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Re: [phenixbb] Optimal settings for finding NCS from density
by Terwilliger, Thomas Charles 06 Jul '15

06 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.

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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

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metal refinement: adps and restraints
by Alexandra Marques 03 Jul '15

03 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

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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

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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)

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Simulated annealing refinement for just one domain
by Appu kumar 01 Jul '15

01 Jul '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

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while doing tar xvzf of nightly build 1.10pre-2089
by Murpholino Peligro 30 Jun '15

30 Jun '15

I get an error >>>> gzip: stdin: unexpected end of file phenix-installer-1.10pre-2089-intel-linux-2.6-x86_64-centos5/modules/phenix_regression/wizards/command_line_rosetta_tests/test_mr_rosetta_ncs.tgz tar: Unexpected EOF in archive tar: Unexpected EOF in archive tar: Error is not recoverable: exiting now <<<< Should I try another version?

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Re: [phenixbb] labelit access in Phenix?
by R.D. Oeffner 29 Jun '15

29 Jun '15

This should have been forward to the mailing list. Rob -------- Original Message -------- Subject: Re: [phenixbb] labelit access in Phenix? Date: 2015-06-26 21:46 From: "R.D. Oeffner" <rdo20(a)cam.ac.uk> To: "Keller, Jacob" <kellerj(a)janelia.hhmi.org> Copy: Aaron Brewster <asbrewster(a)lbl.gov>, Nigel W Moriarty <NWMoriarty(a)lbl.gov> Hi Jacob, Labelit is not present on Windows in the last official release of Phenix from May last year, version 1.9-1692. But it is present in recent pre-releases of Phenix as command line tools. When you install Phenix on Windows a startup group is created that includes a command line prompt which recognises Phenix commands. From there you can execute all labelit command line tools. I think Nigel is about to put the recent Windows pre-release online on the Phenix website. Feel free to get in touch with further questions. Regards, Rob On 2015-06-26 18:44, Aaron Brewster wrote: > Hi Jacob, replying off of the list for now. There is no labelit gui > support in the phenix gui. There may be a batch script you have to > run to get the phenix command line binaries in the path for the cmd > program in win7, but I don't know it. If you can run phenix.refine on > the command line but not labelit, that would be instructive. > > cc'ing Rob who has been working on the phenix windows build. > > -Aaron > > On Thu, Jun 25, 2015 at 7:58 PM, Keller, Jacob > <kellerj(a)janelia.hhmi.org> wrote: > >> 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 >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb [1] >> Unsubscribe: phenixbb-leave(a)phenix-online.org > > > > Links: > ------ > [1] http://phenix-online.org/mailman/listinfo/phenixbb

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phenix-1.9-1692 pymol problem
by ChenWeiFei 27 Jun '15

27 Jun '15

Dear all, I just install phenix and I found phenix-1.9-1692/pymol/install and it says: INSTALLATION of the PyMOL Executable Build for Unix 1) Extract the appropriate archive. tar -zxvf pymol-0_99-bin-linux-x86-glibc23.tgz 2) Change directory into the root level of the archive. cd pymol 3) Run "./setup.sh" which will create "./pymol" with a record of the current working directory. ./setup.sh 4) Link or copy ./pymol into a directory that is in your path. ln -s `pwd`/pymol /usr/local/bin/pymol (or perhaps) cp pymol /usr/local/bin/pymol 5) Now try it! ./pymol I follow it and when I type pymol there comes an error: $ pymol /usr/local/bin/pymol: /usr/local/phenix-1.9-1692/pymol/pymol.exe: /lib/ld-linux.so.2: bad ELF interpreter: No such file or directory Is any one konw how to deal with it? Best, Weifei

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phenix.composite_omit_map
by Dyda 27 Jun '15

27 Jun '15

Dear Phenix list, I have generated an mtz file with phenix.composite_omit_map. It has labels assigned as 2mFo-DFC for F and PH2mFo-DFC for P. Now, I would like to generate a map file. I was trying to convince phenix.maps to use this mtz file to do that, however it didn't seem to like the labels. I tried both the GUI interface of phenix.maps and also tried to force feed it through the command line with a maps.param file. Neither of these worked, so I'm obviously missing something. Btw., Coot can open the mtz file and display the map, and it does look reasonable. This is phenix-1.9-1692 running under RHEL6. Thank you for your help. Fred [32m******************************************************************************* Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular Biology Fax: 301-496-0201 DHHS/NIH/NIDDK e-mail:[email protected] Bldg. 5. Room 303 Bethesda, MD 20892-0560 URGENT message e-mail: 2022476710(a)mms.att.net Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred *******************************************************************************[m

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