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autobuild : use of ncs
by Lepore, Bryan 22 Sep '10

22 Sep '10

i read and see that autobuild finds ncs automatically and uses it. i have one .pdb with one copy of the model for segid's A and B, and chainid's A and B. however, i notice sometimes in density modification that ncs has "NO" flags as to its use, and the output .pdb's have a single chain in them. refinement has sensible .eff's and such for ncs, there's find_ncs_* output, but some .log's suggest it is not specified or used. so just generally, how is ncs used - e.g. is it strict, which would explain a single chain the output .pdb? -bryan

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PDB Tools and CNS formatted structure factors
by Joseph Noel 22 Sep '10

22 Sep '10

Is there anyway with the PDB Tools to renumber protein chains? I have a model that doesn't correspond to the actual sequence, off by a couple of residues and just looking for a quick way to change that. Also, which module in Phenix is used to read in and convert CNS formatted ascii structure factors to the mtz read by phenix other then using ccp4. ___________________________________________________________ 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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FYI : autobuild : "refine_pdb_in.mtz is missing" etc.
by Lepore, Bryan 22 Sep '10

22 Sep '10

here's a google-able post of a *solved problem* for the archive : phenix 1.6.4-486 (latest official release as of 21sep2010) building ends (FINISHED) with error messages (see below). some associated job setup details : phenix.autobuild with CL flag refine_eff_file_list=my_refinement_params.eff cartesian or torsion annealing, or start_temperature work OK in building/refinement. two segid's in .pdb, one chain id etc. SOLUTION : use the latest build. i used phenix-dev-533 GNU/Linux 32-bit. and thanks especially to Tom Terwilliger for the solution. [key error messages]: Failed to carry out AutoBuild_multiple_models: Sorry a subprocess has failed... Failed to carry out AutoBuild_build_cycle: Sorry...the file AutoBuild_run_1_/TEMP0/refine_pdb_in.mtz is missing...

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autobuild : annealing
by Lepore, Bryan 21 Sep '10

21 Sep '10

[ phenix 1.6.4-486 ] looks like autobuild annealing is Cartesian. are there any (simple) tricks to get torsion, b/c seems there are no flags for it. -bryan

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deleting jobs in phenix
by Sebastiano Pasqualato 20 Sep '10

20 Sep '10

Hi all, sorry for the maybe silly question, but I don't seem to find a way to delete jobs from a project in phenix (I'm using ver. 1.6.2-473 on a MacBook Pro). The 'job history' tab on the main window does not allow that, so I was wondering if there's an easy way to do it. Thanks a lot for the great software suite, keep it up guys, ciao s. -- Sebastiano Pasqualato, PhD IFOM-IEO Campus Dipartimento di Oncologia Sperimentale Istituto Europeo di Oncologia via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5094 fax +39 02 9437 5990

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Phenix renewal support
by Paul Adams 20 Sep '10

20 Sep '10

Dear Phenix Users, I hope that Phenix has been helpful in your work. We are in the process of submitting a renewal for funding of the Phenix project and I would be most appreciative of your support for our renewal. If you would be willing to write me a short note, before September 18th, in the form of a signed letter (PDF) that indicates how much Phenix has helped your research, that would be incredibly helpful for our renewal. You can send your letter to me at PDAdams(a)lbl.gov 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: Kathleen Moody [ KLMoody(a)lbl.gov ] [ 1-510-495-2506 ] --

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R factor
by zhangh1＠umbc.edu 19 Sep '10

19 Sep '10

Hi, I want to calculate Fc based on the PDB file and reproduce the R factor in it. I first tried phenix.model_vs_data. It optimized ksol bsol and b_cart, and the output R factor (0.2143) is close enough to that in PDB (0.215). However, it didn't generate mtz files containing the calculated Fc. Then, I take the optimized ksol bsol and b_cart as the input and tried phenix.fmodel. I wrote my own code to calcuate the R factor. However, I got a lower R factor (0.2078). I think the reason might be my R calculation formula (sigma(fo-fc)/sigma(fo)) is wrong; or model_vs_data did more than just did flat solvent correction and anisotropic scaling. So, I am wondering whether phenix can: (1) Do the similar thing as model_vs_data (hope can be somehow faster:), but generate Fc-containing mtz file; (2) Do a simple R factor calculate to see whether my code is wrong (maybe answered already:) Thanks! Best Regards, Hailiang

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generate Rfree flag for twinned crystals with 3 twin fractions
by Zheng Zhou 19 Sep '10

19 Sep '10

Dear all After reading the informative posts in mailing list, I started to deal with my first twinning dataset. The space group is P3. Xtriage found 3 twin laws. R vs R statistics indicated perfect twinning for two twin laws and one is twin with RPS. I realize that twin-related reflections should be in the same work or free group. Could phenix handle the Rfree flag correctly for me when there are more than one twin fraction identified? By applying one twin law, the Rfree dropped from 37% to 28% using phenix. When I use Refmac, the twin fractions are refined and the Rfree is down to 26%. I copied the Rfree flag from phenix to the ccp4 in this case. When I let ccp4 generate Rfree flag automatically, the Rfree is refined to 26% too. Should I label the Rfree at a higher space group? Thanks for your advice Best, Zheng (Joe) Zhou

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Resolve NCS masks
by Florian Schmitzberger 18 Sep '10

18 Sep '10

Dear All, I would have a question regarding the use of masks in Resolve in Phenix for density modification: Is it possible to output the NCS and/or solvent masks Resolve is using during the Autosol run (similar as the options from the stand alone Resolve version) such as: mask_as_mtz ncs_mask_file mask.mtz protein_mask_file What are the best criteria (other than the final maps of course) within the output from Phenix.resolve to judge if the NCS (and/or solvent) mask was chosen adequately? (NCS_overlap?) I am mostly concerned if the masks chosen do include some of the more peripheral parts of my protein molecule and do not flatten these regions. Secondly, it is possible within Phenix Autosol wizard to supply a pdb file (with dummy atoms) for the mask for Resolve to construct the NCS mask? i.e. similar to set mask_pdb file= dummyatom.pdb Regards, Florian ----------------------------------------------------------- Florian Schmitzberger Biological Chemistry and Molecular Pharmacology Harvard Medical School 250 Longwood Avenue, SGM 130 Boston, MA 02115, US Tel: 001 617 432 5602

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Ligand restraints editing with REEL
by Joseph Brock 18 Sep '10

18 Sep '10

Hi all, I'm working on a 1.5A structure that contains a novel ligand within the active site, which is an Arsenic derivative of Glutathione, using the Phenix GUI, version 1.6.4-486. I have been using the 'Molinspiration' webpage (http://www.molinspiration.com/docu/webme/) to generate a smiles string, which I then feed into ELBOW. Although the structure/chemical restraints of Glutathione should be unchanged by the covalent linkage to arsenic through the cysteinyl sulfur, the resulting restraints file consistently restricts one of the dihedrals to a value that is incompatible with the (quite clear) electron density. This occurs regardless of wether i use AM1 optimization, and is unresponsive to using native Glutathione (which refines into the corresponding density extremely well) as an input geometry file with any of the available 'Use geometry for' options (final geometry, initial geometry, etc). I then tried opening the output file in REEL and manually changing the corresponding dihedrals to those of glutathione, however after running simple optimization, the resulting restraints file has the same problem, and upon choosing the 'transer geometry and restraints' option (or any option) midway through running the 'eLBOW optimization' or 'AM1 optimization' options, Phenix consistently crashes. Any advice on how to transfer the origional geometry of native Glutathione to my new ligand effectively would be greatly appreciated. I'm a little confused as to the abilities of REEL, and how to affect them. Thanks so much in advance. Cheers, -Joe.

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