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B(sol) too high
by Matthew Merski 17 Dec '09

17 Dec '09

I am in the process of solving a series of protein/ligand complex structures and ran the Polygon tool on the series. I noticed that, in general, even when all the other statistics were good, the B(sol) term was a bit too high according to Polygon. (The structures with poorer statistics also had high B(sol) values as well.) Since this is a series of multiple structures of the same protein, should this be a concern for me? And if so, what are typical causes of a high B(sol) value? Matt Merski Shoichet Group UCSF

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LigPlot
by Zhou, Tongqing (NIH/VRC) [E] 16 Dec '09

16 Dec '09

Dear Phenix Users, I am trying to get Roman Laskowski's Ligplot, but could not find it on the ftp site he provided in the website below: http://www.biochem.ucl.ac.uk/bsm/ligplot/ligplot.html Does anyone have any information on how and where to get it? Thanks, Tongqing Tongqing Zhou, Ph.D. Staff Scientist Structural Biology Section Vaccine Research Center, NIAID/NIH Building 40, Room 4607B 40 Convent Drive, MSC3027 Bethesda, MD 20892 (301) 594-8710 (Tel) (301) 793-0794 (Cell) (301) 480-2658 (Fax) ****************************************************************** The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. ******************************************************************

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tls matrices etc.
by Bryan W. Lepore 16 Dec '09

16 Dec '09

does phenix compute the center of reaction pretty much like refmac does? i figure the matrices/center of reaction between refmac and phenix are identical - is that true? -bryan

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Rfree refmac5 issue
by anon 16 Dec '09

16 Dec '09

Hi, has anyone had any experience using phenix with refmac5? I seem to be having issues with the Rfree flag. Phenix sets aside 8.1% of the reflection for Rfree. However when i use refmac for refinement, it reports that its using 91.4% of the reflections for Rfree........? thanks

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polygon output (dev-256)
by Bryan W. Lepore 16 Dec '09

16 Dec '09

[ phenix dev 256 ] where - or should we - be looking for the polygon output .png (the one with the polygon)? its obvious in 1.5-2, so i think its dev-256 only... -bryan

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.cif use/restraints
by Bryan W. Lepore 16 Dec '09

16 Dec '09

a ligand is distorting - as if it is ignoring the .cif and i already have the angles tighted up in the .def. what else should i check? what i did : generated some elbow output. the .cif was provided to phenix.refine on cmd line. the .pdb had the H's and CONNECT's removed, but the .cif retains them. the .pdb was incorporated into a single .pdb input file. -bryan

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Firefox problem
by Phil Evans 15 Dec '09

15 Dec '09

Dear Gurus If I click the Help button on the Phenix GUI I get the following fail messages. What am I doing wrong? I'm running 64-bit Phenix on a 64-bit machine, but our Firefox (as I understand it) is 32-bit, since there is no 64-bit Java Best wishes Phil hex_pre> phenix Using browser /usr/bin/firefox (Gecko:3603): Gtk-WARNING **: /lmb/home/public/xtal/Phenix/Phenix64/phenix-dev-2 49/build/intel-linux-2.6-x86_64/base/lib/gtk-2.0/2.10.0/engines/libclearlooks.so : wrong ELF class: ELFCLASS64 (Gecko:3603): Pango-WARNING **: /lmb/home/public/xtal/Phenix/Phenix64/phenix-dev -249/build/intel-linux-2.6-x86_64/base/lib/pango/1.6.0/modules/pango-basic-fc.so : wrong ELF class: ELFCLASS64 Failed to load Pango module for id: 'BasicScriptEngineFc' (Gecko:3603): Pango-WARNING **: /lmb/home/public/xtal/Phenix/Phenix64/phenix-dev -249/build/intel-linux-2.6-x86_64/base/lib/pango/1.6.0/modules/pango-basic-fc.so : wrong ELF class: ELFCLASS64 Failed to load Pango module for id: 'BasicScriptEngineFc' (Gecko:3603): Pango-WARNING **: /lmb/home/public/xtal/Phenix/Phenix64/phenix-dev -249/build/intel-linux-2.6-x86_64/base/lib/pango/1.6.0/modules/pango-basic-fc.so : wrong ELF class: ELFCLASS64 Failed to load Pango module for id: 'BasicScriptEngineFc' (Gecko:3603): Pango-WARNING **: /lmb/home/public/xtal/Phenix/Phenix64/phenix-dev -249/build/intel-linux-2.6-x86_64/base/lib/pango/1.6.0/modules/pango-basic-fc.so : wrong ELF class: ELFCLASS64 .. snip ... Failed to load Pango module for id: 'BasicScriptEngineFc' (Gecko:3603): Pango-WARNING **: /lmb/home/public/xtal/Phenix/Phenix64/phenix-dev -249/build/intel-linux-2.6-x86_64/base/lib/pango/1.6.0/modules/pango-basic-fc.so : wrong ELF class: ELFCLASS64 Failed to load Pango module for id: 'BasicScriptEngineFc' (Gecko:3603): GLib-GObject-CRITICAL **: g_object_get_qdata: assertion `G_IS_OBJE CT (object)' failed (Gecko:3603): Pango-CRITICAL **: pango_font_describe: assertion `font != NULL' f ailed /usr/lib/firefox-3.0.15/run-mozilla.sh: line 131: 3603 Segmentation fault "$prog" ${1+"$@"}

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phenix and refmac5
by anon 15 Dec '09

15 Dec '09

Hi, recently i used phenix (AutoSol and AutoBuild) on a SAD dataset containing Iodine. I was wanting to do my refinement using Refmac instead of phenix.refine. I was wondering where would i be able to locate the correct .mtz file to input into Refmac5 for rounds of refinement? I was under the impression the .mtz file used for refinement was the one produced after scaling, but im not sure where phenix puts this. Also I was wondering if anyone had any issues with phenix.xtriage carrying out its Matthews coefficient calculation? When using Phenix, it gave me a solution with 3 mols/AU, despite there being 4 mols/AU according to the Matthews coeffiecient calculation in CCP4. Looking back at the xtriage log in autosol it has n_residues= 200 (despite me not specifying anywhere the number of residues, my protein has 147 residues). Realising this I re-ran Autosol, inputting my .mtz file along with my sequence this time, and specifying the number of NCS copies as 4. Looking at the phenix.xtriage log this time results in it recognising the correct number of residues, however the matthews coefficient calculation is still incorrect, claiming 1 mol/Au. Any ideas what may be the problem? ##-------------------------------------------## ## Unit cell defined manually, will ignore ## specification in reflection file: ## From file : None ## From input: (140.124, 77.954, 54.519, 90, 98.549, 90) ##-------------------------------------------## ##-------------------------------------------## ## Space group defined manually, will ignore ## specification in reflection file: ## From file : C 1 2 1 ## From input: C 1 2 1 ##-------------------------------------------## Effective parameters: #phil __ON__ scaling { input { asu_contents { n_residues = 588 n_bases = None n_copies_per_asu = 4 } Matthews coefficient and Solvent content statistics ---------------------------------------------------------------- | Copies | Solvent content | Matthews Coef. | P(solvent cont.) | |--------|-----------------|----------------|------------------| | 1 | 0.448 | 2.226 | 1.000 | ---------------------------------------------------------------- | Best guess : 1 copies in the asu | ----------------------------------------------------------------

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input/output error
by Geoffrey Feld 14 Dec '09

14 Dec '09

Greetings fellow crystallographers, This past weekend, I collected some new data on my new project, indexed, scaled it, and found a phaser solution. The resolution is 3.6 A and I need to find one of the protein components, so I'm slowly refining piece-by-piece so I don't overdo it and flatten out the missing protein. To do this, I simply do rigid body and tls refinements for decreasingly smaller pieces of the protein I've already found. This method worked for me in the past for a similar structure. However, this time, as the refinement is finishing up, I get an input/output error and the program shuts down. Sometimes I get similar errors, and I can fix them by simply running the job again, overwriting the failed job, but this time that doesn't seem to be working. Here's the output from my .log file: Traceback (most recent call last): File "/programs/phenix-1.5-2/phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/programs/phenix-1.5-2/phenix/phenix/refinement/command_line.py", line 89, in run call_back_handler=call_back_handler) File "/programs/phenix-1.5-2/phenix/phenix/refinement/driver.py", line 1121, in run call_back_handler = call_back_handler) File "/programs/phenix-1.5-2/phenix/phenix/refinement/strategies.py", line 428, in refinement_machine monitors = monitors) File "/programs/phenix-1.5-2/cctbx_project/mmtbx/refinement/rigid_body.py", line 559, in __init__ out = log) File "/programs/phenix-1.5-2/cctbx_project/mmtbx/refinement/rigid_body.py", line 619, in show translations=t_vec) File "/programs/phenix-1.5-2/cctbx_project/mmtbx/refinement/print_statistics.py", line 161, in show_rigid_body_rotations_and_translations % euler_angle_convention, suffix=frame) File "/programs/phenix-1.5-2/cctbx_project/libtbx/utils.py", line 652, in write file_object.write(str) IOError: [Errno 5] Input/output error Again, the only thing I've done is made a few rigid body and tls groups. Please advise! Thanks, Geoff -- Geoffrey K. Feld Department of Chemistry 492 Stanley Hall University of California, Berkeley "Vigilia pretium libertatis"

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TLS-derived anisoU restraint
by Bryan W. Lepore 14 Dec '09

14 Dec '09

is wxu the easiest - perhaps indirect - way to restrain anisoU's derived from TLS? under the target_weights scope i see : wxu_scale fix_wxu optimize_wxu <-already using this .... b/c i want to pull back some anisoU deviations across C-N. -bryan

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