- phenixbb - phenix-online.org

Weird problem of Coot fetch PDB&Map using PDB_redo
by Xiao Lei 07 Jul '15

07 Jul '15

Hi All, Today I found one weird problem of coot. I have coot installed in different platforms, I have coot 0.8.1 version in Ubuntu 15.04 and coot 0.8.1 version in Mac OS X 10.10.3, and I also have wincoot 0.8.1 in Windows 8.1. When I tried to fetch pdb&map using EDS, coot in all three platforms works very well. However, when I tried to fetch pdb&map using PDB_redo, only the windows wincoot works, which shows "successfully read coordinates...". The coot in mac and Ubuntu failed to fetch and shows "failed to read coordinates file...". I do not think the problem comes from PDB_redo as I tried to fetch the same pdb to compare coot in three platforms, only wincoot works well. I do not know if anyone else has this problem and how to fix it. Thanks ahead. Xiao

2 1

on determination whether a protein is a monomer or complex by phenix
by Smith Liu 07 Jul '15

07 Jul '15

Dear All, Suppose I have got a mtz file, and I know the aa sequence of the protein from which I got the crystal and the corresponding mtz file, will you please tell me which phenix function (program) can tell me whether my protein crystal was formed by protein monomer or by protein complex, and if formed by protein complex, how many subunits existing in the complex? Best regards. Smith

5 6

Re: [phenixbb] phenix rosetta refine
by kaiser 06 Jul '15

06 Jul '15

Thanks, Nigel! <div>-------- Original message --------</div><div>From: Nigel Moriarty <nwmoriarty(a)lbl.gov> </div><div>Date:2015/07/06 14:11 (GMT-08:00) </div><div>To: Jens Kaiser <kaiser(a)caltech.edu> </div><div>Cc: phenixbb(a)phenix-online.org </div><div>Subject: Re: [phenixbb] phenix rosetta refine </div><div> </div>Jens I believe that is all true and correct. Cheers Nigel --- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov On Mon, Jul 6, 2015 at 1:55 PM, Jens Kaiser <kaiser(a)caltech.edu> wrote: Nigel, Sorry for the late reply, I was away from the office last week. Yes, I did follow these instructions. At the moment I'm using rosetta_bin_linux_2015.22.57859_bundle and phenix-1.10pre-2084. I requested 20 models (which I get) but there are rosetta_##.sh files created that are empty and subdirectories _ros_temp?????? that contain files with _adp_refine in their names. I'm just wondering if it is really running as intended. Cheers, Jens On Mon, 2015-06-29 at 10:25 -0700, Nigel Moriarty wrote: > Jens > > > Have you followed the instructions? > > > http://www.phenix-online.org/documentation/reference/rosetta_refine.html > > > Cheers > > > Nigel > > > --- > Nigel W. Moriarty > Building 64R0246B, Physical Biosciences Division > Lawrence Berkeley National Laboratory > Berkeley, CA 94720-8235 > Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov > Fax : 510-486-5909 Web : CCI.LBL.gov > > On Sat, Jun 27, 2015 at 2:38 AM, Jens Kaiser <kaiser(a)caltech.edu> > wrote: > Hey there, > who would be the person to talk about setting up > phenix.rosetta_refine? I tried our SBgrid installation with > overrides to > "nightly" for phenix and rosetta; I tried a clean install of > rosetta and > phenix - production version and nightly's in all combinations > - and all > combinations of compiling (rosetta first, then > rosetta.build_phenix_interface, phenix first, then > rosetta.build_phenix_interface). The problem is that > "phenix.rosetta_refine" seems to run, and produce a log file > that looks > reasonable, but geometry params are worse than with an > ordinary refine. > I think I tracked it down to the fact that the "rosetta_XX.sh" > files are > empty, and rosetta actually does not run. > > Any help is welcome - and any support will be extended. > > Cheers, > > Jens > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org > >

1 0

phenix rosetta refine
by Jens Kaiser 06 Jul '15

06 Jul '15

Hey there, who would be the person to talk about setting up phenix.rosetta_refine? I tried our SBgrid installation with overrides to "nightly" for phenix and rosetta; I tried a clean install of rosetta and phenix - production version and nightly's in all combinations - and all combinations of compiling (rosetta first, then rosetta.build_phenix_interface, phenix first, then rosetta.build_phenix_interface). The problem is that "phenix.rosetta_refine" seems to run, and produce a log file that looks reasonable, but geometry params are worse than with an ordinary refine. I think I tracked it down to the fact that the "rosetta_XX.sh" files are empty, and rosetta actually does not run. Any help is welcome - and any support will be extended. Cheers, Jens

2 3

Re: [phenixbb] Optimal settings for finding NCS from density
by Terwilliger, Thomas Charles 05 Jul '15

05 Jul '15

Hi William, For find_ncs_from_density the shape of the molecule itself is not so important. What matters is if there is some local part of the molecule that is recognizable in both copies. So I would try default parameters first. I assume you did that and it didn't give you a useful answer...so then I would do these things: 1. try many locations : n_center_use=20 This is the best option...it will try 20 times using density at 20 different locations to search. If you have an older version of phenix you may need to download a nightly build to do this. 2. Try varying the resolution 3. Try varying the angular spacing of the search (delta_phi) All the best, Tom T ________________________________ From: CCP4 bulletin board [CCP4BB(a)JISCMAIL.AC.UK] on behalf of William Chao [William.Chao(a)CRICK.AC.UK] Sent: Friday, July 03, 2015 10:24 AM To: CCP4BB(a)JISCMAIL.AC.UK Subject: [ccp4bb] Optimal settings for finding NCS from density Dear all, What would be the best settings to look for NCS using phenix.find_ncs_from_density on an elongated (~150A) molecule? No coordinate is available unfortunately and there should be 2 copies in a P21 space group. Many thanks in advance! William --- The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 215 Euston Road, London NW1 2BE.

2 2

labelit access in Phenix?
by Keller, Jacob 03 Jul '15

03 Jul '15

Dear Phenix list, Does anyone know how to access labelit through Phenix to determine whether the highest possible symmetry has been found? I exclusively use the GUI, and it's on win7. In the labelit documentation/homepage it mentions the command: labelit.check_pdb_symmetry [pdb coordinate file] [data=mtz file] But I did not find any executables called labelit, nor can I figure out how to run Phenix from command line in Win7, short of installing Cygwin or something. JPK

3 2

metal refinement: adps and restraints
by Alexandra Marques 02 Jul '15

02 Jul '15

Hi, I am refining a protein with a Mo in the active site and which is bound to a cofactor and to a water molecule. After each refinement step there is always a lot of positive and negative density around the Mo and the cofactor molecules, although their occupancy refined to 1. I read this message http://www.phenix-online.org/pipermail/phenixbb/2015-May/022031.html, but I still have doubts about how to choose the refinement parameters. I know I have to select the Mo atoms to be refined anisotropically. And the other atoms, do I have to specifically select them to be refined isotropically?. For instance: Isotropic atoms: not element Mo Anisotropic atoms: element Mo I am asking that because I have been using TLS for the protein atoms during refinement, so I am not sure if it is correct to select the other atoms as isotropic or if I leave it in blank… My other problem is with the metal restraints. I am not sure about the ideal distance between the Mo and O atom but based on homologous protein structures I choose the following: refinement.geometry_restraints.edits { bond { action = *add atom_selection_1 = name MO and chain A and resname 4MO and resseq 1 atom_selection_2 = name O and chain A and resname O and resseq 2 distance_ideal = 1.900000 sigma = 0.050 } } However after the refinement this ideal distance interval (1.95-1.85) is not respected; I have 4 active sites and in some of them the Mo-O distance refines to 0.83 A although there is a lot of density for the water molecule to be at 1.9 A. How to make the restrainst work? Am I missing something? Thank you very much, Alexandra

3 2

accept MR solution even if the number of clashes is above the threshold
by Almudena Ponce Salvatierra 02 Jul '15

02 Jul '15

Hi everyone, I am running Phaser (from Phenix) and while checking the .log file (it is still running) I realize that it found some solutions with a TFZ score over 7, but it won't take them I guess because the number of clashes is higher than allowed (>12, I guess they're not so many either). My models are poor and for so I would like to check these solutions that for now Phaser will reject. However in the input I don't want to increase the allowed number of clashes because this will then affect all the other solutions and this will take forever... So my question is: can I tell phaser somehow to write down/save the solutions for which the TFZ score will be higher than 7? Even though the clashes Thanks a lot in advance All the best, Almu -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany

3 2

C-beta RMSD
by Kaushik Hatti 02 Jul '15

02 Jul '15

Hi, Is there a tool which can calculate C-beta RMSD for equivalent amino acids of homologous structures, post C-alpha superposition? Sorry if its off topic, Thanks, Kaushik -- Stupidity is everyone’s birthright. However, only the learned exercise it! --Kaushik (28Oct2014)

3 2

Simulated annealing refinement for just one domain
by Appu kumar 30 Jun '15

30 Jun '15

Hello All, I was wondering if there is a simulated annealing refinement for the just one domain and keeping the other domain fix. I have a structure where the electron density is poorly defined which could be because of the some conformation of domain is different. Although the resolution of the data is 4A but channel has well defined density in the TM domain. Thanks in advance for your advice and suggestions. Appu

2 1