[ccp4bb] problem of conventions

ied? With best wishes, Anita Anita Lewit-Bentley Unité d'Immunologie Structurale CNRS URA 2185 Département de Biologie Structurale & Chimie Institut Pasteur 25 rue du Dr. Roux 75724 Paris cedex 15 FRANCE Tel: 33- (0)1 45 68 88 95 FAX: 33-(0)1 40 61 30 74 email: ale...@pasteur.fr

[ccp4bb] buccaneer crashes

Dear CCP4 folks, I am trying to run Buccaneer to build a substantial part of my structure: I have a model for one protein domain, but not for the other, though there is clear density for it in a MR-Buster map. I'm using CCP4 6.1.13 on a Mac-Pro under OS X 10.5.8 with a CCP4Interface 2.0.6

Re: [ccp4bb] Arp/wArp error

these annoying obstacles can get removed from the path of - otherwise really happy - CCP4 users! Thanks again, Anita Bonne chance Jan On Tue, Dec 1, 2009 at 8:41 AM, Anita Lewit-Bentley wrote: Dear all, I have a nice MAD map produced by Sharp and would like to trace a chain into it

[ccp4bb] Arp/wArp error

2 and Arp 7.0.1, with the CCP4Interface version 2.0.5 running on Mac OSX version 10.5.8. Any advice will be extremely welcome! Anita Anita Lewit-Bentley Unité d'Immunologie Structurale CNRS URA 2185 Département de Biologie Structurale & Chimie Institut Pasteur 25 rue du Dr. Roux 757

[ccp4bb] packing diagrammes

Dear all, thanks to everybody who offered their experience and hints. The most convenient way of preparing a packing diagramme, at least for me, was via PyMol as suggested by Michael Klein (see below). One can do something similar with the CCP4 graphics package, but for some reason the pro

[ccp4bb] packing diagrammes

so as to visualise the continuity of solvent channels etc. Thanks for any leads! Anita Anita Lewit-Bentley Unité d'Immunologie Structurale CNRS URA 2185 Département de Biologie Structurale & Chimie Institut Pasteur 25 rue du Dr. Roux 75724 Paris cedex 15 FRANCE Tel: 33- (0)1 45 68

Re: [ccp4bb] LSQKAB error

side effect of forcing the program to read in the XYZINF input file. Norman From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Anita Lewit-Bentley Sent: 16 March 2009 14:59 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] LSQKAB error Dear all, I am trying to compare several

[ccp4bb] LSQKAB error

sion of the programme somewhere? If not, what other programme could do the same thing (in a simple way...)? Thanks for any suggestions! Anita Anita Lewit-Bentley Unité d'Immunologie Structurale CNRS URA 2185 Département de Biologie Structurale & Chimie Institut Pasteur 25 rue du Dr.

Re: [ccp4bb] TLS refinement in Refmac gets stuck

pe along if I remember to copy the .tmp files accross to my working directory. Better than nothing! Thanks for your hint. Cheers, Anita -Original Message- From: owner-ccp...@jiscmail.ac.uk [mailto:owner- ccp...@jiscmail.ac.uk] On Behalf Of Anita Lewit-Bentley Sent: 23 Febru

[ccp4bb] TLS refinement in Refmac gets stuck

Any help will be appreciated! Thanks, Anita Anita Lewit-Bentley Unité d'Immunologie Structurale CNRS URA 2185 Département de Biologie Structurale & Chimie Institut Pasteur 25 rue du Dr. Roux 75724 Paris cedex 15 FRANCE Tel: 33- (0)1 45 68 88 95 FAX: 33-(0)1 40 61 30 74 email: ale...@pasteur.fr

[ccp4bb] more REFMAC problems

the end, one has to edit the pdb file output by Coot before running Refmac - not very automatic. Best wishes for Christmas and the New Year, anyway! Anita Anita Lewit-Bentley Unité d'Immunologie Structurale CNRS URA 2185 Département de Biologie Structurale & Chimie Institut Pas

Re: [ccp4bb] Atom labels in PDB file for Refmac

Thanks to all who answered - and so fast! - MET residues should become MSE (i.e. Se-MET instead of S-Met) - ' SD ' atom name should become 'SE ' - remove the columns 77-80 I had changed S to SE and that's fine Simply using an editor I changed the pdb file - and it works!! Thanks again, A

[ccp4bb] Atom labels in PDB file for Refmac

introduce the Se atom within the Met residue, so as to provide a correct description of the molecule. What format/syntax should I use for Refmac to recognise it? SED (with SE in he last column) does not work, nor does just simple SE left- shifted. Thanks for any hint! Anita Anita Lewit