[ccp4bb] Setting default PDB viewer to PyMOL in CCP4i
Dear CCP4 developers and all,
CCP4i of CCP4 version 6.1.3 can set the default PDB viewer to PyMOL
(Default Viewers section in Preferences dialog). I have not noticed this
function in previous versions.
But viewing PDB file with PyMOL fails. It shows message dialog ERROR
could not start PyMol.
So, I modified the souce of fileviewer. It is here.
$ diff -u fileviewer.tcl.orig fileviewer.tcl
--- fileviewer.tcl.orig 2009-09-17 19:18:25.0 +0900
+++ fileviewer.tcl 2010-03-08 21:27:16.0 +0900
@@ -654,7 +654,7 @@
}
#-
-proc RunPyMol { $args } {
+proc RunPyMol { filename } {
#-
#d_sum Run PyMol lto display coordinates
#d_arg filename Input PDB coordinate file
---
This modification will fix the problem.
Please check this patch.
# Apologies in solution if this is already-answered question.
Thanks.
Nobuo OKAZAKI
[ccp4bb] Don't understand output of refmac with tlso addu option
I'm trying to come to grips with the recent PDB policy for depositing files which have the TLS model expanded out into individual ANISOU records. Up until now I've been using tlsextract/tlsanl to prepare such files, but now I've just tried using the new refmac option TLSO ADDU and I'm confused. My structure was refined using a pure TLS model. That is, all Biso terms for protein atoms were fixed at the Wilson B, and then refmac refined the TLS parameters and an overall aniso B correction. I took my previous final refinement run in refmac, added the TLSO ADDU keyword to the input script, and reran it. So now I have two parallel PDB files: the first one produced by refmac/tlsextract/tlsanl (no TLSO option) the second one produced by refmac (TLSO ADDU option) The BISO and ANISOU records in these are not quite the same. Not wildly different, but more than I can attribute to round-off error. Even more confusing, the water molecules in the second file have their own ANISOU records. Parvati analysis shows their descriptions are not even close to being isotropic. How/what/why did my waters get subject to aniso refinement? They are not part of any TLS group, and I didn't ask for any individual B refinement of any sort! -- Ethan A Merritt Biomolecular Structure Center University of Washington, Seattle 98195-7742
[ccp4bb] older version of CCP4 Program Suite vs newer!
Dear All, I wonder if anyone has come across the differences seen between the statistics obtained from scala output files using CCP4 Program Suite 6.0.2 CCP4Interface 1.4.4.2 versus CCP4 Program Suite 6.1.2 CCP4Interface 2.0.5 (which is obviously a more recent version). The reason I ask is that I am seeing a difference in the statictics especially when it comes to Rsym and MeanI/sigmaI values; using the more recent version of CCP4 the values are worse at the same resolution. I would appreciate your inputs. Many thanks, Arefeh Arefeh Seyedarabi, PhD Postdoctoral research assistant School of Biological and Chemical sciences Queen Mary, University of London Mile End road London E1 4NS
Re: [ccp4bb] crystallization of a macromolecular complex
Hi Jan-- What is the composition of your protein buffer? Thanks! annie Annie Hassell Glaxo Smithkline 5 Moore Drive RTP, NC 27709 919/483-3228 919/483-0368 (FAX) annie.m.hass...@gsk.com Jan Rash jan...@googlemail.com Sent by: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK 05-Mar-2010 09:02 Please respond to Jan Rash jan...@googlemail.com To CCP4BB@JISCMAIL.AC.UK cc Subject [ccp4bb] crystallization of a macromolecular complex Dear All, This is about the crystallization of the macromolecular complex which is highly soluble and shows no signs of the aggregation (even at high concentration). We have tried several salts, precipitants and even high protein concentration (around 20g/L) for its crystallization without any genuine hit. Any suggestions for growing the crystals of this macromolecular complex will be highly appreciated. Thanks, Jan
[ccp4bb] Multiple conformations of disulfide-linked cysteines
Dear CCP4BB, I am building a protein structure containing a pair of cysteines linked via disulfide bond. This disulfide bond (i.e. the cysteine S-gamma atoms) refines well at 2/3 occupancy, however the electron density suggests that these cysteines each adopt a second, unlinked conformation (presumably at 1/3 occupancy). I have no trouble building the alternate conformers; however, refinement causes both conformers to disulfide-bond. I would like to know if there is a way (and how) to specify individual conformers (or individual atoms) in the SSBOND record of a PDB. Thank you in advance, David A. Critton Graduate Student, Page Laboratory Department of Molecular Biology, Cell Biology Biochemistry Brown University Providence, RI
Re: [ccp4bb] Don't understand output of refmac with tlso addu option
On Monday 08 March 2010 09:28:15 Ethan Merritt wrote: I'm trying to come to grips with the recent PDB policy for depositing files which have the TLS model expanded out into individual ANISOU records. Up until now I've been using tlsextract/tlsanl to prepare such files, but now I've just tried using the new refmac option TLSO ADDU and I'm confused. Update: Mitchell Miller pointed out to me that there is another relevant keyword, one that isn't shown in the GUI: TLSDETAILS WATERS EXCLUDE Adding that to the input script did indeed cause my waters to remain isotropic. The result is slightly unexpected, however: RfactRfree FOM -LL rmsBOND rmsANGL No keywords: 0.2385 0.2884 0.649272372.0.01091.282 TLSO ADDU 0.2385 0.2884 0.649272372.0.01091.282 TLSDETAILS WATERS EXCLUDE + TLSO ADDU 0.2393 0.2903 0.685272462.0.00991.223 It doesn't surprise me that the R factors are slightly different (0.3% change) depending on whether the waters are included in the TLS treatment. But why does the geometry change? And in particular why such a relatively large change in FOM? (6% change) Request: I think the GUI needs a tick box for the include/exclude waters option, if only so that the user is aware of what's going on. It is IMHO very bad that nowhere in the PDB file or even the refmac log file is there any record of _which_ TLS group a water was placed in. This is a defect in the current PDB ATOM record format! We really need a field that says I belong to TLS group #N. Ethan My structure was refined using a pure TLS model. That is, all Biso terms for protein atoms were fixed at the Wilson B, and then refmac refined the TLS parameters and an overall aniso B correction. I took my previous final refinement run in refmac, added the TLSO ADDU keyword to the input script, and reran it. So now I have two parallel PDB files: the first one produced by refmac/tlsextract/tlsanl (no TLSO option) the second one produced by refmac (TLSO ADDU option) The BISO and ANISOU records in these are not quite the same. Not wildly different, but more than I can attribute to round-off error. Even more confusing, the water molecules in the second file have their own ANISOU records. Parvati analysis shows their descriptions are not even close to being isotropic. How/what/why did my waters get subject to aniso refinement? They are not part of any TLS group, and I didn't ask for any individual B refinement of any sort! -- Ethan A Merritt Biomolecular Structure Center University of Washington, Seattle 98195-7742 -- Ethan A Merritt Biomolecular Structure Center University of Washington, Seattle 98195-7742
Re: [ccp4bb] Multiple conformations of disulfide-linked cysteines
I have a similar situation so I am also curious for the answer. Refmac will always try to form a disulfide bond with both conformers for me as well. On Mon, Mar 8, 2010 at 4:55 PM, Critton, David david_crit...@brown.eduwrote: Dear CCP4BB, I am building a protein structure containing a pair of cysteines linked via disulfide bond. This disulfide bond (i.e. the cysteine S-gamma atoms) refines well at 2/3 occupancy, however the electron density suggests that these cysteines each adopt a second, unlinked conformation (presumably at 1/3 occupancy). I have no trouble building the alternate conformers; however, refinement causes both conformers to disulfide-bond. I would like to know if there is a way (and how) to specify individual conformers (or individual atoms) in the SSBOND record of a PDB. Thank you in advance, David A. Critton Graduate Student, Page Laboratory Department of Molecular Biology, Cell Biology Biochemistry Brown University Providence, RI -- Jim Fairman, Ph D. Post-Doctoral Fellow National Institutes of Health - NIDDK Cell: 1-865-748-8672 Lab: 1-301-594-9229 E-mail: fairman@gmail.com james.fair...@nih.gov
[ccp4bb] python install issues?
Hi, I'm simultaneously installing ccp4 on a MacBook Pro running Snow Leopard and on a MacPro running Leopard. On both machines, the command: source /sw*/bin/init.csh (where /sw* is either /sw64 on the machine running 10.6, or /sw on the machine running 10.5) gives the error: *** Fatal Error: Incomplete libtbx environment! *** Please re-run the libtbx/configure.py command. I've seen this phenomenon mentioned on the ccp4bb before, but I'm not clear on how those earlier posts relate to my current situation (alright, to be honest, I didn't really understand the previous posts). Details:Installing ccp4-6.1.2 using either fink or precompiled binaries from UC SantaCruz (thanks again, a thousand times, to Bill Scott!) One machine has python 2.5.1, the other has 2.6 Any help welcome. Thanks, Pat --- Patrick J. Loll, Ph. D. Professor of Biochemistry Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pat.l...@drexelmed.edu
