- phenixbb - phenix-online.org

Duration of a phenix.elbow run
by Dirk 21 Jul '09

21 Jul '09

Hi, I'm trying to create restraints for a carbohydrate ligand using phenix.elbow. If I run it without the --opt command everything works fine, but I'm not completely happy with the geometry of my ligand after refinement. I tried to get an optimized cif by using --opt command, but the program just runs up to the following output: MoleculeClass : H:38 C:23 N: 1 O:19 (PDB format) 81 atoms 83 bonds 151 angles 238 dihedrals -------------------- Time Energy delta E RMS Max Step size and then nothing happens for several hours. Does the optimization needs such a long time and if I let it run overnight (or perhaps longer) I will get an output or is something going wrong? The input is a pdb (I tested several) and I tried both the stable phenix release (1.3) and the current version (1.4). Any help would be very appreciated Thanks Dirk

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Unable to produce kicked maps
by Schubert, Carsten [PRDUS] 17 Jul '09

17 Jul '09

Hi , I am trying to make some kicked maps in 1.4.106. At the end of the run all I am getting is Sorry: Duplicate mtz_label_amplitude FOFCWT Any workaround, except not to use kicked maps? Here the diff_params output for easer debugging. Cheers Carsten <<diff.def>>

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autosol
by sbiswas2＠ncsu.edu 16 Jul '09

16 Jul '09

Hi, I was trying to run autosol using gui however it crashed with the following message: Floating-point error (Python and libc call stacks above) This crash may be due to a problem in any imported Python module, including modules which are not part of the cctbx project. To disable the traps leading to this message, define these environment variables (e.g. assign the value 1): BOOST_ADAPTBX_FPE_DEFAULT BOOST_ADAPTBX_SIGNALS_DEFAULT Is this again a version problem? I am running version 1.4-6 Any help will be appreciated, Shya

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rigid body refinement in phenix.refine
by Pavel Afonine 16 Jul '09

16 Jul '09

To PHENIX users who asked about this: I recall several people (unfortunately, I don't remember who exactly) asked me about the details of rigid-body refinement implementation in phenix.refine (MZ protocol) and I promised to let them know when the corresponding paper is published. So here it is: J. Appl. Cryst. (2009). 42, 607-615 Automatic multiple-zone rigid-body refinement with a large convergence radius P. V. Afonine, R. W. Grosse-Kunstleve, A. Urzhumtsev and P. D. Adams http://journals.iucr.org/j/issues/2009/04/00/dd5048/index.html Pavel.

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error message
by zachcp 15 Jul '09

15 Jul '09

A Python error was detected. This is almost certainly a bug; please send an email containing this message to phenixbb(a)phenix-online.org so we can fix it. Thanks! SorryException : No array of observed xray data found. Traceback: Traceback (most recent call last): File "/usr/local/phenix-1.4-3/phenix/wxGUI2/Xtriage.py", line 158, in OnExcept raise event.data SorryException: No array of observed xray data found.

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Average B-factor and ML error
by Leo Sazanov 15 Jul '09

15 Jul '09

Hi, phenix.refine outputs "WILSON B" value into PDB header after refinement, which is not the same as average B-factor of all the atoms in the structure, and not exactly the same as Wilson B-factor from SCALA scaling. How exactly is Wilson B-factor for phenix header calculated and would it be possible to output there also the average B-factor of all the atoms in the structure? Also, deposition into PDB requires only Luzzati coordinate errors, while phenix produces only ML based ones. Presumably ML estimate is better than Luzzati?, but it looks like often people just ignore PDB input for errors. It seems that it would it be useful in future to have ML option in the PDB submission process? Or should Phenix produce Luzzati errors as well? (I know that one can calculate av. B-fac in other programs or ask PDB to add some data to the deposition, but if the idea is to streamline the process...) Thanks, -- Dr. Leonid A. Sazanov Research group leader Medical Research Council Mitochondrial Biology Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-mbu.cam.ac.uk Tel: +44-1223-252910 Fax: +44-1223-252915 -- Dr. Leonid A. Sazanov Research group leader Medical Research Council Mitochondrial Biology Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-mbu.cam.ac.uk Tel: +44-1223-252910 Fax: +44-1223-252915

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Anyone have a phenix.resolve script for after Phaser ?
by Phil Jeffrey 15 Jul '09

15 Jul '09

Although my usual m.o. is SHELX -> SHARP I'm exploring HYSS -> PHASER -> RESOLVE to see if the maps are any more interpretable. I think I've got good scripts for the first two steps but I'm not sure about my resolve script which stands at: phenix.resolve << EOD hklin myp3_auto.mtz LABIN FP=F SIGFP=SIGF PHIB=PHIB FOM=FOM HLA=HLA HLB=HLB HLC=HLC HLD=HLD hklout resolve.mtz solvent_content 0.45 seq_file myp3.pir EOD This runs, but I could not tell from delving into the documentation if this was ideal or not. Thanks Phil Jeffrey (a Luddite and not using the GUI) Princeton

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Re: [phenixbb] refine occupancy of partially overlapping ligands
by Chris Ulens 14 Jul '09

14 Jul '09

Hi, I'm trying to refine the occupancy of 2 ligands that occupy the same binding pocket in 2 *partially* overlapping orientations. Let's assume I would define the ligands in 2 separate "chains" termed A and B. Could the experts point me to the proper syntax to define the correct group restraints to refine the occupancy? Thank you. Chris +++++++++++++++++++++++++++++++ Chris Ulens, Ph.D. Lab of Structural Neurobiology Division of Pharmacology Campus Gasthuisberg, ON1 Herestraat 49, PB 601 B-3000 Leuven Belgium Tel +32 16 345812 Fax +32 16 345699 Telepathy 2.69 GHz +++++++++++++++++++++++++++++++

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can't find phaser_mtz.hand.mtz?
by Pei-Chun Lin 14 Jul '09

14 Jul '09

Hi, I am the beginner of crystallography and have a 3.5A map generated by MAD method using phenix GUI. I already traced and built 2/3 of my protein. I wish to use this partial model combined with SAD to generate a new map and see if the new map can help me to deal with the rest of the structure. Does it sound reasonable to you? However, after running AutoSol. I got this error message: Failed to carry out AutoSol_score_ha_solutions: [Errno 2] No such file or directory: 'AutoSol_run_1_/TEMP0/phaser_mtz.hand.mtz' What should I do now? Can't phenix automatically calculate it? PC _________________________________________________________________ Windows Live™: Keep your life in sync. Check it out! http://windowslive.com/explore?ocid=TXT_TAGLM_WL_t1_allup_explore_012009

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tightening geometry
by Patrick Loll 10 Jul '09

10 Jul '09

Hi, I'm a little baffled. We have a 3 Å structure, and while the R values seem OK, I'd like to tighten up the rmsd values for the geometry. However, altering wxc_scale seems to have no effect. Specifics: In a clean directory, I run the following command phenix.refine X.mtz Y.pdb Z1.cif Z2.cif Z3.cif wxc_scale=0.??? strategy=group_adp (the cif files are libraries for different ligands) When I vary wxc_scale from 0.5 to 0.005, the geometry doesn't change at all, which makes no sense to me: For wxc_scale=0.5 r_work = 0.2672 r_free = 0.2900 bonds = 0.028 angles = 3.151 For wxc_scale=0.05 r_work = 0.2672 r_free = 0.2900 bonds = 0.028 angles = 3.151 For wxc_scale=0.005 r_work = 0.2672 r_free = 0.2900 bonds = 0.028 angles = 3.151 ...you get the idea. These were run with phenix-1.4-3. With phenix-1.4-56, we get subtly different r values, but the bonds and angles numbers are the same as shown above (to 3 decimal places!), and the numbers don't change upon changing wxc_scale. Am I missing something here? Is there a better way to tighten up the geometry? Thanks, Pat --------------------------------------------------------------------------------------- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pat.loll(a)drexelmed.edu

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