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Solvent in Auto_Build
by Jeff Bush 11 Sep '06

11 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 06 Sep '06

06 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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Phenix 1.24.1 update/reinstall
by Noinaj 02 Sep '06

02 Sep '06

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

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Strategies is not working on IRIX
by Pramod Kumar JRF 01 Sep '06

01 Sep '06

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

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Re: [phenixbb] phase extension through phenix
by Tom Terwilliger 12 Aug '06

12 Aug '06

Hi Pramod, >I have one more question. Is any way in phenix GUI through which i can do >phasing to lowere resolution, further phase extension to higher >resolution? Becouse, my SAD data with single SeMet in whole protein of >3.5 Ang which have somewhat better phases and FOM at 5.0 ang resolution >than 3.5 Ang resolution. Is it possible through phenix? >If anybody have any one can help me? In the version you have, unfortunately the AutoSol keywords res_phase and resolution do almost the same thing, so you cannot do what you are asking for. This is fixed for the next version. An update patch will be available shortly to do it as well. I'm sorry for the problem! -Tom T Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.tbgenomics.org

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SAD and autosol
by Tom Terwilliger 11 Aug '06

11 Aug '06

Hi Pramod, >Hi all I am new user of the phenix. I am using autosol for the SAD data of >the 3.5 Ang of resolution data of spacegroup P42212. After running autosol >with all inputs , during Hyss autosol is not able to move forard with >display of followimg information: > > >Top solution : # 2 Dataset #1 >score: -1000 Fom: 0.19 sites:1 > > >Failed to carry out Autosol_score_ha_solutions: >list index out of range >STEP: Autosol_score_ha_solutions I'm sorry about this problem. I haven't seen it before, and I would like to track it down. I assume you are using version 1.24.1b, is that correct? If you would like to send me the data for this (as a .tar or .tgz file, renamed to ".txt") I will try it out on my computer. All the best, Tom T Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.tbgenomics.org

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phase extension through phenix
by Pramod Kumar JRF 11 Aug '06

11 Aug '06

Hi all I have one more question. Is any way in phenix GUI through which i can do phasing to lowere resolution, further phase extension to higher resolution? Becouse, my SAD data with single SeMet in whole protein of 3.5 Ang which have somewhat better phases and FOM at 5.0 ang resolution than 3.5 Ang resolution. Is it possible through phenix? If anybody have any one can help me? 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

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SAD and autosol
by Pramod Kumar JRF 11 Aug '06

11 Aug '06

Hi all I am new user of the phenix. I am using autosol for the SAD data of the 3.5 Ang of resolution data of spacegroup P42212. After running autosol with all inputs , during Hyss autosol is not able to move forard with display of followimg information: Top solution : # 2 Dataset #1 score: -1000 Fom: 0.19 sites:1 Failed to carry out Autosol_score_ha_solutions: list index out of range STEP: Autosol_score_ha_solutions 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

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a few questions
by Jianghai Zhu 07 Aug '06

07 Aug '06

Hi all, I have a structure refined to 2.5 A. After simulated annealing (start temp = 5000, cool rate = 25, final temp = 100, include TLS refinement and NCS restraint), my R and Rfree are 24.6% and 28.7% respectively. I then turned off the SA in the generated def file and carried on the combined refinement. My R and Rfree went up to 25% and 29.2% respectively. Why did the Rfree go up after refinement? In the remarks of the output pdb file, I have one line, "REMARK twinned : True". What does this mean? The RMSD of bonds and angles after either SA or combined refinement are about 0.006 and 0.851 respectively. Don't you guys think the geometry restraints are too tight? How do I change the weight in PHENIX? 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: 618-278-3030 +++++++++++++++++++++++++++++++

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