- phenixbb - phenix-online.org

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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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 06 Aug '06

06 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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Autobuild peptide?
by ckielkop 02 Aug '06

02 Aug '06

Hi, We have a molecular replacement RNA structure with a bound peptide. I'd like phenix autobuild the peptide, because only a portion of it is bound and we'd like an unbiased, silicon opinion about what that portion is. It's not clear to me how to proceed with this in phenix- we have a beautiful electron density map from CNS, coordinates for the RNA portion, and peptide sequence. Thanks for any guidance! -- Clara L. Kielkopf Assistant Professor Biochemistry and Molecular Biology Johns Hopkins University Rm. W8708 BSPH 615 N. Wolfe St. Baltimore, MD 21205 Ph. 443-287-4546

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Build problems: 1.24.1b on SLES9
by Chris Richardson 01 Aug '06

01 Aug '06

Dear all, I've just been trying to install 1.24.1 beta on a new server running SuSE Linux Enterprise Server 9. The machine's a dual Xeon, so I've been using the 64-bit linux 2.6 build. I'm invoking install with ./install --prefix=/common/app/phenix-1.24.1b Installation fails with the message configuring PHENIX components Error configuring: see /common/app/phenix-installer-1.24.1b/ build-binary/intel-linux-2.6-x86_64/zaltu/log/binary.log for details Looking at the log file, the last few lines are ./iotbx/iotbx/shelx/from_ins.py ./iotbx/iotbx/shelx/write_ins.py ./ccp4io_502_cci/ ./ccp4io_502_cci/lib/ ./ccp4io_502_cci/lib/src/ ./ccp4io_502_cci/lib/data/ ./ccp4io_502_cci/lib/data/symop.lib ./ccp4io_502_cci/CCI_DIFFS python: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory SLES v9 uses libstdc++.so.5. Python works fine on this machine and is linked to libstdc++.so.5. I assume (probably incorrectly) that the error comes from some component of Phenix that is linked to the later version of the library. Does anybody have handy hints for installation on SLES? I would try it with SLES v10, but that would conflict with other packages we have running on that machine. TIA, Chris -- Dr Chris Richardson - sysadmin, Structural Biology Section, icr.ac.uk

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Problems running demo
by Miguel Ortiz Lombardia 31 Jul '06

31 Jul '06

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear all, Sorry if this kind of problems have been posted before, I tried unsuccessfully to find a relevant FAQ. I'm new to Phenix, so I thought it would be a good idea to run the GUI demo first. I installed, set up the programs and copied the data in a directory and did as instructed in the demonstration sequence page. I find two problems: 1. When I call the GUI I don't see the Tasks tab (well, perhaps not a problem, just a misunderstanding) 2. After I load the AutoSol wizard and press "Continue" the wizard doesn't turn to green. Instead, it remains blue and get this message in the console: (...) SUMMARY Input files dataset #1 peak.sca Creating new Data Storage /home/miguel/tests/phenix_demo/PDS/AutoSol.1 Traceback (most recent call last): File "/usr/local/phenix-1.24.1b/phenix/phenix/pds_server/ProcessMaster.py", line 269, in ? run() File "/usr/local/phenix-1.24.1b/phenix/phenix/pds_server/ProcessMaster.py", line 193, in run tasklist = strategyDataStorage.getObject(ProcessKey) File "/usr/local/phenix-1.24.1b/phenix/phenix/server/PDSClient.py", line 146, in getObject return self.loader(pickle_string) File "/usr/local/phenix-1.24.1b/phenix/phenix/server/PDSClient.py", line 27, in loader self.loader(pickle_string) File "/usr/local/phenix-1.24.1b/phenix/phenix/server/PDSClient.py", line 17, in loader return cPickle.loads(pickle_string) ValueError: could not convert string to float Any ideas of what may be wrong? 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/ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Je suis de la mauvaise herbe, Braves gens, braves gens, Je pousse en liberté Dans les jardins mal fréquentés! Georges Brassens -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.1 (GNU/Linux) iD8DBQFEzgoeF6oOrDvhbQIRAn6SAJ4zmtiWyYJhmB7hdJeEGUp3kr0MtACfYffg ZvyFTX9ExvysvTOav35k0pg= =nS7A -----END PGP SIGNATURE-----

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Re: [phenixbb] (no subject)
by Petrus H Zwart 28 Jul '06

28 Jul '06

The easiest way is to run the AutoBuild wizard. It will do modelbuilding and density modification for you. HTH Peter Zwart ----- Original Message ----- From: sroy(a)mbu.iisc.ernet.in Date: Friday, July 28, 2006 4:57 am Subject: [phenixbb] (no subject) > Hi all, > I am first time using phenix GUI. I have a moleculat > replacementsolution. PDB file contain a polyala model. I want to > do density > modification using resolve in phenix. how to do? > please help > sidhu > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb >

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(no subject)
by sroy＠mbu.iisc.ernet.in 28 Jul '06

28 Jul '06

Hi all, I am first time using phenix GUI. I have a moleculat replacement solution. PDB file contain a polyala model. I want to do density modification using resolve in phenix. how to do? please help sidhu

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