepack? I can't get it to recognize the 'cell' keyword. Thanks in advance, Rebecca

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restricted simulated annealing
by Raja Dey 13 Nov '08

13 Nov '08

Dear Friends, How can I restrict simulated annealing in phenix on part of my molecule, say 2 chains out of 3 or part of a particular chain? Thanking you in advance for your reply... Raja

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Failed to carry out AutoBuild
by Joao Renato Carvalho Muniz 12 Nov '08

12 Nov '08

Dear Phenix community, I started an AutoBuild run using the Phenix GUI (ver 1.3 final) on linux. However, I noticed 2 weird things: 1st, Phenix seems that can not handle with alignment between the residues from pdb and sequence.seq, flagging the "Rebuild in place not recommended as identity * fraction_aligned is 0.0%" message but still trying to build the structure with the option "include_input_model=False" I guess(?)... and 2nd, after quite a while I obtained the following error message: ******************************************************************************** Failed to carry out AutoBuild_build_cycle: child process stderr output: command: 'csh /someplace/somedir/somedir2/AutoBuild_run_2_/TEMP0/RUN_FILE_1' /someplace/somedir/somedir2/AutoBuild_run_2_/TEMP0/RUN_FILE_1.log: File exists. ******************************************************************************** The alignment between MR.1.pdb and sequence.seq should be something like 80%+! Also tried to run using the followed command line: phenix.autobuild data=MR.1.mtz model=MR.1.pdb include_input_model=True n_cycle_rebuild_max=5 seq_file=sequence.seq Same problem as above. Could anyone please tell me what to do to prevent this error and get phenix get its job finished? Many thanks in advance, Joao.

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refine occupancies for MET/MSE double conformations
by Anastassis Perrakis 12 Nov '08

12 Nov '08

Hi there - I was pleased to read in the manual: if no selections are provided (refine.occupancies.individual=None and refine.occupancies.group=None) then phenix.refine by default will refine individual occupancies for atoms that have partial occupancy values in input PDB file (except zeros) and it will perform group constrained occupancy refinement for all atoms in alternative conformations. Occupancies of all other atoms will be fixed. If selections are provided (refine.occupancies.individual=atom_selection or refine.occupancies.group=atom_selection) then the selected atoms will be added to the list of atoms defined above (atoms with partial occupancies or those in alternative conformations). See this document for examples of atom_selection syntax. However, I want to refine my MET residues in double conformations, one as MET (AMET) and the other one as MSE (BMSE) with each 0.5 occupancy to start with. When I try that I get: == ----------Initial model statistics (before refinement)---------- ... |-Occupancies statistics------------------------------------------------------| Sorry: There are atoms with negative occupancies. Check input PDB file. === The PDB file has 0.5 and 1.0 occupancies only. I am also using: == refinement.refine.strategy=tls+individual_sites+individual_adp +group_anomalous refinement.refine.adp.tls="chain A" refinement.refine.adp.tls="chain B" refinement.main.number_of_macro_cycles=4 refinement.simulated_annealing.start_temperature=5000 refinement.refine.adp.individual.anisotropic =" chain C" refinement .input .xray_data .labels=I_Mystery(+),SIGI_Mystery(+),I_Mystery(-),SIGI_Mystery(-),merged refinement.refine.anomalous_scatterers { group { selection = "name ZN " f_prime = -0.3 f_double_prime = 2.5 refine = *f_prime *f_double_prime } group { selection = "name SE " f_prime = -5.2 f_double_prime = 3.8 refine = *f_prime *f_double_prime } } == Any hints on how to proceed ? Should I define groups for the occupancy refinement explicitely and not rely to automatic assignment? And if so how? How do people treat this partial Se-Met issue ? We solved the structure with SeSAD ... if I out MSE I get pretty large negative density peaks on the Se ... if I put MET I get positive peaks ;-) And there are good reasons to believe in partial Se- substitution in this case. Thanks in advance, Tassos

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cis peptide
by Jianghai Zhu 09 Nov '08

09 Nov '08

Hi, Does phenix.refine restrain cis peptide? How do I know if the refined pdb file contain any cis peptide? Thanks. -- Jianghai

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User proposal submission for Collaborative Crystallography at BCSB
by Banumathi Sankaran 05 Nov '08

05 Nov '08

Dear Users, Through the Collaborative Crystallography Pilot Program (CC) at the Advanced Light Source, scientists can send protein crystals to Berkeley Center for Structural biology (BCSB) staff researchers for data collection and analysis. The CC Pilot Program can provide a number of benefits to researchers: * Obtain high quality data and analysis through collaborating with expert beamline researchers; * Rapid turn around on projects; * Reduced travel costs. Thumbnail Description: ====================== The Collaborative Crystallography program will be piloted on beamlines 5.0.1 and 5.0.2 for one year; if successful it will be implemented on a permanent basis. CC proposals will go through the regular ALS General User proposal review process for beamtime allocation. Proposals will be reviewed and ranked by the Proposal Study Panel, and beamtime will be allocated accordingly. BCSB staff will schedule the projects to fit into the available resources. Only non-proprietary projects will be accepted. As a condition of participation, BCSB staff researchers who participate in data collection and/or analysis must be appropriately acknowledged - typically being included as authors on publications and in PDB depositions. Please consult the website for additional information at: http://bcsb.als.lbl.gov/wiki/index.php/Collaborative_Crystallography ============= How To Apply: To submit a proposal, go to: http://www-als.lbl.gov/als/quickguide/independinvest.html Click on "protein crystallography" to begin proposal. For question 3 select "Collaborative PX 501/502." For question 9, please describe a specific research project with a clear end point. In order to request CC time for January/February 2009 allocation period, proposals must be submitted by November 15, 2008. The deadline for CC proposals for the time period March/April 2009 will be January 15, 2009. Regards, Banumathi Sankaran

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weight optimization
by Raja Dey 03 Nov '08

03 Nov '08

Hi, I was trying to optimize weights as follows, but it came out with the error given below. Can anyone tell me what's wrong? I used phenix.refine ../p65_nat.mtz ../p65_136.1.pdb optimize_wxc=true optimize_wxu=true output.prefix=136.1 ----------xray term weight optimization (wxc)---------- 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 449, in refinement_machine log = log) File "/usr/local/phenix-1.3b-rc6/phenix/phenix/refinement/weight_xray_chem.py", line 256, in __init__ self.wxc_optimization() File "/usr/local/phenix-1.3b-rc6/phenix/phenix/refinement/weight_xray_chem.py", line 511, in wxc_optimization wxc = self.holder.wxc AttributeError: weight instance has no attribute 'holder' Thanks... Raja

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