June 2010 - phenixbb - phenix-online.org

Geometry problem with sugars refined in phenix
by Tirumala Kumar Chowdary 03 Mar '11

03 Mar '11

Hi, I have refined a structure with NAGs linked to ASNs at 3 places in my structure. I used the right link definitions and the NAG definitions are from Phenix library. Phenix refined all the sugars right and made the right links between the NAGs. However, while submitting, PDB found problem with the geometry of NAGs linked to the ASN at two places. This is the issue -the atoms around C1 atom of the sugar molecule NAG A #810 and NAG A #1670 are on a plane and the C1 atom center is far off to be tetrahedral. Please, verify the chirality of C1 and provide the correct coordinates if necessary.- Any ideas on how to fix the geometry of these sugars will be of great help. Regularization and real space refine in Coot is not working or I don't know how to do it. I am looking for alternative ways to fix this problem. Thank You Tirumal

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Problem with Autobuild
by Claudia Scotti 12 Jan '11

12 Jan '11

Dear List, Sorry fo r the easy question, but I have a problem with Autobuild. I'm trying to rebuild a scFv, composed of two domains linked by a linker. I've managed to find an MR solution with a polyalanine model deprived of the loops, which is my starting model for rebuilding. I've given Autobuild three input files: the mtz, the model coordinates and the sequence of the scFv, asking to model only the beta strands and helices. Problem is that in the final model Autobuild seems to guess incorrectly the density of two beta-strands, inserting the linker there instead of the expected side chains. Any suggestions on how to correct this? Shall I manually rebuild this part to avoid problems? Or is it crucial to prevent errors, for example, that the model and the sequence are numbered so that they are in register? Thanks in advance, Claudia Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673 _________________________________________________________________ Hotmail: Trusted email with powerful SPAM protection. https://signup.live.com/signup.aspx?id=60969

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Can PHENIX write the peak list to a PDB file?
by Joe Krahn 04 Dec '10

04 Dec '10

PHENIX has an option to find positive and negative peaks, but only lists them in the log file along with the residue they are closest to. Is it possible to write out the actual peak coordinates, such as to a PDB file? Thanks, Joe Krahn

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Bad ligand parameters
by Joe Krahn 21 Oct '10

21 Oct '10

I found that residue TRS has different dihedral target angles for the three hydroxyl oxygens, which are actually all equivalent. They have a periodicity of 1, but should have a periodicity of 3. What is the best way to handle such discrepancies? Most ligand parameters are probably auto-generated based on a reference structure, and there is probably a lot of conformation bias. In this case, it seems that parameterization should have been able to detect symmetry. It would be nice if parameters could include information about whether a human has done any validation. Actually, a ligand Wiki might be nice, where people can easily put comments, even if they are not sure about how to improve the parameters. Joe Krahn

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Re: [phenixbb] phenix.automr ensemble/component question
by Thomas C. Terwilliger 24 Jul '10

24 Jul '10

Hi Scott, Your first command looks good to me. It is saying that the composition of the crystal is 2 copies of each chain: component_1.component_copies=2 component_2.component_copies=2 and you want to search for 2 copies of each of your search models: ensemble_1.copies_to_find=2 ensemble_2.copies_to_find=2 All the best, Tom T > Hi Phenixers, > > I'm a bit confused about the proper syntax for my phenix.automr job. > This is probably a simple concept, but I'm running on 3 hours of sleep > as my kid was up all night, and my synapses aren't working so good. > > I expect 2 copies of my protein per AU > > My protein is composed of two domains > > I have a single PDB search model for each domain > > is either of these commands correct? > > phenix.automr data=mydata.sca \ > ensemble_1.coords=domain1.pdb \ > ensemble_1.identity=95 \ > ensemble_1.copies_to_find=2 \ > component_1.mass=40579 \ > component_1.component_copies=2 \ > ensemble_2.coords=domain2.pdb \ > ensemble_2.identity=95 \ > ensemble_2.copies_to_find=2 \ > component_2.mass=13410 \ > component_2.component_copies=2 > > > or > > > phenix.automr data=mydata.sca \ > ensemble_1.coords=domain1.pdb \ > ensemble_1.identity=95 \ > ensemble_1.copies_to_find=1 \ > component_1.mass=40579 \ > component_1.component_copies=2 \ > ensemble_2.coords=domain2.pdb \ > ensemble_2.identity=95 \ > ensemble_2.copies_to_find=1 \ > component_2.mass=13410 \ > component_2.component_copies=2 > > > essentially I'm not really using an ensemble of search models, I only > have a single PDB for each domain. So should ensemble_1.copies_to_find > and ensemble_2.copies_to_find be set to 1 or 2? > > > Thanks, > Scott > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Scott Classen, Ph.D. > SIBYLS Beamline 12.3.1 > http://bl1231.als.lbl.gov > Advanced Light Source > Lawrence Berkeley National Laboratory > 1 Cyclotron Rd > MS6R2100 > Berkeley, CA 94720 > C) 510.206.4418 > O) 510.495.2697 > Beamline) 510.495.2134 > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb >

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writing composite omit maps in .xplor
by Susan Tsutakawa 23 Jul '10

23 Jul '10

Hi all, Continuing the conversation on looking at Phenix maps in pymol, what is the best way to generate .xplor maps in Autobuild. I would like to generate a figure in pymol with an omit map. I wasn't able to find documentation explicitly stating how this can be done. Sincerely, Susan

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Reference for phenix.elbow
by Michael Hothorn 01 Jul '10

01 Jul '10

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

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NCS constraints in phenix
by Kenneth Verstraete 01 Jul '10

01 Jul '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

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SAD dataset
by sbiswas2＠ncsu.edu 29 Jun '10

29 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

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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

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