- phenixbb - phenix-online.org

hi
by intekhab alam 06 Jul '10

06 Jul '10

I am a new user to phenix and have just started with Phenix.refine using GUI. I want to fix the co-ordinate of ligand atoms in my structure and then refine it. can anyone help me to do that in phenix GUI. Thanks in advance Regards INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL

4 3

Computational Crystallography Newsletter - Issue 1
by Paul Adams 05 Jul '10

05 Jul '10

Dear Colleagues, I am pleased to announce the publication of the first issue of the Computational Crystallography Newsletter: http://www.phenix-online.org/newsletter/ It features articles, meeting announcements and reports, information on research and other items of interest to crystallographers and users of crystallographic software. The target audience is structural biologists including both students and experts. Anyone interested in publishing articles or other items in the newsletter is encouraged to contact the editor at any time. Submission of text by email using the word-processing templates available online is requested. Cheers, Paul -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Marian Harris [ MSHarris(a)lbl.gov ] [ 1-510-486-6886 ] --

1 0

queueing system support in GUI
by Nathaniel Echols 05 Jul '10

05 Jul '10

The most recent nightly build (dev-457) adds the ability to run jobs on Sun Grid Engine. To activate this feature, go to Preferences->Processes and click "Activate queueing system support"; this will add a queue job option to the menu that appears when you click the Run button. I'm hoping that the default command-line arguments I picked are suitable for most environments. Obviously the filesystem that you run jobs on must be visible both to the host machine and to the machines in the queueing system. The same PHENIX installation must also be accessible from both. You need to be able to submit jobs from the machine that you're running the GUI on. (FYI, you could be running everything on a single multi-core computer - there's no reason why this has to be done on a cluster, but that's what I'm testing it on.) You can view the current queue status from the main GUI via "Show queue status" in the utilities menu. (You can't actually delete jobs from there yet, despite the misleading button that I forgot to remove.) Some caveats: - This should, in theory, run on heterogeneous clusters, but I haven't tried this because all of our systems are 64-bit Linux. - I haven't tried it on Mac either. - There will probably be some weirdness associated with closing the GUI and resuming jobs while still running, especially if you try to abort them. - The built-in parallelization of AutoBuild and the ligand identification program will not play nice with the queueing system when using this mechanism (this is really a defect in queueing systems, not AutoBuild). I think it will be relatively easy to fix this, but for now, you're better off using a single multiprocessor machine for parallel AutoBuild runs in the GUI. - If the queueing system or remote host crashes, the GUI will still think the job is running. Those of you who are interested in using this, please let me know how it works and what features are missing. As always, I fully expect that this will break on some setups. thanks, Nat

2 1

Which is the better way to combine the dataset from different crystals?
by fn1＠rice.edu 02 Jul '10

02 Jul '10

Hi all, I have a question on how to combine two dataset from different crystal of the same protein. The first way I could think of is that, 1) Merge two dataset seperately; 2) Scale them to see whether they are consistent with each other enough as indicated by the R-factor; 3) If the R is low enough, say below 10 or 15%, then take the average for both the F and SIGF. The other way is that, 1) Take the unmerged file from MOSFLM, and reset their batch number; 2) Run SCALA to scale these two unmerged dataset at the same time. Could anyone tell which way is the better or the correct way? Thank you in advance! Alphar

1 0

Reference for phenix.elbow
by Michael Hothorn 30 Jun '10

30 Jun '10

Hi, is there a reference for phenix.elbow? Thanks Michael

3 2

NCS constraints in phenix
by Kenneth Verstraete 30 Jun '10

30 Jun '10

Dear all, I am working on a low resolution dataset (4.2 angstrom) of a multidomain complex. Using MR and density modification with NCS I obtained map in which I am extending/modifying my MR-models for the different domains. I tried to build the mainchain as a polyala model (extending on my MR-models) and then refined my new model in phenix.refine using torsion angle refinement. I have fourfold NCS and I think a this point it would be advantageous to use NCS-constraints instead of restraints. Is this possible in phenix? If I set the coordinate_sigma in de .def file to zero will this result in constrained NCS-refinement? ncs { restraint_group { reference=XXX selection=YYY coordinate_sigma=0.00 b_factor_weight=10 } Thank you very much for your advice, kind regards, Kenneth

2 1

SAD dataset
by sbiswas2＠ncsu.edu 28 Jun '10

28 Jun '10

Hi all, I was trying to run autosol with a sca file. I get the following error message: GUESS FILE TYPE MERGE TYPE sca premerged TARGET LABELS ['IPLUS', 'SIGIPLUS', 'IMINU', 'SIGIMINU'] Unit cell: (45.947, 88.031, 129.436, 90, 90, 90) Space group: F 2 2 2 (No. 22) CONTENTS: ['AutoSol_run_26_/TEMP0/F222peak_PHX_I_476(+).sca', 'sca', 'premerged', 'F 2 2 2', [45.947000000000003, 88.031000000000006, 129.43600000000001, 90.0, 90.0, 90.0], 2.000299364734313, ['IPLUS', 'SIGIPLUS', 'IMINU', 'SIGIMINU']] File F222peak_PHX_I_476(+).sca RES: 2.0 Guess of most complete dataset: 1 with resolution of 2.0 for dataset 1 FILE IS: AutoSol_run_26_/LAST.LOG ******************************************************************************** Failed to carry out AutoSol_scale_and_analyze_mad: None of the solve versions worked I guess this has something to do with the column label of sca file. How do I fix this? Any help is appreciated. thanks, Shya

1 0

Molecule will not load into coot from Phenix 1.6.2-432
by Subhangi Ghosh 26 Jun '10

26 Jun '10

Hi, I'm using Phenix version 1.6.2-432. When I run phenix.refine, coot opens up, but my molecule does not load. If I open in coot after refinement, molecule still does not load in coot. Please help. Thank you, Subhangi

2 6

NAG clashes: C2 with ND2
by Sam Stampfer 25 Jun '10

25 Jun '10

Hi, I'm in the process of preparing 4 structures for submission to rcsb, and the validation server has pointed out numerous issues with the N-acetyl-glucosamine moieties on my structures. While I have fixed the torsion angles accordingly (using CARP from http://www.glycosciences.de/tools/carp/ as a validation checker) and they stay fixed after phenix refinement, phenix keeps generating 2-2.2 Angstrom clashes between ND2 on asparagine with C2 on the NAG (the linkage is ND2-C1 and the usual distances are at least 2.28 Angstroms). Occasionally, the ND2 to C2 distance is as low as 1.8 Angstroms. This is happening in all my structures and happens independently of the setting of wxc_scale (even for wxc_scale=0.05!) My NAG groups fit the density well, both pre- and post- refinement. Any suggestions? Will rcsb care? These clashes are present in 12 out of 39 NAG moieties. Thanks! -Sam

3 3

PHENIX refine: detached sidechain atoms
by Oliver King 25 Jun '10

25 Jun '10

Hi All, I've noticed that when refining a model in phenix.refine using a PDB file from Refmac, the sidechain atoms of certain residues become detached from the rest of the molecule and appear to float on their own, at least when viewing in Coot. I think this is down to the format of the PDB file. For example the atoms of a Leu residue from a phenix.refine file which displays well is of the form: ATOM 1 N LEU A 8 50.022 -34.247 -5.817 1.00 58.12 N ATOM 2 CA LEU A 8 49.788 -34.905 -4.539 1.00 55.84 C ATOM 3 C LEU A 8 48.339 -35.358 -4.348 1.00 60.39 C ATOM 4 O LEU A 8 48.008 -36.016 -3.360 1.00 68.40 O ATOM 5 CB LEU A 8 50.219 -34.011 -3.373 1.00 57.98 C ATOM 6 CG LEU A 8 51.690 -34.126 -2.975 1.00 65.66 C ATOM 7 CD1 LEU A 8 52.014 -33.170 -1.836 1.00 59.99 C ATOM 8 CD2 LEU A 8 52.020 -35.566 -2.594 1.00 68.57 C where as from a Refmac PDB which also behaves well, it is of the form: ATOM 1 N LEU A 8 50.453 -35.722 -5.617 1.00 20.00 N ATOM 2 CA LEU A 8 49.649 -35.131 -4.482 1.00 20.00 C ATOM 3 CB LEU A 8 50.190 -33.735 -4.147 1.00 20.00 C ATOM 4 CG LEU A 8 51.461 -33.755 -3.275 1.00 20.00 C ATOM 5 CD1 LEU A 8 52.556 -32.768 -3.741 1.00 20.00 C ATOM 6 CD2 LEU A 8 51.082 -33.546 -1.799 1.00 20.00 C ATOM 7 C LEU A 8 48.166 -35.063 -4.824 1.00 20.00 C ATOM 8 O LEU A 8 47.822 -34.257 -5.568 1.00 20.00 O but after refinement in phenix it becomes ATOM 1 N LEU A 8 50.734 -35.936 -5.935 1.00 54.45 N ATOM 2 CA LEU A 8 49.846 -35.185 -4.892 1.00 51.89 C ATOM 3 CB LEU A 8 50.377 -33.761 -4.516 1.00 51.22 C ATOM 4 CG LEU A 8 51.550 -33.730 -3.431 1.00 59.27 C ATOM 5 CD1 LEU A 8 52.457 -32.407 -3.635 1.00 60.88 C ATOM 6 CD2 LEU A 8 51.120 -34.090 -1.879 1.00 55.50 C ATOM 7 C LEU A 8 48.268 -35.042 -5.221 1.00 47.92 C ATOM 8 O LEU A 8 47.989 -34.282 -6.195 1.00 47.32 O and the CD2 atom is now too far away to be part of the residue in Coot Is there an easy way to convert a PDB from Refmac into one which will behave itself when put through phenix.refine? I've tried using phenix.pdb_tools and also putting the model through Molprobity and hoping that that the output would be corrected. Thanks, Olly King

6 8