December 2010 - phenixbb - phenix-online.org

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

15 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 14 Dec '10

14 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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phenix.phaser ep_sad mode
by Bryan Lepore 09 Dec '10

09 Dec '10

dev-601 i found an ep_sad script on the phaser wiki^[1] that works ok^[2] for old versions. for the dev-601 phaser, i think it comes down to me not understanding this line : LLGComplete CRYStal insulin COMPLETE ON SCATtering ELEMent S i tried jumbling the commands/arguments around^[3], leading to syntax errors for each attempt (output excerpt below). if this "should work", i'll gladly return to the manual - or is there something unusual between versions, am i missing something, etc.... -Bryan [1]http://www.phaser.cimr.cam.ac.uk/index.php/Experimental_Phasing#Combined_MR_and_SAD_Phasing [2] seem not to write ATOM records in the .pdb when sites are in fact found. [3]http://www.phaser.cimr.cam.ac.uk/index.php/Keywords#LLGCOMPLETE output excerpt : MODE EP_SAD TITLe sad phasing insulin with best AutoMR solution HKLIn truncate.mtz CRYStal insulin DATAset sad LABIn F+=F(+) SIG+=SIGF(+) F-=F(-) SIG-=SIGF(-) ! LLGComplete CRYStal insulin COMPLETE ON SCATtering ELEMent S LLGComplete CRYStal  <B><FONT COLOR="#FF8800"> $TEXT:Warning: $$ Baubles Markup $$ ------------------------------------------------------------------------------------- SYNTAX ERROR: Use (optionally) COMPLETE TYPE SCATTERER ELEMENT CLUSTER SIGMA NCYC CLASH ANOM REAL MAPS or METHOD -------------------------------------------------------------------------------------

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phaser ep_sad zscore
by Bryan Lepore 09 Dec '10

09 Dec '10

dev-601 in phaser ep_sad mode, i tried ZSCORE SOLVED 0 to get more sites output, and i can see a peak of about Z=4 in the stdout, but no peaks are written to the .pdb am i applying ZSCORE wrong here? -Bryan

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reflection outliers detection in phenix.refine
by guanrj＠foxmail.com 08 Dec '10

08 Dec '10

Hi All I have a question regarding reflection outliers detection in phenix.refine: in my input reflection file, there are 24432 reflections, but only 22769 of them were used in refinement. I checked the log file and saw 1663 outliers. (below if from the log) basic_wilson_outliers = 14 extreme_wilson_outliers = 18 beamstop_shadow_outliers = 0 model_based_outliers = 1657 total = 1663 What is the "model_based_outliers"? What causes so many reflections rejected and not used in the refinement? Thanks Rongjin

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Multistart simulated annealing refinement
by Joseph Noel 08 Dec '10

08 Dec '10

Hi All, I'm sure this has already been addressed but is there a way through the PHENIX GUI to carry out multistart simulated annealing refinement either with different starting seeds (velocities) or temperatures automatically or does one have to start a fresh run each time? Thanks! Joe P.S. Similar procedure as described in the PNAS paper: "Multistart simulated annealing refinement of the crystal structure of the 70S ribosome" ___________________________________________________________ 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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