- phenixbb - phenix-online.org

Two groups per residue and multiple trajectories for simulated annealing
by Stephen Graham 02 Mar '07

02 Mar '07

Hi all, I am taking my first tentative steps into the world of phenix.refine with a somewhat problematic 3 A data set and I had a few questions that Google couldn't answer. I am running phenix.refine version 1.24.1b (intel-linux-2.6) from the command line. Firstly, is it possible to do 'grouped' adp refinement with 2 groups per residue (like the good old bgroup.inp of CNS)? Secondly, is it possible to specify multiple starting trajectories for simulated annealing? I often find it handy to do 10 runs of simulated annealing and overlay the output co-ordinates to see where the 'wobbly' bits are. Lastly, can the latest version of phenix.refine do SA omit maps? Thanks, Stephen P.S. My .def file is the default (from phenix.refine --dry-run) w/ the following changes: 86,87c86,87 < refine_adp_individual = True < refine_adp_group = False --- > refine_adp_individual = False > refine_adp_group = True 92c92 < simulated_annealing = False --- > simulated_annealing = True -- Dr Stephen Graham Nuffield Medical Fellow Division of Structural Biology Wellcome Trust Centre for Human Genetics Roosevelt Drive Oxford OX3 7BN United Kingdom Phone: +44 1865 287 549

2 1

Phased anomalous difference map
by Luca Jovine 28 Feb '07

28 Feb '07

Hello, Is it possible to calculate a phased anomalous difference map with phenix.refine? Thanks, Luca

1 0

Re: [phenixbb] phenix.refine crash
by Ralf W. Grosse-Kunstleve 24 Feb '07

24 Feb '07

> Anyone has any idea what is happening? Thanks. It is a bug that we've fixed already. We will release a new cci apps in the next couple of days that will include the fix. In the meantime, could you try removing the ANISOU cards (grep -v ANISOU xxx.pdb)? I think that should work around the problem. Ralf

1 0

Re: [phenixbb] input HA
by Tom Terwilliger 13 Feb '07

13 Feb '07

Hi Morton, I'm sorry to make it difficult! Here are 2 formats that should work: 1. PDB format (I'm not sure why the one from cns failed...can you send me a line or two from that so I can make it work?): HETATM 1 SE SE 3 73.920 0.324 3.857 0.92 54.60 Se HETATM 2 SE SE 4 39.591 8.262 2.158 0.55 60.00 Se 2. Plain fractional xyz, with or without the word "xyz". For example see: $PHENIX/examples/gene-5-mad/sites.xyz : xyz 0.0271 0.8074 0.0657 xyz 0.0239 0.0116 -0.0965 Please let me know if this doesn't do it! -Tom T At 03:52 AM 2/13/2007, Morten Grøftehauge wrote: >Ok, I give up. > >What is the correct format for a heavy atom file >for AutoSOL? I've tried both the outputs from >FFT, CNS pdbs and sdbs and I've tried just >putting them on a line like you do for SHARP: >ATOM Br - 0.0120 0.5731 0.2740 >but none of them are accepted by Phenix. >Any help please? > >-- >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 ><http://www.bioxray.dk>www.bioxray.dk > >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://www.phenix-online.org/mailman/listinfo/phenixbb 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.doe-mbi.ucla.edu/TB

1 0

input HA
by Morten Grøftehauge 13 Feb '07

13 Feb '07

Ok, I give up. What is the correct format for a heavy atom file for AutoSOL? I've tried both the outputs from FFT, CNS pdbs and sdbs and I've tried just putting them on a line like you do for SHARP: ATOM Br -0.0120 0.5731 0.2740 but none of them are accepted by Phenix. Any help please? -- 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

1 0

CCI Apps
by Noinaj 26 Jan '07

26 Jan '07

Hi, Quick question. I am trying to refine occupancy of a ligand and was attempting to do this using the method outlined under the CCI Apps documentation for phenix.refine. a.. Refinement of one occupancy factor per selected group of atoms (group occupancy refinement): % phenix.refine data.hkl model.pdb strategy=group_occupancies \ refine.occupancies.group="chain A and resid 1"Yet, when I type the commands, I keep getting an error saying that something is wrong with my commands: strategy, group, etc. I have not (at least I don't recall) loading the updated CCI Apps and only have what was installed with Phenix 1.24b installation. Am I doing something wrong here or do I need to update the CCI Apps? Thanks in advance for all 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

2 1

New CCI Apps
by Ralf W. Grosse-Kunstleve 25 Jan '07

25 Jan '07

On behalf of the Phenix development team I'm pleased to announce the release of a new CCI Apps version: http://phenix-online.org/download/cci_apps/ Version 2007_01_24_2154 Simultaneous use of NCS restraints and automatic water picking. Individual anisotropic ADP restraints (similar to SHELXL SIMU). Bug fix in processing of multiple apply_cif_link blocks applied to the same residue. Send bug reports to: bugs(a)phenix-online.org For help write to: help(a)phenix-online.org

1 0

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

6 13

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

1 0

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

1 0

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.

1 0

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-----

4 4

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

2 1

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-----

2 1

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

2 1

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 > > =

1 0

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

1 0

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

2 1

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.

2 1

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

2 1

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

3 2

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

3 2

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 +++++++++++++++++++++++++++++++

3 2

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 +++++++++++++++++++++++++++++++

2 1

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

2 1