- phenixbb - phenix-online.org

refining a twin
by Bryan W. Lepore 21 Nov '06

21 Nov '06

i see there are map utilities for twinned data. but before i go try refinement of a twin - will phenix.refine refine against twinned data? if so, is alpha determined each time, thus, alpha is not specified in the .def? -bryan

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HA clusters
by Morten Grøftehauge 14 Nov '06

14 Nov '06

Hi, This is probably a stupid question but how do I tell AutoSol to look for a heavy-atom cluster rather than individual atoms? Or should I just find the cluster as a superatom in CNS and input the refined co-ordinates? Thanks, -- Morten K Grøftehauge PhD student Department of Molecular Biology Gustav Wieds Vej 10 C 8000 Aarhus C - Denmark Phone: +45 89 42 50 10 Fax: +45 86 12 31 78 www.bioxray.dk

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fixing atoms during refinement
by Gregers Andersen 02 Nov '06

02 Nov '06

Is there anyway through selection to fix selected atoms during minimisation/sim annealing in phenix.refine? Gregers Rom Andersen Associate Professor, Ph.D. Dep. Molecular Biology Gustav Wiedsvej 10C DK8000 Aarhus C Denmark phone +4589425024 fax +4586123178 <http://www.bioxray.dk/research_gra_uk.php> http://www.bioxray.dk/research_gra_uk.php Please notice new email: <mailto:[email protected]> gra(a)mb.au.dk

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a few questions
by Jianghai Zhu 23 Oct '06

23 Oct '06

Hi All, I have a few questions about phenix.refine and I couldn't find the answer in the manual. 1) How to generate the ligand library in phenix.refine? 2) Can phenix.refine calculate an OMIT COMPOSITE map? 3) When I used ML as the target, I couldn't find the output of LLG or similar number in the log file. How do I know the refinement is converged? Thanks. Jianghai +++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++

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a few questions
by Jianghai Zhu 22 Oct '06

22 Oct '06

Hi All, I have a few questions about phenix.refine and I couldn't find the answer in the manual. 1) How to generate the ligand library in phenix.refine? 2) Can phenix.refine calculate an OMIT COMPOSITE map? 3) When I used ML as the target, I couldn't find the output of LLG or similar number in the log file. How do I know the refinement is converged? Thanks. Jianghai +++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++

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Phenix 1.24 and Fedora Core 5_64
by Nicholas Noinaj 09 Oct '06

09 Oct '06

Hi, I have loaded PHenix 1.24 onto a system with Fedora Core 5 (ix86_64). THe computer has an AMD X2_64 4400+ processor, 2 GB RAM, 3X120GB Sata HDs, ASUS A8N-Sli Premium Mobo, and an Nvidia 7600 GT graphics card. When I install PHenix, everything seems to load okay, except it seems to take a bit longer to install than with RHEL3 did, stalling for bit on one of the modules (sorry, can't remember which one exactly). Then after a while, the installation completes without any errors and I setup the environment as instructed for /bin/bash. I then type [phenix] to start the program, but again nothing happens for a very long time (30 minutes or more), and then the Phenix interface finally loads. But then, everything is very sluggish and takes a very long time to load or even stops responding (setup/parameter windows in particular). I have installed Phenix 1.24 on RHEL3 and not experienced any of these problems, so I am a bit clueless. FUrther, I am a Linux 'newbie' and this was my first time installing Fedora Core 5 (64), so it is possible that i haven't installed everything that Phenix needs, yet I did not experience any problems at all with the FC5 installation, ran smoothly. If you have any suggestions or insights as to what my problem or mistake may be, I thank you in advance for your feedback and assistance. I am eager to get Phenix purring away on my latest PC. Cheers, Nick the environment as instructed for /bin/bash. I then type [phenix] to start the program, but again nothing happens for a very long time (30 minutes or more), and then the Phenix interface finally loads. But then, everything is very sluggish and takes a very long time to load or even stops responding (setup/parameter windows in particular). I have installed Phenix 1.24 on RHEL3 and not experienced any of these problems, so I am a bit clue ________________________________________ Nicholas Noinaj University of Kentucky College of Medicine Department of Molecular and Cellular Biochemistry The Center for Structural Biology Biomedical Biological Sciences Research Building, Rm 236 741 S. Limestone Lexington, Ky 40536 Lab: 859-323-8183 Cell: 859-893-4789 Home: 859-228-0978 noinaj(a)uky.edu noinaj.com

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Re: [phenixbb] Solvent in Auto_Build
by Thomas C. Terwilliger 10 Sep '06

10 Sep '06

Hi Jeff, I think if you edit the file to replace 'ATOM ' with 'HETATM' for all the HOH records then it should work. Please let me know if it doesn't! -Tom T > Dear Dr. Adams, and/or other Phenix experts, > > > > I have done water-picking in CNS and some refinement in Refmac-5 in > ccp4 and subsequent manual adjustments of waters in Coot and O. I have > discovered that CNS seems to like the format 'OH2 TIP' for listing waters, > whereas refmac only likes HOH. When I then run Auto_Build in the Phenix > GUI, I get the following error message: > > > > Input failed > > Sorry, the PDB file /path/filename.pdb has an incomplete residue (or > conformer/residue combination) in conformer ' ' chain S residue HOH 733 > because the conformer is missing the following main chain atoms: [ 'N', > 'CA', 'C' ]. > > > > The first water in my pdb file is indeed the one in question above. > Apparently Phenix is thinking that this water should be a protein residue > instead of solvent. Can anyone help me with this and tell me what I need > to > edit in the pdb file so that Phenix recognizes it as solvent instead of > protein, or do I need to delete all waters and repick them in Phenix. I > have tried changing the segid to from A to S with no success. > > > > Many Thanks, > > > > Jeff B. > > > > > > > > > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb >

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Solvent in Auto_Build
by Jeff Bush 10 Sep '06

10 Sep '06

Dear Dr. Adams, and/or other Phenix experts, I have done water-picking in CNS and some refinement in Refmac-5 in ccp4 and subsequent manual adjustments of waters in Coot and O. I have discovered that CNS seems to like the format 'OH2 TIP' for listing waters, whereas refmac only likes HOH. When I then run Auto_Build in the Phenix GUI, I get the following error message: Input failed Sorry, the PDB file /path/filename.pdb has an incomplete residue (or conformer/residue combination) in conformer ' ' chain S residue HOH 733 because the conformer is missing the following main chain atoms: [ 'N', 'CA', 'C' ]. The first water in my pdb file is indeed the one in question above. Apparently Phenix is thinking that this water should be a protein residue instead of solvent. Can anyone help me with this and tell me what I need to edit in the pdb file so that Phenix recognizes it as solvent instead of protein, or do I need to delete all waters and repick them in Phenix. I have tried changing the segid to from A to S with no success. Many Thanks, Jeff B.

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Re: [phenixbb] phenixbb Digest, Vol 10, Issue 1
by Pramod Kumar JRF 05 Sep '06

05 Sep '06

Hi I am running structure solution strategy- solve MAD and 'top' is also doesnot shows that anything is running. and also 'Task' is also never appered on the taskbar alongwith wizards and strategies. thanks in advance Pramod Kumar, c/o Dr. Shekhar C. Mande Lab of structural biology Center for DNA Fingerprinting and Diagnostics ECIL Road, Nacharam, Hyderabad-500076 India On Fri, 1 Sep 2006 phenixbb-request(a)phenix-online.org wrote: > Send phenixbb mailing list submissions to > phenixbb(a)phenix-online.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.phenix-online.org/mailman/listinfo/phenixbb > or, via email, send a message with subject or body 'help' to > phenixbb-request(a)phenix-online.org > > You can reach the person managing the list at > phenixbb-owner(a)phenix-online.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of phenixbb digest..." > > > Today's Topics: > > 1. Strategies is not working on IRIX (Pramod Kumar JRF) > 2. Re: Strategies is not working on IRIX (Paul Adams) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 1 Sep 2006 08:51:24 -0700 > From: Pramod Kumar JRF <pramod(a)cdfd.org.in> > Subject: [phenixbb] Strategies is not working on IRIX > To: phenixbb(a)phenix-online.org > Message-ID: > <Pine.SGI.4.44.0609010841320.231393-100000(a)www.cdfd.org.in> > Content-Type: TEXT/PLAIN; charset=US-ASCII > > Hi > I have installed the IRIX version of the phexinx1.24b.I am able to run > the wizards on my sgi but not strategies. Even after several hours its not > turning green,which is an indication that its not running.what could be > the problem? > > thanks in advance > > With regards > Pramod Kumar, > c/o Dr. Shekhar C. Mande > Lab of structural biology > Center for DNA Fingerprinting and Diagnostics > ECIL Road, Nacharam, > Hyderabad-500076 > India > > > > > > > ------------------------------ > > Message: 2 > Date: Fri, 01 Sep 2006 08:58:41 -0700 > From: Paul Adams <PDAdams(a)lbl.gov> > Subject: Re: [phenixbb] Strategies is not working on IRIX > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Message-ID: <44F858B1.3000507(a)lbl.gov> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi, > > which strategy are you trying to run. Does 'top' show anything running? > > Cheers, > Paul > > Pramod Kumar JRF wrote: > > Hi > > I have installed the IRIX version of the phexinx1.24b.I am able to run > > the wizards on my sgi but not strategies. Even after several hours its not > > turning green,which is an indication that its not running.what could be > > the problem? > > > > thanks in advance > > > > With regards > > Pramod Kumar, > > c/o Dr. Shekhar C. Mande > > Lab of structural biology > > Center for DNA Fingerprinting and Diagnostics > > ECIL Road, Nacharam, > > Hyderabad-500076 > > India > > > > > > > > > > _______________________________________________ > > phenixbb mailing list > > phenixbb(a)phenix-online.org > > http://www.phenix-online.org/mailman/listinfo/phenixbb > > -- > Paul Adams > Senior Staff Scientist, Physical Biosciences Division > Head, Berkeley Center for Structural Biology > Deputy Principal Investigator, Berkeley Structural Genomics Center > > Building 64, Room 248 > Tel: 510-486-4225, Fax: 510-486-5909 > http://cci.lbl.gov/ > > Lawrence Berkeley Laboratory > 1 Cyclotron Road > BLDG 64R0121 > Berkeley, CA 94720, USA. > -- > > > ------------------------------ > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb > > > End of phenixbb Digest, Vol 10, Issue 1 > *************************************** >

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Re: [phenixbb] Phenix 1.24.1 update/reinstall
by Petrus H Zwart 02 Sep '06

02 Sep '06

No way to update, just reinstall from scratch. Remove the sourcing of the phenix_env file from the .cshrc file (or so) and replace iot with what the phenix installer tells you. You can leave the old phenix sources sitting on your disc for senstimental reasons, or just remove it. A small tip, source your phenix distribution after you source ccp4. This will ensure that the most upto date version of various cctbx command line utilities will be used (otherwise you might have to call mmtbx.xtriage_1.24.1b instead of mmtbx.xtriage) HTH Peter Hi, i have Phenix 1.1 installed on a Linux workstation and would like to update it to Phenix 1.24.1. Is there a way to just update the old version or do I need to uninstall Phenix 1.1 and then install Phenix 1.24.1? If I need to uninstall Phenix 1.1, what is the best approach to accomplish this (sorry, Linux newbie)? Thanks in advance for all your feedback! Cheers, Nick ________________________________________ Nicholas Noinaj University of Kentucky School of Medicine Department of Molecular and Cellular Biochemistry Biomedical Biological Sciences Research Building, Rm 236 741 S. Limestone Lexington, Ky 40536 Lab: 859-323-8183 Home: 859-228-0978 noinaj(a)uky.edu www.noinaj.com _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://www.phenix-online.org/mailman/listinfo/phenixbb

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