- phenixbb - phenix-online.org

questions
by Jianghai Zhu 17 Jan '07

17 Jan '07

Hi, Got some questions in using phenix.refine. 1) Can phenix.refine use the ligand library generated by refmac5? 2) How do I use elbow to generate the ligand library when I have more than one kind of ligands? When I used --residue=xxx more than once, elbow will only generated library for the last ligand. If I use elbow multiple times to generate multiple libraries, how do I read the libraries in? Should I combine them to one file? 3) When I ran phenix.refine, I found the following message in the log. Number of residues, atoms: 32, 418 Unusual residues: {'NAG': 22, 'MAN': 10} Classifications: {'undetermined': 32} Link IDs: {None: 31} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 32 Number of residues, atoms: 18, 28 Unusual residues: {'GOL': 2, ' MG': 2, ' CA': 14} Classifications: {'undetermined': 18} Link IDs: {None: 17} I already gave the cif library for NAG. Looks like nothing happened. How come phenix.refine doesn't recognize Glycerol, Mg, and Ca? 4) The refinement (TLS + ML + B individual) went through, I got reasonable R, Rfree, rmsdBOND, rmsdANGLE. But the B factors are pretty low. The B factor of the backbone is much lower than the side chain, some have numbers like 4. Some metal atoms also have B factors around 4. What did I do wrong? Thanks. Jianghai

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Re: [phenixbb] phenix.hyss
by Ralf W. Grosse-Kunstleve 17 Jan '07

17 Jan '07

Hi Jianghai, I think the large memory consumption is due to the large number of triplet phase relations. Using the --real_space_squaring option may help. > The MAD data only goes to 4 A. I tried SOLVE and based on the CC > table output from SOLVE, the anomalous signal goes to 4.3 A. I > believe the cut of CC in SOLVE is 0.3. Unfortunately, the native > data is not isomorphous. Finding 50 Se given only 4.3 A resolution is difficult. I'm sorry to say I'm not very hopeful, but I'd try all tools out there. I'd also play with the resolution cutoff. hyss used 4 A in your case. I'd try 4.5 and maybe even all cutoffs 4.4, 4.3, 4.2, 4.1 if you can afford the CPU time, with --real_space_squaring first, without it if nothing worked still. Another question is the space group. You cannot distinguish I222 and I212121 from the systematic absences. Are you certain it is I212121? To find a cluster, lower the resolution significantly. I've had success with 6 A cutoff (--resolution=6). The atom type doesn't really matter, Ta should be fine. If it works, hyss will give you atoms around the centers of the clusters. You have to fit the whole cluster yourself. I'm not sure about the best approach for this (inspecting the map with coot and place the cluster manually?). Maybe someone else can help? How many clusters do you expect? In general, the more you expect the more data you need. I.e. a 6 A cutoff may work for finding a couple of sites, but for say 10 sites you'd need 5 A. -- These numbers are just to convey the idea. What works exactly depends highly on the available data. Hope this helps. Cheers, Ralf

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Re: [phenixbb] phenix.hyss
by Ralf W. Grosse-Kunstleve 17 Jan '07

17 Jan '07

Hi Jianghai, phenix.hyss isn't normally using that much memory. To help me understand what is happening, could you please email me the complete output (I will keep it confidential if you email to rwgk(a)cci.lbl.gov directly). Thanks! Ralf

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mmtbx.twin_map_utils utility
by Jorge Iulek 03 Jan '07

03 Jan '07

Hallo, This must be a naive question, but following Dr. Zwart's previous post and as I found in the web (http://www.phenix-online.org/phenix_wiki/mmtbx.twin_map_utils) this should be a utility to calculate a detwinned map. I just installed phenix and everything seemed to be fine during installation. But, where is this utility ? I cannot find it. Thanks, *********************************************************************** Prof. Jorge Iulek, Ph. D. Protein Purification and 3D Structure Determination Group State University of Ponta Grossa Telephone: ++ 55 - 42 - 3220-3062 Fax: ++ 55 - 42 - 3220-3262 iulek(a)uepg.br iulek(a)interponta.com.br *********************************************************************** !!!!!!!!!!!!!!!!!!!!!!!!!!Hi Brian, There are map utilities for twinned data indeed. mmtbx.twin_map_utils carries out refinement of the overall, anisotropic scale, bulk solvent parameters and twin fraction. It spits out the maps afterwards. Unfortunately, refniement against twinned data is not yet fully implemented in phenix.refine but we are working on that. HTH Peter > 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 > _______________________________________________ > phenixbb mailing list > phenixbb at phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb > -- Esta mensagem foi verificada pelo sistema de antivírus e acredita-se estar livre de perigo.

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full omit maps
by Miguel Ortiz Lombardia 29 Dec '06

29 Dec '06

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hello everyone, I'm trying to obtain a full omit map as it was described by Tom Terwilliger in a previous post: http://www.phenix-online.org/pipermail/phenixbb/2006-October/000108.html However, when I run the AutoBuild strategy asking for no rebuilding / no refinement all I get in the FULL_OMIT directory is a collection of pdb files named 'overall_best.pdb_OMIT_REGION_x' where 'x' correspond to each of the 'omit regions'. But I get no 'resolve_composite_map.mtz' whatsoever. Surely I'm missing something. I would appreciate your guidance. Have all of you an excellent year 2007! All the best, Miguel - -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 email: molatwork(a)yahoo.es www: http://www.ysbl.york.ac.uk/~mol/ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Le travail est ce que l'homme a trouvé de mieux pour ne rien faire de sa vie. (Raoul Vaneigem) -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) iD8DBQFFlNB7F6oOrDvhbQIRAuBpAJwK4/+sj+5PowBBIvNVE0Tvyin7wwCdHFOS QHrtAM+9afN+2RTGshFB8KU= =IXga -----END PGP SIGNATURE-----

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Re: [phenixbb] CCI apps bundles upgrading
by Ralf W. Grosse-Kunstleve 20 Dec '06

20 Dec '06

Hi Miguel, Thanks for asking the question! I just added this information to the CCI Apps download page: Please do NOT install CCI Apps inside an existing Phenix installation. It is best to install the CCI Apps bundle in a new, separate, empty directory. To override the Phenix commands with more recent equivalents in CCI Apps (e.g. phenix.refine), source cci_apps_build/setpaths.csh AFTER source phenix_env. Sorry for not explaining this earlier. It is just one of the things we don't usually think about as developers. Please let us know if there are other issues like this. Cheers, Ralf

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CCI apps bundles upgrading
by Miguel Ortiz Lombardia 20 Dec '06

20 Dec '06

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear all, This is a pretty newbie question. I have phenix installed at: /usr/local/phenix-1.24.1b and have downloaded the new version of the CCI Apps. I would like to install/upgrade them in my current installation (I have a backup, of course ;-) Should I simply run: python /PATH-TO/cctbx_sources/libtbx/configure.py phenix in the /usr/local/phenix-1.24.1b directory and then do the: source setpaths.csh libtbx.scons or it should be done differently to keep the phenix installation working? Thank you! Cheers, Miguel - -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 email: molatwork(a)yahoo.es www: http://www.ysbl.york.ac.uk/~mol/ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Le travail est ce que l'homme a trouvé de mieux pour ne rien faire de sa vie. (Raoul Vaneigem) -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) iD8DBQFFiVtPF6oOrDvhbQIRAkcKAJ414Qrsa+8DSj67uFQ6gv56Sc7TRQCfY8xG 7jXKhu+xv6nCc90xYjXt0T8= =2vZq -----END PGP SIGNATURE-----

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Anisotropic ADP
by James Fraser 16 Dec '06

16 Dec '06

Hello, We've just started using phenix.refine and I'm a bit confused about whether anisotropic ADP's are actually being used or not. On the wiki (http://www.phenix-online.org/phenix_wiki/phenix.refine) it says: << phenix.refine is the macromolecular refinement engine of the Phenix suite. It features * Individual as well as grouped B factor refinement * Anisotropic or isotropic+anisotropic B factor refinement * TLS refinement >> However, the documentation says (http://www.phenix-online.org/download/documentation/phenix/phenix/structure…): << Current limitations * No restrained individual anisotropic ADP refinement >> In my .def file I can set: adp { individual { isotropic = None anisotropic = chain a force_all_to_be_refined_isotropically = True } and get ANISO lines in my output pdb. But I'm confused as to whether this is actually refining with individual anisotropic b's for chain a (analagous to refining with anisotropic temperature factors in refmac). Should I be resetting the force_all... to false? Can someone with more knowledge clarify this? Thanks, the program seems to be working great otherwise! James Alber Lab UC Berkeley

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Re: [phenixbb] questions / TLS+NCS bug
by Pavel Afonine 14 Dec '06

14 Dec '06

Hi Jianghai, Thanks for the .log file ! I looked at it and now I think I now what's the problem: this is the bug in phenix.refine that we will fix for the next release. The bug arises when you try to refine using TLS and NCS at once. Sorry for this. The possible solution is to split your refinement into 2 parts: 1) First, refine coordinates and isotropic B-factors. Use NCS restraints. DO NOT refine TLS. 2) At the end, as the final tune up, refine ONLY isotropic B-factors + TLS and do not refine coordinates. For this run, please REMOVE all NCS information (NCS selections) from the command file. This refinement run should be the final one. Once again, sorry for the inconvenience. This will be fixed in the next release of CCI APPS and PHENIX. Once this fixed, you will be able to run everything in "one go" and in any combination. Please let me know if what I suggested helped you. Any further questions are welcome! Cheers, Pavel. Jianghai Zhu wrote: > Here is the log file. Thanks. > > Jianghai > > = > ------------------------------------------------------------------------ > > > > On Dec 14, 2006, at 12:50 PM, Pavel Afonine wrote: > >> Hi Jianghai, >> >> could you please send us .log file from your refinement run, so we >> can analyze what's going on. >> >> In general, "bad" B-factors can be: >> - misplaced model; >> - inadequate TLS model (= domains chosen for TLS do not correspond to >> the reality). >> >> If you are using like 2 months old or older version of phenix.refine, >> you may want to get the latest CCI APPS since we made lots of >> improvements. Just goto http://www.phenix-online.org/download/cci_apps/ >> >> Pavel. >> >> >> Jianghai Zhu wrote: >>> The resolution is 2.5 A. The wilson B is about 50. I know B factor >>> of the backbone is lower than that of the sidechian. But a B factor >>> like 4 is definitely wrong. >>> >>> Jianghai >>> >>> >>> On Dec 14, 2006, at 12:11 PM, Peter Zwart wrote: >>> >>>> >>>>>> 4) The refinement (TLS + ML + B individual) went through, I got >>>>>> reasonable R, Rfree, rmsdBOND, rmsdANGLE. But the B factors are >>>>>> pretty low. The B factor of the backbone is much lower than the >>>>>> side >>>>>> chain, some have numbers like 4. Some metal atoms also have B >>>>>> factors around 4. What did I do wrong? >>>> >>>> What is the resolution of your data? >>>> >>>> Backbone B-s usually are lower than the main chain. >>>> >>>> What is the Wilson B value reported by phenix.refine? >>>> You could re-refine and randomize all B-values and see what happens (I >>>> have to get back to you to to get the exact command for this). >>>> Maybe it >>>> is useful to obtain a copy of the latest verison of phenix.refine by >>>> downloading cci_apps from our server http://www.phenix-online.org. >>>> >>>> >>>> If your B-values still come out lowish, try growing crystals that >>>> do not >>>> diffract very well, that usually does the trick. >>>> >>>> HTH >>>> >>>> Peter >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> phenixbb mailing list >>>> phenixbb(a)phenix-online.org <mailto:[email protected]> >>>> http://www.phenix-online.org/mailman/listinfo/phenixbb >>> >>> ------------------------------------------------------------------------ >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org >>> http://www.phenix-online.org/mailman/listinfo/phenixbb >>> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org <mailto:[email protected]> >> http://www.phenix-online.org/mailman/listinfo/phenixbb > > =

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Re: [phenixbb] questions
by Ralf W. Grosse-Kunstleve 14 Dec '06

14 Dec '06

> 3) When I ran phenix.refine, I found the following message in the log. > > Number of residues, atoms: 32, 418 > Unusual residues: {'NAG': 22, 'MAN': 10} > Classifications: {'undetermined': 32} "Unusual" means "not peptide, rna/dna, or water". It is just for information. If phenix.refine cannot find matching CIF restraint definitions, it will report "Unknown residues". Ralf

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NCS in phenix.refine
by Alessandro S. Nascimento 13 Dec '06

13 Dec '06

Hi all, I've searched in phenix manuals but I didn't find how to deal with ncs in parameter file. Also, how to prepare simulated annealing keeping ncs restraints? Is it already possible in 1.24b version? Any idea? thanks, - alessandro

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Maybe a bug?
by Zhongli Cui 22 Nov '06

22 Nov '06

Phenix is a quite useful suite in solving protein structure. But I met a problem during running phenix1.24.1b on a suse 10.1 environment. When I try to load pdb file from the window, the phenix GUI will close automatically. But it runs OK, if I input the file name manually into the window.

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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 13 Nov '06

13 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 01 Sep '06

01 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 01 Sep '06

01 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 11 Aug '06

11 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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