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phenix.refine with simulated annealing
by zhangh1＠umbc.edu 17 Dec '10

17 Dec '10

Hi there, I was trying to perform a SA refinement for PDB# 2VZ8 using the following phenix script: random_seed=2679941 phenix.refine 2VZ8.pdb 2vz8.mtz simulated_annealing=true main.random_seed=${random_seed} output.prefix=${random_seed} >${PDB}-phx-sa.log where 2VZ8.pdb was downloaded from rcsb, and 2vz8.mtz was converted from the cif file by ccp4-cif2mtz. But it ended up with: ******************* =============================== refinement start ============================== Traceback (most recent call last): File "/users/hz9/TOOLS/PHENIX/phenix-1.6.4-486/phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/users/hz9/TOOLS/PHENIX/phenix-1.6.4-486/phenix/phenix/refinement/command_line.py", line 89, in run call_back_handler=call_back_handler) File "/users/hz9/TOOLS/PHENIX/phenix-1.6.4-486/phenix/phenix/refinement/driver.py", line 1182, in run call_back_handler = call_back_handler) File "/users/hz9/TOOLS/PHENIX/phenix-1.6.4-486/phenix/phenix/refinement/strategies.py", line 229, in refinement_machine xray_structure = model.xray_structure,) File "/users/hz9/TOOLS/PHENIX/phenix-1.6.4-486/phenix/phenix/refinement/strategies.py", line 133, in extract_from_pdb_header xray_structure = xray_structure) File "/users/hz9/TOOLS/PHENIX/phenix-1.6.4-486/cctbx_project/mmtbx/f_model.py", line 302, in __init__ twin_law_xyz = sgtbx.rt_mx(symbol=self.twin_law, r_den=12, t_den=144) RuntimeError: cctbx Error: Parse error: unexpected character: NULL ************************ I tried another smaller system and it works well. Not sure what happens, and thanks for any suggestion! Hailiang

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phenix.map_to_object for HA sites
by Michael Hothorn 16 Dec '10

16 Dec '10

Hi, I have a .pdb with heavy atoms that are dispersed all over the unit cell. I would like to move all of them (about 40) as close as possible to my refined structure. Could phenix.map_to_object do that for all heavy atoms at once, or would I need to do this in an atom by atom manner? Thanks Michael

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Map filenames are not honored [dev-610]
by Schubert, Carsten [PRDUS] 15 Dec '10

15 Dec '10

Hi, I just noticed that v610 does not honor map file names defined in the .def file. Instead it constructs its own file name from the prefix, serial and map_type settings. That works fine for run-of-the-mill fofc and 2fofc maps, but causes a clash in map filenames when one also computes kicked maps or other maps with non-default settings beside the default fofc and 2fofc maps. Cheers, Carsten

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phenix.find_tls_groups: a new tool for automated partitioning a model into TLS groups
by Joseph Noel 15 Dec '10

15 Dec '10

Pavel or Nat, Can you point me to the button in the GUI to use to run this? I am pretty much a GUI guy although not adverse to running things through the command like like the old days (yes, I was a command like geek when I started at Yale in 1990 and until I stopped (temporarily) doing anything worthwhile around 2001. Now that I am back in the lab doing work (but probably still not worthwhile) I have become addicted to GUIs and buttons. Blame my daughters! LOL Joe ___________________________________________________________ Joseph P. Noel, Ph.D. Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________

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phenix.find_tls_groups: a new tool for automated partitioning a model into TLS groups
by Pavel Afonine 14 Dec '10

14 Dec '10

PHENIX users: starting dev-610 (development version of PHENIX) there is a new tool available for completely automated partitioning a model into TLS groups: http://www.phenix-online.org/download/nightly_builds.cgi To run: phenix.find_tls_groups model.pdb or if you have a multiple CPU machine: phenix.find_tls_groups model.pdb nproc=N where N is the number of CPUs available (thanks Nat for parallelization!). There is no parameters that a user is supposed to tweak (except defining the number of CPUs, if desired). The result of running the above command are atom selections that define TLS groups. These atom selections are ready to use in phenix.refine. This is available from PHENIX GUI too, where automatically defined TLS groups can be readily visualized and checked on the graphics (thanks Nat!). The algorithm is fast. For example, for a GroEL structure (3668 residues, 26957 atoms, 7 chains) it takes only 135 seconds using 1 CPU, and 44 seconds using 10 CPUs. Analogous job takes 3630 seconds using TLSMD server. For a lysozime structure it takes 9.5 seconds with one CPU, and 2.5 seconds using 10 CPUs. The timing results may vary depending on the performance of your computer. There is ongoing work that will slightly improve phenix.find_tls_groups within the next few weeks / a month; however the current version is functional and can be tried now. An example of such improvements are analyzing (scoring) user-defined TLS groups (for example, TLS groups from PDB file header), automated combining cross-chain TLS groups (non-contiguous segments) that will be obtained through connectivity analysis, better handling non-protein chains, and more. Integration with phenix.refine is also planned. Any feedback is very much appreciated! Thanks, Pavel.

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request for openmp compile comments
by Bryan Lepore 14 Dec '10

14 Dec '10

if anyone has specifically gotten automr to run on an openmp-compiled phenix installation with something like the specs i give below, i would appreciate any details you could offer. (in my hands, automr always crashes, refine works.) -Bryan any recent nightly release with --openmp gcc/g++ 4.4.5 (or thereabouts) 2.6.35-23-generic SMP i686 (or thereabouts) amd, intel, (or thereabouts) Ubuntu (recent - but not Fedora)

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phenix.refine use_experimental_phases vs target=mlhl
by Francis E Reyes 13 Dec '10

13 Dec '10

Are these settings redundant? i.e. what happens when you have target=mlhl, use_experimental_phases=False? Thanks! F --------------------------------------------- Francis E. 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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AutoSol/PhaserSAD with more than one anomalously-scattering atom produces error...
by Francis E Reyes 13 Dec '10

13 Dec '10

Hi all I'm getting an error... "'InputEP_SAD' object has no attribute 'addSCAT_TYPE'" from autosol. Facts: - phenix-1.6-289 - SAD experiment with two types of anomalous scatterers in the xtal, data is the peak wavelength of one of the anomalous scatterers. - sites are input from a previous phaser run (ha_x.pdb_formatted.pdb) - the atom positions are likely correct, but the atom types are all the same atom (I'd like phenix/phaser to go through the list and reannotate/refine based on the proper heavy atom identities) - additional atom types/f'/f'' defined in autosol.eff, Using the documentation example "SAD with more than one anomalously-scattering atom" (http://www.phenix-online.org/documentation/autosol.htm). Thanks! F --------------------------------------------- Francis E. 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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changing test set flag
by Michael Hothorn 11 Dec '10

11 Dec '10

Dear all, I used phenix.refine to generate the test set flag for my dataset which it did with a value of 1. I now use a program that expects the test set flag in the mtz file to be 0. Is there a simple way to change the flag from 1 to 0 keeping the flagged reflections identical? Thanks! Michael

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Help needs: SAD-phasing for Cobalt ion
by YoungJin 10 Dec '10

10 Dec '10

Dear helpers in phenix, I have anomalous data (Co; wavelength: 1.609A) that I want to use its Phase information from SAD-phasing method (autosol). As I have a native data (from nomal wavelength ~1A) with higher resolution (~2A) than SAD data (~2.5A), I wanted to apply phase information to this native data for further refinement: My goals were 1. I want to confirm where is my heavy metal is; 2. I want to refine further using native data as has higher resolution. At first, when I did autosol, it didn't give me perfect result. So far what I tired is as following: 'SAD peak' from imosflm generated mtz file (scaled), 'Phases' from first refmac generated mtz file from the native data, and 'MIR native' from the native data mtz file (imosflm and scaled). FOM: 0.186; overall score was 10.75 +/- 12.33. FYI. I input 2 sites and result suggested 3 sites. Each molecule has one binding site of metal ion. I was using old Mac version:1.6.4-486 Anyway, I simply passed the result over Autobuild. It ran and gave me better statistics as following: R/Rfree=0.2734/0.3312; CC 0.76. However (I have two molecules/ASU) one of models was not great. But this time, anomalous density map well phased(?!) to 2Fo-Fc map and I could see - it was before only one heavy metal I clearly could see- 2 heavy metal signal from 2 molecules and those positions are well matched with native density maps. So I continued phenix.refine using Autobuild made 'expt_fobs_phase_freeR_flags_1.mtz'. The question is the statistics from anomalous data itself (it has slight dispcrepancy between anomalous map and 2Fo-Fc/Fo-Fc map due to phase problem) or even those from native data is better than my current model which came from native data set (SAD-phased as described above) with higher resolution. I think one of main reasons is one of molecule has a lid that does not perfectly fit into current density map. However, in terms of heavy metal position and the active site is better from current map (Autobuild generated model). FYI: current model has R/Rfree=0.21/0.27(best was 0.21/0.26); 0.19/0.24 (for native data only used model) .... Am I too concerning for statistics or is there something I am missing? Now my questions are as following plus any suggestions are welcome: 1. For SAD-phasing, could you tell me which is best way to do so with my case (one data from the edge of heavy metal (lower resolution) and native data (higher resolution) or where is the point I can convince. Also I tried to use DANO/SIGDANO column (from hkl2000 and ccp4) but seems like it (Autosol) doesn't take them into account. Could you tell me how can I improve phase by using anomalous data? 2. In case of Co, does anyone have experience about coordination numbers? I thought it should have 6 (or 4) coordination numbers. The question what I have now is about the numbers and their lengths ... I though it should be within 2A, but not true for my current models (And somehow distorted octahedron or else with 2.07-3.28A). I also searched PDB files, and found that many deviations from 1.98 to 2.82A (depending on corresponding atoms and resolutions: 3KOI, 3KON, 2DD5, and 2XJM). I would appreciate if you can give me any tips regarding this issue. Many thanks in advance, Young-Jin

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