- phenixbb - phenix-online.org

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 15 Dec '09

15 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 15 Dec '09

15 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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Re: [phenixbb] How to extend R-free set to higher resolution by new phenix-1.5.2
by Thomas C. Terwilliger 14 Dec '09

14 Dec '09

Hi PC, >> >> Hi, >> >> I know this topic was discussed before, but I am still confused and still >> unable to refine my map merged from hires data because phenix.refine >> complains "No array of R-free flags found" >> >> The command was used to generate a hires map. >> phenix.autobuild data=resolve_1.mtz hires_file=hires.sca >> \seq_file=sequence.dat maps_only=True >> >> So, now I have "exptl_fobs_phases_freeR_flags.mtz", "cycle_best_1.mtz", >> "overall_best_denmod_map_coeffs.mtz"...several files in my autobuild >> folder, What this command has done is to take the phases in resolve_1.mtz and combined them with amplitudes from hires.sca and added free R flags to generate exptl_fobs_phases_freeR_flags.mtz . Additionally the file overall_best_denmod_map_coeffs.mtz now contains the above amplitudes along with some kind of density-modified phases. I would caution that this is probably not what you really wanted to do. Instead: Almost always you should use for "data=" a file that contains experimental phases only (not density-modified phases). So it would be better to use the command: phenix.autobuild data=phaser_1.mtz hires_file=hires.sca \ eq_file=sequence.dat maps_only=True which would instead density modify using hl coeffs from modify phaser_1.mtz, extending phase information to the data in hires.sca . Now you will have exptl_fobs_phases_freeR_flags.mtz with (a) experimental amplitudes from hires.sca (b) experimental phases and hl coefficients (where available) from phaser_1.mtz (c) free R flags to the full resolution of hires.sca and overall_best_denmod_map_coeffs.mtz with coefficients for a density-modified map at the resolution of hires.sca. >> >> How do I merge low and high resolution data by >> "phenix.reflection_file_editor"? What files (input and output arrays) >> should I choose? I think reflection_file_editor will only copy arrays (or columns) of data, and not merge several columns of data into one. Note that merging high and low resolution data requires (1) a scale factor between the datasets and (2) possibly a b-factor or anisotropic b-factor relating the two datasets. It cannot be properly done simply by merging reflection files. The reflection_flle_editor will add free R flags if they are missing or extend them for you if they are present only to low resolution, however. This allows you to take a low-res dataset with free R flags and a high-res dataset with no free R and to transfer the existing low-res free R flags to the high-res dataset and to extend them to full resolution. If you want, you can use phenix.solve to scale low and high resolution data by pretending that they are part of a mad dataset: make a file "scale.csh" like this, after editing to match your case: #!/bin/csh -f cp $PHENIX/solve_resolve/ext_ref_files/c2.sym . phenix.solve<<EOD resolution 20 3.0 cell 76 28 42 90 103 90 symfile c2.sym readdenzo ! readformatted/readdenzo/readtrek/readccp4_unmerged premerged ! premerged/ unmerged read_intensities ! read_intensities/read_amplitudes lambda 1 mad_atom c fprprv_mad 1. fprimv_mad 1. rawmadfile low.sca rawmadfile high.sca skip_solve sad EOD Then run with chmod +x scale.csh ./scale.csh Now solve_1.sca should have your scaled, merged data. I hope that helps! -Tom T

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How to extend R-free set to higher resolution by new phenix-1.5.2
by Pei-Chun Lin 12 Dec '09

12 Dec '09

Hi, I know this topic was discussed before, but I am still confused and still unable to refine my map merged from hires data because phenix.refine complains "No array of R-free flags found" The command was used to generate a hires map. phenix.autobuild data=resolve_1.mtz hires_file=hires.sca \seq_file=sequence.dat maps_only=True So, now I have "exptl_fobs_phases_freeR_flags.mtz", "cycle_best_1.mtz", "overall_best_denmod_map_coeffs.mtz"...several files in my autobuild folder, How do I merge low and high resolution data by "phenix.reflection_file_editor"? What files (input and output arrays) should I choose? Detail description will be very appreciate. Thanks for answer my question. PC _________________________________________________________________ Windows Live: Make it easier for your friends to see what you’re up to on Facebook. http://www.microsoft.com/middleeast/windows/windowslive/see-it-in-action/so…

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Side chain at special position
by Nate Nicely 12 Dec '09

12 Dec '09

I have a structure wherein the data show alternate conformations for a particular Trp side chain. The problem is that each of these conformations also occupies a special position: rotamer A clashes with rotamer A of the symmetry object, and similar for rotamer B. I'm attaching a screenshot wherein I tried to capture what's going on. The prerefined structure has a yellow carbon backbone, and you can see how refinement pushes rotamer A out of its rightful place in the map. I readjusted it and added the alternate conformation as seen in the green carbon backbone, but refinement after that just pushes apart both rotamers (not shown). I'd appreciate advice how to handle refining this structure in phenix. Thanks, Nate N

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Re: [phenixbb] structural validation and deposit format
by Pavel Afonine 12 Dec '09

12 Dec '09

On 12/11/09 12:55 PM, rui wrote: > SO in the output pdb file, there are another set of lines start with > ANISOU, what are those, should I keep those? These are ADPs - Atomic Displacement Parameters, or B-factors. They are as important as atomic coordinates (almost) stored in ATOM records -:) > I turned on the optimze_wxc and optimize_wxu flags in the GUI, it does > give better R/Rfree. Do I need to turn on every time or just use the > optimized weights, where I can find those optimized weight? In log file? Optimization of weights is usually time consuming and the default weights are just good most of the time. So I usually recommend running weights optimization as the last step to tune up your model. Of course there might be exceptions. Since optimal weight may be different from run to run, they are not stored in .def file for the next runs. Pavel.

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structural validation and deposit format
by rui 12 Dec '09

12 Dec '09

Hi, All, Sorry for this stupid question. When I tried to use phenix to validate the structure, it generate geometry outliers, model validation, real-space correlations and a phenix_map_coeffs.mtz file which I assume could be open in coot. How should I use this generated mtz file? When I open in coot, it tellls me core dump. I'm wondering if phenix will automatically do the corrections or should I look one by one in the log file and modify? It also generate a test_reduced.pdb, should I use this reduced pdb ( H added) for next round of refinement? Thanks. Is the format from phenix.refine ready for deposit?

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refinement
by r n 12 Dec '09

12 Dec '09

Hi all I do have very low resolution data (around 4 ang), what are the efficient way of doing refinement, either rigid body alone or rigidbody and tls or individual with group_adp. I did both, but not much significant changes in Rfree stays around 48/50%. Also I do have other questions 1. While doing rigid body refinement, phenix complaint about the special position and could not perform rigid body refinement, whereas individual site refinement is working fine. I do have to delete the atom in special position for rigid body refinement? Thanks

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How to reload a project into the gui
by Dirk 11 Dec '09

11 Dec '09

Hi, during a phenix refinement the gui froze and I had to kill the process. After restarting the gui the project I was working with was disappeared - all other projects are still there. Is there a way to reload the project into the gui? All files including the project folder still exists but are somehow not recognized by the gui. I'm using dev-249 64bit. Greetings Dirk

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Re: [phenixbb] How to reload a project into the gui
by Thomas C. Terwilliger 11 Dec '09

11 Dec '09

Hi Dirk, Try phenix.refine --gui Refine_xx/refine_xx.eff where xx is the run number of your refinement. That should preload all the parameters you had set at least. All the best, Tom T >> Hi, >> >> during a phenix refinement the gui froze and I had to kill the >> process. After restarting the gui the project I was working with was >> disappeared - all other projects are still there. Is there a way to >> reload the project into the gui? All files including the project folder >> still exists but are somehow not recognized by the gui. >> I'm using dev-249 64bit. >> >> Greetings >> >> Dirk >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

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Are sigma cutoffs for R-free reflections cheating?
by Joe Krahn 11 Dec '09

11 Dec '09

Using a sigma cutoff in refinement is almost always a bad idea. It appears that some people still use them. The problem is that sigma cutoffs almost always improve R-factors, because it increases the denominator in the error/average equation. Some people incorrectly think that the reduced R-factor means that the cutoff was an improvement in the structure quality. The result of a sigma cutoff is that the R-factor can be made to look better than it really is. I think that this should be prevented by never excluding any R-free reflections by any sort of cutoff criteria. That keeps the R-free value unbiased. If culling R-free is required for proper error analysis, or just because the culled data are almost certainly bogus values, then the un-culled R-free could be a separate value. Now days, most people use a sigma cutoff of zero, so it is normally not a big problem. However, it appears that PHENIX still throws out many reflections where Fobs==0, which can be a significant fraction in the last shell with anisotropic data. Unfortunately, the exclusion of weak reflections depends on how amplitudes were derived. If using CCP4 Truncate, those weak reflections will be inflated a bit to a non-zero value, and a zero-sigma cutoff will have a significantly different affect. Therefore, I think that the default should be to use reflections with Fobs==0, with SigFobs > 0 as the criterion for non-absent reflections in reflection files without a missing number flag (i.e. CNS format). Joe Krahn

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cif_as_mtz : column labels
by Bryan W. Lepore 11 Dec '09

11 Dec '09

a .cif has a bunch of labels (see below). the output .mtz has three: FOBS, SIGFOBS, R-free-flags ... without getting anyones' hands dirty, are the F's merged from the four correct columns, viz. F_plus, F_minus, (and sigmas)? -bryan (for pdb code, pls. off-list) labels in .cif : _refln.F_meas_au _refln.F_meas_sigma_au _refln.F_calc _refln.phase_calc _refln.pdbx_F_plus _refln.pdbx_F_plus_sigma _refln.pdbx_F_minus _refln.pdbx_F_minus_sigma _refln.pdbx_HL_A_iso _refln.pdbx_HL_B_iso _refln.pdbx_HL_C_iso _refln.pdbx_HL_D_iso

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Clearing old NCS group definitions
by John Pascal 09 Dec '09

09 Dec '09

Hello, I am using NCS restraints in phenix.refine, and I am defining the restraints in a parameter file that I read into the GUI interface. After modifying the ncs parameters file, I see in the log file that phenix.refine has used the updated NCS groups, but also retains the old restraints settings. Therefore, the number of NCS groups doubles each time I make an edit. Is there a way to erase the previous NCS restraints? I see that the restraints are accumulating in the project_data/*.eff files. Are those read in by default on consecutive runs? I am probably missing something obvious, but I would appreciate any advice. Thanks. Best, John -- John Pascal, PhD ph 215.503.4596 Assistant Professor fx 215.923.2117 Thomas Jefferson University Biochemistry & Molecular Biology 233 South 10th Street, BLSB 804 Philadelphia, Pennsylvania 19107 ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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Is it possible to do Molecular Replacement for synthesized "small" molecule X-ray data?
by Yves Wang 09 Dec '09

09 Dec '09

Hi PHENIX users, We've got a synthesized molecule, called Cucurbit[7]uril, molecular weight 1163 Da. We were able to grow crystals of cucurbit[7]uril with one of its ligand. This crystal diffracted to 1.5A at our X-ray machine. The dilemma is that, at this resolution, we can't use small molecule crystallography softwares to solve the structure (correct me if I'm wrong, we need at least 1A resolution?), while macromolecular X-ray softwares are really not designed for synthesized molecules. We have collected diffraction data of this crystal with decent quality. So I'm wondering if there's any way we can put a known crystal structure of cucurbit[7]uril and solve the structure of the complex. We have tried AutoMR but the solution is not very encouraging. Any suggestion will be gratefully appreciated. Best, -- Yi(Yves) Wang Department of Biochemistry Structural Biology & Biophysics Program Duke University BS: University of Science and Technology of China School of Life Sciences, National Laboratory for Physical Sciences at Microscale Tel: +1-919-236-3307 (Cell) +1-919-684-0235 (Lab 1) +1-919-660-1634 (Lab 2) Office: A20 LSRC / 5301 FFSC E-Mail: yves.wang(a)duke.edu Mail: Box 90317, Chemistry Department

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Re: [phenixbb] Problem using MOSFLM-integrated MAD data
by Chen, Yu Wai 08 Dec '09

08 Dec '09

Dear All, Thanks to all those who have responded to my previous query. The problem was due to I used MOSFLM raw data without scaling or sorting. I put the MOSFLM data through SORTMTZ and SCALA and output as "unmerged intensities in SCALEPACK format" and that error I mentioned earlier in the BB has gone. SOLVE completed successfully with some possible solutions. But now I have another problem. When RESOLVE tries to run DM, it reported another problem which seems to indicate it cannot read the scala-produced file correctly. The last bit of the log file before AutoSol stopped is as follows. I also print out the first few lines of the scala-produced SCALEPACK-format data file at the bottom for your diagnosis. Can you advise me what went wrong (and how to fix it)? Thanks a lot. Regards. Wai ##################### AutoSol_build AutoSol Run 22 Mon Dec 7 17:07:41 2009 SOLUTION FOR MODEL-BUILDING: Solution 2 using HYSS on /home/wai/dbe15_sh/SeM8/phnx/sem8_peak.hkl_ano_1.sca and taking inverse. Dataset #1 SG="P 21 21 21" SOLUTION FOR MODEL-BUILDING: Solution 1 using HYSS on /home/wai/dbe15_sh/SeM8/phnx/sem8_peak.hkl_ano_1.sca. Dataset #1 SG="P 21 21 21" DM SOLUTION USED FOR MODEL-BUILDING 1:Solution 2 using HYSS on /home/wai/dbe15_sh/SeM8/phnx/sem8_peak.hkl_ano_1.sca and taking inverse. Dataset #1 SG="P 21 21 21" WARNING: As the experimental data have been corrected for anisotropy and no input_refinement_file is available, no refinement will be carried out. Model-building will continue without refinement. Trying to guess refinement file for later use from ['/home/wai/dbe15_sh/SeM8/phnx/sem8_peak.hkl'] Choosing guess of refinement file for later use from all files: ['/home/wai/dbe15_sh/SeM8/phnx/sem8_peak.hkl'] FILE TYPE scalepack_no_merge_original_index GUESS FILE TYPE MERGE TYPE sca unmerged TARGET LABELS ['I', 'SIGI'] CONTENTS: ['/home/wai/dbe15_sh/SeM8/phnx/sem8_peak.hkl', 'sca', 'unmerged', 'P 2 2 2', None, None, ['I', 'SIGI']] File /home/wai/dbe15_sh/SeM8/phnx/sem8_peak.hkl ******************************************************************************** Failed to carry out AutoSol_build: float argument required, not NoneType ******************************************************************************** ########################### SeM8/phnx> more sem8_peak.hkl 4 P222 1 0 0 0 1 0 0 0 1 0 0 0 -1 0 0 0 -1 0 0 0 1 0 0 0 1 0 0 0 -1 0 0 0 -1 0 0 0 -1 0 0 0 1 0 0 0 -1 0 0 0 0 -1 -2 0 1 2 2 0 0 1 608.6 133.4 0 -1 -2 0 1 2 179 0 0 1 660.0 138.4 0 1 -2 0 1 2 176 0 0 2 519.0 130.9 0 -1 -3 0 1 3 4 0 0 1 1409.6 239.7 0 -1 -3 0 1 3 179 0 0 1 1525.0 251.0 -- Yu Wai Chen, PhD........................................Lecturer King's College London, Randall Division +44-207-848-8206 New Hunt's House, Guy's Campus, London SE1 1UL, U.K.

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Problem using MOSFLM-integrated MAD data
by Yu Wai Chen 07 Dec '09

07 Dec '09

> > Message: 3 > Date: Fri, 4 Dec 2009 15:54:13 -0800 > From: Nathaniel Echols <NEchols(a)lbl.gov> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] Problem using MOSFLM-integrated MAD data > Message-ID: <7B4AA329-8759-4603-BC26-9FD0A9120FC2(a)lbl.gov> > Content-Type: text/plain; charset=us-ascii > > On Dec 4, 2009, at 3:44 PM, Yu Wai Chen wrote: > >> > .... >> > Unable to analyze /home/wai/dbe15_sh/SeM8/phnx/sem8_remo.mtz with xtriage >> > (a total of 3 instances of this) >> > . . . >> > Testing anisotropy in /home/wai/dbe15_sh/SeM8/phnx/sem8_peak.mtz ... >> > Applying overall anisotropic B correction to /home/wai/dbe15_sh/SeM8/phnx/sem8_peak.mtz to yield AutoSol_run_8_/TEMP0/ANISO_sem8_peak.mtz.sca >> > Overall B set to minimum of the trace of B values >> > Unable to get range of aniso B from xtriage output >> > Multiple equally suitable arrays of observed xray data found. >> > >> > wavelength { >> > data = sem8_peak.mtz >> > labels = "I, SIGI, M_ISYM" >> > } >> > > What happens when you specify the labels as simply "I SIGI"? > > The same errors resulted. Any advise please? Wai -- Yu Wai Chen, PhD........................................Lecturer King's College London, Randall Division +44-207-848-8206 New Hunt's House, Guy's Campus, London SE1 1UL, U.K.

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Re: [phenixbb] P32 twin or p3221?
by lauren 06 Dec '09

06 Dec '09

Hi Peter, Thanks for your reply. >This data can be processed to P3 or P321 with the R-fac almost the same >After that, I used Bales to do the MR, two solutions were found in P32 >(dimmer) and one in P32 21 (monomer) >Then, I refine the structure using phenix.refine in both P32 and P32 21 sets, but the R/Rfree stopped at 0.19/0.25 and never goes down. >However, if I treat the P32 data as a twin (with twin law h,-h-k,-l ), the R/Rfree can down to 0.12/0.18. >Do an R vs R analysis by loading up a model as well in xtriage to get a clue about the extend of the pseudo symmetry. I do the R vs R analysis with P32 in xtriage, but the R value seems very close to zero. And the D_ncs is high (0.95) in resolution range 9.9841-4.2623, which may indicate an incorrect point group? The results are as follow. --------------------------------------------- Analysing possible twin law : h,-h-k,-l --------------------------------------------- mean |H| : 0.018 (0.50: untwinned; 0.0: 50% twinned) mean H^2 : 0.001 (0.33: untwinned; 0.0: 50% twinned) Estimation of twin fraction via mean |H|: 0.482 Estimation of twin fraction via cum. dist. of H: 0.487 Britton analyses Extrapolation performed on 0.47 < alpha < 0.495 Estimated twin fraction: 0.455 Correlation: 0.9777 R vs R statistic: R_abs_twin = <|I1-I2|>/<|I1+I2|> Lebedev, Vagin, Murshudov. Acta Cryst. (2006). D62, 83-95 R_abs_twin observed data : 0.022 R_abs_twin calculated data : 0.090 R_sq_twin = <(I1-I2)^2>/<(I1+I2)^2> R_sq_twin observed data : 0.001 R_sq_twin calculated data : 0.006 Perfoming correlation analyses The supplied calculated data are normalized and artificially twinned Subsequently a correlation with the observed data is computed. Results: Correlation : 0.832594802609 Estimated twin fraction : 0.49 Maximum Likelihood twin fraction determination Zwart, Read, Grosse-Kunstleve & Adams, to be published. The estimated twin fraction is equal to 0.478 Log[likelihood]: 78991.418 twin fraction: 0.443 D_ncs in resolution ranges: 9.9841 -- 4.2623 :: 0.950 4.2623 -- 3.4280 :: 0.694 3.4280 -- 3.0083 :: 0.655 3.0083 -- 2.7394 :: 0.885 2.7394 -- 2.5466 :: 0.853 2.5466 -- 2.3986 :: 0.824 2.3986 -- 2.2800 :: 0.817 The correlation of the calculated F^2 should be similar to the estimated values. Observed correlation between twin related, untwinned calculated F^2 in resolutiuon ranges, as well as ewstimates D_ncs^2 values: Bin d_max d_min CC_obs D_ncs^2 1) 9.9841 -- 4.2623 :: 0.981 0.902 2) 4.2623 -- 3.4280 :: 0.970 0.482 3) 3.4280 -- 3.0083 :: 0.958 0.429 4) 3.0083 -- 2.7394 :: 0.954 0.783 5) 2.7394 -- 2.5466 :: 0.964 0.728 6) 2.5466 -- 2.3986 :: 0.953 0.679 7) 2.3986 -- 2.2800 :: 0.963 0.667 Best Regards, Lauren

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Re: [phenixbb] Phenix installation issue
by smoniot＠chemie.fu-berlin.de 05 Dec '09

05 Dec '09

Well, I've dowloaded the installer again and changed my use of tar from -xvf to -xf option. Then reran the installation It went through and everything seems to work now. The only thing is that i'm normally running bash shell and that phenix doesn't work so. sourcing the phenix_env does not work under bash (setenv) Did I miss something or switching to tcsh is necessary ? Thanks for your help installing Seb > just a thought: > > if /net/anaconda is an nfs-shared drive, and you are trying to sudo > something on it from another workstation, it will fail because sudo > grants administrative privileges on the workstation, not on the server > where drive is housed. > > On Fri, 2009-12-04 at 04:59 +0100, smoniot at chemie.fu-berlin.de wrote: > Hi, > > I'm trying to install phenix on my computer (Linux distribution Kubuntu 64 > bits (virtual machine but it should not be an issue)) but the installation > failed after some minutes ... > the last lines on the installation log file are : > > /bin/tar: ./build/intel-linux-2.6-x86_64/base/bin/wx-config : un lien > symbolique ne peut pas être créé vers > «/net/anaconda/scratch1/phenix/phenix-1.5-2/build/intel-linux-2.6-x86_64/base/lib/wx/config/gtk2-ansi-release-2.8»: > Opération non permise > > It's in french but basiccaly it can't create a symbolic link to > /net/anaconda.... not allowed. > > I don't get it since I did try both the sudo ./install command and the su > - root. > > If anyone experienced this and get to fix it I would be glad to know :) > > Thanks in advance > > Sebastien > _______________________________________________ > phenixbb mailing list > phenixbb at phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb

2 1

Problem using MOSFLM-integrated MAD data
by Yu Wai Chen 05 Dec '09

05 Dec '09

Dear All, I am trying to use a set of MAD data integrated with MOSFLM in phenix. But when I ran autosol, I've got the following error in the log file: .... Unable to analyze /home/wai/dbe15_sh/SeM8/phnx/sem8_remo.mtz with xtriage (a total of 3 instances of this) ... AutoSol_setup_for_scaling AutoSol Run 8 Fri Dec 4 23:18:59 2009 Shifting to Automatic mode.... RESOLUTION 2.5 SOLVENT_FRACTION 0.54 RESIDUES 364 MAD-N-HA 14 NCS-COPIES 2 Setting up for scaling dataset resolution: 2.5 solvent_fraction: 0.54 Scoring criteria will be: ['SKEW', 'CORR_RMS'] Scoring method will be: BAYES-CC AutoSol_scale_and_analyze_mad AutoSol Run 8 Fri Dec 4 23:18:59 2009 scale_and_analyze_mad for dataset 1 file type :ccp4_unmerged ccp4_unmerged merge type :unmerged Testing anisotropy in /home/wai/dbe15_sh/SeM8/phnx/sem8_peak.mtz ... Applying overall anisotropic B correction to /home/wai/dbe15_sh/SeM8/phnx/sem8_peak.mtz to yield AutoSol_run_8_/TEMP0/ANISO_sem8_peak.mtz.sca Overall B set to minimum of the trace of B values Unable to get range of aniso B from xtriage output Multiple equally suitable arrays of observed xray data found. ******************************************************************************** Failed to carry out AutoSol_scale_and_analyze_mad: Sorry, there is something wrong with the file /home/wai/dbe15_sh/SeM8/phnx/sem8_peak.mtz ... xtriage cannot analyze it? ******************************************************************************** THIS IS MY parameters input to phenix.autosol: autosol { seq_file = dbe15.seq sites = 14 atom_type = Se crystal_info { resolution = 2.5 space_group = P212121 } wavelength { data = sem8_peak.mtz labels = "I, SIGI, M_ISYM" lambda = 0.9794 f_prime = -7.83 f_double_prime = 5.97 } wavelength { data = sem8_edge.mtz labels = "I, SIGI, M_ISYM" lambda = 0.9796 f_prime = -9.72 f_double_prime = 3.08 } wavelength { data = sem8_remo.mtz labels = "I, SIGI, M_ISYM" lambda = 09719 f_prime = -4.11 f_double_prime = 3.85 } } Can some guru help me? I can send the mtz file if needed. -- Yu Wai Chen, PhD........................................Lecturer King's College London, Randall Division +44-207-848-8206 New Hunt's House, Guy's Campus, London SE1 1UL, U.K.

2 1

Phenix installation issue
by smoniot＠chemie.fu-berlin.de 05 Dec '09

05 Dec '09

Hi, I'm trying to install phenix on my computer (Linux distribution Kubuntu 64 bits (virtual machine but it should not be an issue)) but the installation failed after some minutes ... the last lines on the installation log file are : /bin/tar: ./build/intel-linux-2.6-x86_64/base/bin/wx-config : un lien symbolique ne peut pas être créé vers «/net/anaconda/scratch1/phenix/phenix-1.5-2/build/intel-linux-2.6-x86_64/base/lib/wx/config/gtk2-ansi-release-2.8»: Opération non permise It's in french but basiccaly it can't create a symbolic link to /net/anaconda.... not allowed. I don't get it since I did try both the sudo ./install command and the su - root. If anyone experienced this and get to fix it I would be glad to know :) Thanks in advance Sebastien

3 3

(no subject)
by John Pascal 04 Dec '09

04 Dec '09

Hello, I am looking for advice on how to best refine the structure of a complex that has one component that can adopt two completely different conformations (a DNA duplex). I can model both conformations and set occupancies to 0.5, and try to constrain_group their occupancies, but in phenix.refine the two conformations are interpreted as major clashes. Thanks. Best, John -- John Pascal, PhD ph 215.503.4596 Assistant Professor fx 215.923.2117 Thomas Jefferson University Biochemistry & Molecular Biology 233 South 10th Street, BLSB 804 Philadelphia, Pennsylvania 19107 ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

4 5

P32 twin or p3221?
by lauren 03 Dec '09

03 Dec '09

Hi everyone, I have a dimmer protein diffract to 1.6 A resolution. After processing the data, the Linear R-fac was 0.26/0.038 (last/all), the data quality seems good. This data can be processed to P3 or P321 with the R-fac almost the same After that, I used Bales to do the MR, two solutions were found in P32 (dimmer) and one in P32 21 (monomer) Then, I refine the structure using phenix.refine in both P32 and P32 21 sets, but the R/Rfree stopped at 0.19/0.25 and never goes down. Rfree 25% seems a little bit too high for a 1.6 resolution data. However, if I treat the P32 data as a twin (with twin law h,-h-k,-l ), the R/Rfree can down to 0.12/0.18. I use P3 to run the phenix.xtriage (see bellows), it looks like the L-test says it is not a twin data. So, I am wondering is it a twin data or not? The results are as follow. "Twinning and intensity statistics summary (acentric data): --------------------------------------------------------------------------- Statistics independent of twin laws - <I^2>/<I>^2 : 2.105 - <F>^2/<F^2> : 0.773 - <|E^2-1|> : 0.757 - <|L|>, <L^2>: 0.508, 0.344 Multivariate Z score L-test: 2.013 Statistics depending on twin laws ------------------------------------------------------------------ | Operator | type | R obs. | Britton alpha | H alpha | ML alpha | ------------------------------------------------------------------ | -h,-k,l | M | 0.484 | -0.003 | 0.022 | 0.022 | | h,-h-k,-l | M | 0.026 | 0.454 | 0.479 | 0.478 | | -k,-h,-l | M | 0.507 | -0.004 | 0.026 | 0.022 | ------------------------------------------------------------------ Patterson analyses - Largest peak height : 8.386 (corresponding p value : 0.29163) The largest off-origin peak in the Patterson function is 8.39% of the height of the origin peak. No significant pseudotranslation is detected. The results of the L-test indicate that the intensity statistics behave as expected. No twinning is suspected. Even though no twinning is suspected, it might be worthwhile carrying out a refinement using a dedicated twin target anyway, as twinned structures with low twin fractions are difficult to distinguish from non-twinned structures. The correlation between the intensities related by the twin law h,-h-k,-l with an estimated twin fraction of 0.45 % is most likely due to an NCS axis parallel to the twin axis. This can be verified by supplying calculated data as well." Thanks! Lauren

2 1

High B Factors
by Miles Pufall 03 Dec '09

03 Dec '09

Hello All - I am working on a kinase:inhibitor complex with some interesting properties. First, it is a long, thin unit cell (45x45x300) that has highly anisotropic B-factors (60 in two dimensions and 35 in the other according to xtriage). We had a fair amount of trouble collecting data for these complexes due to somewhat high mosaicity (1.5) and overlap trouble, mostly due to the long unit cell. As a result, although we get diffraction out to ~2.3 A with good signal (I/sigma of 3), the completeness is only OK - dropping off from a high of 95% around 3.5 A pretty much linearly to 75% at 2.3. As a result, the maps look only OK for 2.3A data, but clearly show the interactions between the inhibitor and the kinase that we are looking to define. In that sense, the experiment worked just fine. That said, the structure looks pretty good, although about 1/3 shows poor density for sidechains, which I wouldn't expect at this resolution. But as I put the finishing touches on the structure a couple of things have worried me - first, there is consistently a larger than average gap between R and Rfree (Typically in the R~22 and Rfree~29). This, according to Polygon, is within the range of reported structures, so I think that's OK. What is odd is that despite having an average B caluclated from the reflection of ~50, the average B after refinement is ~80, which is very much on the high end of what has been reported. I have played around a lot with the wxc/wxu balance, and although this can change the Rs and tends to tighten the geometry perhaps inappropriately (rms bond ~0.003, rms angle ~0.7), the B factors stay very high. My question is, should I worry about this? And if so, what can you recommend trying. As usual, I'm happy to provide data if it help elucidate the problem. Thanks in advance - M Miles Pufall Postdoctoral Scholar Yamamoto Lab UC San Francisco Cellular and Molecular Pharmacology Mail Stop 2280 600 16th Street, Genentech Hall S-574 San Francisco, California 94158-2517 (415)476-4480

2 1

Atom Selection for Conformers
by John Pascal 03 Dec '09

03 Dec '09

Hello, What is the syntax for selecting one conformer of a residue? for example, if there are two arginine alternate conformations labeled A and B, how do you select just one of them. Thanks. Best Regards, John -- John Pascal, PhD ph 215.503.4596 Assistant Professor fx 215.923.2117 Thomas Jefferson University Biochemistry & Molecular Biology 233 South 10th Street, BLSB 804 Philadelphia, Pennsylvania 19107 ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

2 1

phenix server upgrade
by Ralf W. Grosse-Kunstleve 01 Dec '09

01 Dec '09

Over the weekend we've moved the phenix web server and mailing list to new hardware. If you notice any problems with the web content, the downloads, or the mailing list, please let us know. Ralf

1 0

Re: [phenixbb] sigma cutoff
by Kay Diederichs 01 Dec '09

01 Dec '09

> > > Hi, > > According to the Phenix manual, phenix.refine uses no sigma cutoff by > default. Since I haven't changed this manually, why do I see in my pdb > file MIN(FOBS/SIGMA_FOBS) 1.340? > > Thanks for help, > Karolina > > This one I can answer because I asked myself the same question recently. The answer is that Phenix does not impose any sigma cutoff, but rather your data are such that the minimum value of Fobs/Sigma_Fobs is 1.34 . You can verify this for yourself by going through your reflection file, line by line, and calculating Fobs/Sigma_Fobs for each reflection. You will find that all your reflections have a Fobs/Sigma_Fobs larger or equal to 1.34 . So it has nothing to with phenix; phenix just reports a property of your data. An easier way than doing it "manually" is using CCP4 sftools for calculating a new column "ratio", writing out the resulting MTZ file, and looking at this with mtzdmp. HTH, Kay -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: Kay.Diederichs(a)uni-konstanz.de Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universitaet Konstanz, Box M647, D-78457 Konstanz

2 1

Re: [phenixbb] Confused by the output from Phenix autobuild jobs
by Thomas C. Terwilliger 30 Nov '09

30 Nov '09

Hi Serah, You are right that the coefficients that you want for a difference map are not present in the overall_best_refine_map_coeffs.mtz file. The coefficients in that file (labelled FP PHIM) are the same as 2FOFCWT PH2FOFCWT from the refinement output, but there are no difference map coefficients. I will change this. In the meantime, I would do this after the end of autobuild: phenix.refine AutoBuild_run_1_/overall_best.pdb \ AutoBuild_run_1_/exptl_fobs_phases_freeR_flags.mtz and then you will have your map coefficients. >> I'm still wondering about the overall_best_*.* outputs - are these the >> really final output, or do we go for cycle_best_3.* series? The overall_best_xxx files are copied from the cycle_best_xxx files which are copied from the original files, all of which are in the TEMP0/ subdirectory. Thanks for pointing out that the difference coefficients are not present in the autobuild map file. I will fix the output to have the original refinement map file available. All the best, Tom T

1 1

alternate conformation
by subhash bihani 26 Nov '09

26 Nov '09

Hi, I am refining a structure with ligand in alternate conformations. I tried giving them A and B, it worked. but I feel that this doesnot make interactions between alternate conformations absolutely zero. Is there any command in phenix similar to Igroup statement in CNS which can be used for such cases. Regards subhash -- Subhash Bihani Scientific Officer Solid State Physics Division Bhabha Atomic Research Centre Trombay, Mumbai-85 Ph. 25594688 (o) alternate email: subhashbihani(a)yahoo.co.in

5 10

R-free rules
by Bryan W. Lepore 25 Nov '09

25 Nov '09

in the phenix.reflection_file_editor gui not sure i understand this: [x] Extend existing R-free array(s) ... [R-free flags generation] <--+ | | | | +-if this is checked, then do NOT check "Generate R-free flags" in here ... because "extend" is not the same as "generate", right? ... and thanks for the help before. -bryan

12 35

Age Concern edition of the Computing Commission and Teaching Commission newsletter
by Ralf W. Grosse-Kunstleve 25 Nov '09

25 Nov '09

Posted on behalf of Lachlan Cranswick: The Computing Commission and Teaching Commission has produced a joint November 2009 newsletter on the theme of "Age Concern", which deals with issue concerning "the slow march towards retirement of the major generation of crystallographic programmers", as further explained by David Watkin within the newsletter. http://www.iucr.org/resources/commissions/crystallographic-computing/newsle… or via http://www.iucr.org/resources/commissions/crystallographic-teaching/newslet… --------------------------- This issue's articles include : - the latest background and information from the UK based EPSRC funded Age Concern Project. - history and science within the Caltech based CRYRM single crystal suite; DIMS - Direct methods In Multidimensional Space software; Crunch 1.5 Direct Methods Software; the Glasgow based GX single crystal suite; the Italian based CAOS structure refinement software; Ton Spek's Platon; and a list of programs archived at Armel Le Bail's Crystallography Source Code Museum. - experience in conversion of large crystallographic Fortran-77 to C++; as well as the place of the Quick and Dirty Crystallographic Computer Program - Historical group photographs from some of the Crystallographic Computing and Teaching School of the 1970's. - Archived manuals and source code from the above mentioned software. - Teaching material of Isabella L. Karle, as she presented at the 1978 Erice School on Direct Methods for Solving Crystal Structures - A reprint of the The Analytical Theory of Point Systems (1923) by J. D. Bernal (1901-1971) Further Computing Commission newsletters are intended on theme of Age Concern : capturing the history and the crystallographic science behind past and present Small Molecule, Powder Diffraction, Protein and other crystallographic software. Submissions on this topic are welcome and encouraged. - Lachlan Cranswick ( lachlan.cranswick(a)nrc.gc.ca )

1 0

Confused by the output from Phenix autobuild jobs
by Serah Wangari 24 Nov '09

24 Nov '09

Dear Phenix users, I have run a number of Autobuild jobs using the Phenix GUI and in all cases, I'm not sure what output I should proceed with to the next step. - The first job was for rebuilding a loop section in the model (rebuild-in-place) - As far as I can remember, there was no mtz generated from this job, I had to generate map coefficients with the overall_best pdb and an old mtz using another refinement program. Did I miss something during the job input step, so that no mtz was generated, or how would I proceed in such a case? - The next job involved rebuilding the whole model (rebuild-in-place) - in this case, I took the overall_best pdb, but when I tried to open the overall_best_refine_map_coeffs.mtz in coot, I got this error that coot failed to find F/Phi columns in the mtz file. Then I checked in the TEMPO directory, and I managed to open a random mtz from one of the refinement cycles with coot, but I wasn't confident building into that, so again I had to generate map coefficients using overall_best pdb and an old mtz in another program. - The other job was rebuilding (rebuild-in-place) another model with composite maps generation - Here, in addition to the 12 mtz and pdb files from the 12 omit regions, I got resolve_composite_map.mtz I should assume as the only final output; and no final pdb. Again, this mtz file doesn't have the F/Phi columns as I got the same error as above in coot. I'm not sure how to proceed with this mtz...... I would really appreciate if someone could point me to the right direction or at least direct me to some literature where the output from Phenix autobuild jobs is explained - as I haven't come across such info yet. Thank you in advance, Serah --

3 2

Clean Jobs
by tea.pavkov＠uni-graz.at 24 Nov '09

24 Nov '09

Dear all, I would have a general question - how can I clean the Jobs (in the Job history list and all corresponding directories) in the new GUI? Thank you in advance! Best regards, Tea ----------------------- Dr. Tea Pavkov-Keller KF Uni Graz, ZMB Structural Biology Group Humboldtstr. 50/III 8010 Graz Austria

3 3

Problem installing on Leopard PowerPC G5
by Satpal Virdee 24 Nov '09

24 Nov '09

Hi, I am trying to install the latest 1.5-2 official release on an iMac PowerPC G5 running OSX 10.5.8. During installation I get the error: " Relocating Python framework. . . /usr/bin/install_name_tool: object: libwx_mac-2.8.0.5.0.dylib malformed object (unknown load command 20) Error: see /Users/Sat/Downloads/phenix-installer-1.5-2/build-binary/ mac-ppc-osx/cpemac406-18/log/binary.log for details " Inspection of the binary.log files reveals this: " libfreetype.6.3.10.dylib: /usr/local/phenix-1.5-2/build/mac-ppc-osx/ base/lib/libfreetype.6.3.10.dylib --> /usr/local/phenix-1.5-2/build/mac-ppc-osx/base/lib/libfreetype. 6.3.10.dylib libfreetype.6.dylib libfreetype.6.dylib: /usr/local/phenix-1.5-2/build/mac-ppc-osx/base/ lib/libfreetype.6.dylib --> /usr/local/phenix-1.5-2/build/mac-ppc-osx/base/lib/libfreetype. 6.dylib libfreetype.dylib libfreetype.dylib: /usr/local/phenix-1.5-2/build/mac-ppc-osx/base/lib/ libfreetype.dylib --> /usr/local/phenix-1.5-2/build/mac-ppc-osx/base/lib/libfreetype.dylib libwx_mac-2.8.0.5.0.dylib fix_mac_python: caught error - exiting. " Any help would be most appreciated. Regards, Satpal

2 1

baton build in coot
by Raja Dey 23 Nov '09

23 Nov '09

Dear Friends, How does CA ZONE > MAIN CHAIN under 'other modeling tools' in coot work? I was trying to rebuild main chain atoms for 3 residues(8,9,10) using CA ZONE > MAIN CHAIN. when I click on one atom in residue 8 and then one atom in residue 10, it failed with a message that says the zone is too short. I increased the zone to 5 residues, still same failed message. Also, is it possible to move an atom in coot? Thanking you in advance for your reply. Raja

2 1

phasing power value in Autosol/Autobuild
by vennila Natesan 20 Nov '09

20 Nov '09

Dear all... I need toknow the phasing power value for my solved structure. Where can i find it out in the output files of autosol and autobuild? I am using phenix1.14.4b and also i need to know the weighted mean phase errors vs resolution. Thanking you.

3 2

I vs F data input
by gerwald jogl 19 Nov '09

19 Nov '09

Hi All, A quick question about diffraction data input. I just noticed that phenix.refine uses Imean/SIGImean and converts these by default in my refinements. Is this the preferred way or would it be better to use F/SIGF (after CCP4)? Thanks, Gerwald

2 1

external ncs reference structures?
by Cathy Lawson 19 Nov '09

19 Nov '09

Dear Phenix developers, We are finishing up refinement of some multiprotein-DNA complex structures at 3-3.5 A resolution and I am wondering if it would be possible with phenix.refine to supply one or more external sets of coordinates from higher-resolution determinations to serve as the ncs references. If so what would be the best way to set this up? thanks, Cathy ********************************** Catherine Lawson, Ph.D. Rutgers University Chemistry & Chemical Biology 610 Taylor Rd Piscataway, NJ 08854 732 445 5494 cathy.lawson(a)rutgers.edu http://roma.rutgers.edu **********************************

2 1

Mac OSX Phenix GUI
by Miguel Ortiz Lombardia 19 Nov '09

19 Nov '09

Hi, This is a question/request to the phenix developers. Are there any plans to make the new phenix GUI to use an X11 python interface instead of the Aqua one? The reason I ask is that we use Mac OSX servers for calculations here and an X11 interface would be a lot more appropriate for this configuration. That way users could export the GUI to their local workstations. As it is implemented now this use of the GUI is impossible on Mac OSX. Before someone makes the suggestion: Remote Desktop simply allows to share the only Aqua desktop that the server can produce, that is, only one user can access the Aqua desktop, whether remotely or locally. We would be happy to test any X11 version you might be willing to develop. Thanks for your great software, which we can use anyway from the command line :-) Best regards, -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR6098) CNRS, Universités d'Aix-Marseille I & II Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 e-mail: miguel.ortiz-lombardia(a)afmb.univ-mrs.fr Web: http://www.pangea.org/mol/spip.php?rubrique2

2 1

Phaser output and error messages
by Ian Stokes-Rees 18 Nov '09

18 Nov '09

I'm having some discussion with a colleague about phaser output (we're using Phaser 2.1.4). We haven't been able to find any documentation which can clarify our situation, and I'm hoping someone on the list can help answer these questions. I should mention that I am relatively new to Phaser. 1. PHASER.sol files: Which "SOLU SET" does Phaser consider to be the best? The first or the last? Or the one with the highest LLG, wherever that may be? In our experience of running Phaser over several MTZ files with a range of models the best Phaser solution has always been the first, and this has had the highest LLG. Note: this is with "untuned" Phaser settings for identity, solvent fraction, or number of search models in ASU -- our goal is to do a first run with "generic" settings for these over a larger set of models, then (from TFZ and LLG scores) select a subset for which we will tune Phaser parameters and PDB search model variations. 2. If we are right that the first "SOLU SET" entry is indicative of the potential for the search model to form a good MR candidate, then is it the case that the first entry is the first Phaser solution that is computed? Or is the PHASER.sol file a sorted list output at the end of the run? From my reading of the documentation it is output in order of computation, and *for our purposes* (if my first statement in this question is correct) Phaser can stop after it outputs this first solution. Is there some way to tell Phaser to stop after the first solution is output? I realize that this doesn't sound like it makes sense (how could Phaser know to pick the best solution first, and even if it could, why would it ever continue past this point), however I ask because we have put a 10 minute timeout into our Phaser runs and we have many situations where we get a timeout but PHASER.sol has already been generated and the best LLG solutions are output first. It leaves me wondering why it didn't just stop on its own after outputting the first result instead of being aborted by our (external) timeout that terminates the process? 3. PHASER.sol files: For single domain search models, we usually get output of the form: SOLU SET RFZ=4.5 TFZ=5.2 PAK=0 LLG=14 LLG=14 SOLU 6DIM ENSE model1 EULER 242.049 45.040 326.088 FRAC -0.09425 0.50268 0.42575 however we see three variations: i) No LLG: SOLU SET RFZ=3.1 TFZ=5.0 PAK=0 SOLU 6DIM ENSE model2 EULER 59.983 69.335 319.701 FRAC -1.17131 -0.70030 0.23150 ii) One LLG: SOLU SET RFZ=3.7 TFZ=4.6 PAK=0 LLG=25 SOLU 6DIM ENSE model3 EULER 293.943 128.068 332.147 FRAC 0.06273 0.13175 0.25054 iii) Two LLG entries, but with different values: SOLU SET RFZ=3.8 TFZ=4.1 PAK=0 LLG=21 LLG=20 SOLU 6DIM ENSE model4 EULER 278.058 129.347 33.292 FRAC 0.28446 0.29011 -0.07986 4. Occasionally we get an error that we don't understand: FATAL RUNTIME ERROR: No scattering in pdbfile model1.pdb What does this mean? Is there a problem with the PDB file? We can't see anything obvious in the ones which produce this error. Thanks, Ian -- Ian Stokes-Rees, Research Associate SBGrid, Harvard Medical School http://sbgrid.org

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Request: read definitions from stdin
by Joe Krahn 16 Nov '09

16 Nov '09

I want to be able to run PHENIX in a shell script, where stdin is accepted as a definition input file. It could be simply specified as the usual POSIX syntax where "-" defines stdin in place of an input file. If the front-end is based too heavily on file suffix mappings, you could add a flag "--stdin=SUFFIX" to define reading stdin as if it had the given SUFFIX. It would also be nice to avoid the duplication of output to both stdout and the .log file. Output can always be sent to /dev/null, but it would be nicer to have either a --quiet flag to suppress stdout, or a DEF option to disable the .log output, or both options to let the user decide. Most other computational programs can be run this way, so I assume that other people would find this useful, especially for running PHENIX from scripts. Hopefully, it is also a fairly easy feature to implement. Thanks, Joe Krahn

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R-free rules
by Bryan W. Lepore 14 Nov '09

14 Nov '09

[ phenix.refine v1.5 rel. tag 2 intel linux 2.6 ] if i provide the test set .mtz (flag = "1") in refinement separately from the data .mtz, it looks like reflection_file_converter.py does not flag the work set as "0", if the work set lacks such a flag -- is that right? i.e. when providing the test set, it looks like all observed data must be in the test set, however the work set has flag "0". -bryan (some error output below) Sorry: R-free flags not compatible with F-obs array: missing flag for 22206 F-obs selected for refinement:

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November 15, 2009 deadline- User proposal submission for Collaborative Crystallography at BCSB
by Banumathi Sankaran 13 Nov '09

13 Nov '09

Dear Users, The deadline for October/November/December 2009 Collaborative Crystallography proposals will be *November 15, 2009. * ------------------------------------------------------------------------ Through the Collaborative Crystallography Program (CC) at the Advanced Light Source (ALS), scientists can send protein crystals to Berkeley Center for Structural Biology (BCSB) staff researchers for data collection and analysis. The CC 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; and * Reduced travel costs. To apply, please submit a proposal through the ALS General User proposal review process for beamtime allocation. Proposals are reviewed and ranked by the Proposal Study Panel, and beamtime is allocated accordingly. BCSB staff schedule the CC projects on Beamlines 5.0.1 and 5.0.2 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 learn more, go to: http://www-als.lbl.gov/als/quickguide/independinvest.html To submit a proposal, go to: http://alsusweb.lbl.gov/. Scroll down to "*Structural Biology beamlines (includes protein SAXS)*" and click on "New Proposal." Enter your proposal information, with attention to the following details: * For question 3/First choice, select "5.0.1 (Monochromatic);" for question 3/Second choice, select "5.0.2 (MAD)." * Check box (yes) in response to question "Do you want collaborative crystallography (beamline 5.0.1 or 5.0.2 only) * In question 9, please describe a specific research project with a clear end point. In order to request CC time for October/November/December 2009 allocation period, proposals must be submitted by *November 15, 2009.* The deadline for CC proposals for the time period March/April 2010 will be January 15, 2010. Regards, Banumathi Sankaran

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sulfate on a 2 fold axis
by David Cobessi 13 Nov '09

13 Nov '09

Hi, I am finishing to refine a structure using Phenix. A sulfate ion is located on a 2 fold axis. When I refine the structure with Refmac, the geometry of the ion is well conserved, while when I use Phenix the geometry is destroyed and the sulfate ion is like a cross!! Any idea to keep the good geometry of this ion in Phenix during the refinement? Thanks in advance, David -- David Cobessi Institut de Biologie Structurale 41, Rue Jules Horowitz 38027 Grenoble Cedex-1, France Tel:33(0)438789613 33(0)608164340 Fax:33(0)438785122

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phenix.cif_as_mtz
by Bryan W. Lepore 13 Nov '09

13 Nov '09

[ v. 1.5 release tag 2 intex-linux-2.6 redhat-e4.8 ] `phenix.cif_as_mtz file.cif --symmetry=FILE.pdb --show-log --show-details-if-error` .. reports "No data extracted from input cif file.", nothing else. command works w/ other .cif/.pdb's, CRYST1 lines, etc. look comparable between them,... not sure where to look next. thanks for any suggestsions. -bryan

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Nino Campobasso is out of the office.
by Nino.2.Campobasso＠gsk.com 12 Nov '09

12 Nov '09

I will be out of the office starting 11-Nov-2009 and will not return until 12-Nov-2009.

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Failed to make map after phenix.refine
by Zhou, Tongqing (NIH/VRC) [E] 12 Nov '09

12 Nov '09

Hi, All I am having problem with the new 1.5.2. After few rounds of refinement, the program failed to write out maps. It ended with: "Sorry: Duplicate mtz_label_amplitudes:FOFCWT" Here is the portion in my param file which worked fine before: electron_density_maps { map_format = *xplor map_coefficients_format = mtz *phs suppress = None map { mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" likelihood_weighted = True obs_factor = 2 calc_factor = 1 } map { mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" likelihood_weighted = True obs_factor = 1 calc_factor = 1 } } Thanks in advance for your help. Tongqing

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