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mlhl refinement
by Florian Schmitzberger 28 Sep '10

28 Sep '10

Dear All, I am running Phenix version 1.6.4.-486 on imac. I just wanted to refine (phenix.refine) a model with MLHL target and experimental phase information. Strange thing is when I load the mtz file, as written out from Phenix Autosol (overall_best_denmod_map_coeffs.mtz) into the GUI, the Phenix refine GUI does not seem to any phase information. Only picks up FP and SIGFP labels; but not the Hendrickson-Lattman coefficients, which are present. The following message comes up when I try to chose mlhl refinement: " You have selected 'mlhl' as the refinement target, but no experimental phases were supplied. If you wish to use phase restraints in refinement, please add or select experimental phases, or choose another target function". I guess it is not such a major problem as I can save the .eff file and manually edit it to include the HL coefficients and then run Phenix (as long as Phenix then recognizes them from the mtz file). I would also like to refine f' and f'', as the data are from a selenomethionine derivatized protein. From what I can see the default in Phenix.Autosol seems to be not to keep the F+/- and Dano labels for the output mtz file? So I suppose I do need to provide the initial mtz file or is there a way to change the output options for the coefficients in Phenix Autosol? Cheers, 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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Does Phenix have the library or program to maintain bond angle and bond length to create an extended chain?
by Rojan Shrestha 28 Sep '10

28 Sep '10

Hello: I am wondering whether Phenix has the library or program to maintain the ideal bond length and bond angle. The torsion angles of residue and xyz of each atoms are already known. I want to juxtapose residue or residues to create an extended chain. Thanks Regards, Rojan

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CCP4 Study Weekend 2011: "Model Building and Refinement and Validation"
by ronan.keegan＠stfc.ac.uk 24 Sep '10

24 Sep '10

Dear All, We're pleased to announce that registration for this coming January's CCP4 Study Weekend meeting is now open. The meeting will take place from January 5th to 7th, 2011 at University of Warwick in the UK. The topic of the meeting will be "Model building and Refinement and Validation". This year's organisers, Roberto Steiner and Bernhard Rupp, have arranged the usual mix of interesting and stimulating lectures from some of the foremost speakers in the field along with the opportunity to see demonstrations of the latest software developments from CCP4 during the lunch-time bytes sessions. For more information on the program and registration details please go to the Study Weekend website: http://www.cse.scitech.ac.uk/events/CCP4_2011/ We look forward to seeing you in Warwick. Best wishes, The CCP4 team -- Scanned by iCritical.

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separate amino acid chains
by Florian Schmitzberger 23 Sep '10

23 Sep '10

Dear All, Quick question regarding the handling of different amino acid chains in the Phenix Autobuild GUI. From the manual I understand that different amino acid chains are separated by > ? I pasted the my amino acid chains in the GUI separated with > ; I don't think in my case Phenix recognizes the different chains as such, but as one contiguous protein. Am I missing anything obvious? 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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autobuild : use of ncs
by Lepore, Bryan 23 Sep '10

23 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 23 Sep '10

23 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 22 Sep '10

22 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 21 Sep '10

21 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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