Re: [ccp4bb] how to model glycosylated residues?

Hi Jiamu, You can use Sketcher to make the library for Coot. You'd better to get the PDB file from http://www.dkfz.de/spec/glycosciences.de/tools/pdbcare/ . Good luck! liu Jiamu Du wrote: Thanks for all the replies above. I have pasted the figure of the electrondensity map in the attachment.

Re: [ccp4bb] How to refine large moleculars?

Have you tried TLS and NCS? Maybe these can lower the R free a little. But ,the quality of your model depends on the quality of your data and completeness of your model etc. Yongchao Li wrote: I have a large molecule to refine.There are about three thousand residues in one asymmetric unit.

[ccp4bb] REFMAC 5.4.0034

I keep finding that the Refmac version from 5.4.0034 is more stable at least with full anisotropic refinement at 1.35 Å resolution. The R- factor stays relatively similar and there is a slow decrease of R- free with R-work. It doesn't jump around compared with an identical refinement in

[ccp4bb] Any programs other than GRASP have a surface scribing function?

Dear CCP4'ers, Any Windows/Linux/OS X programs have a surface scribing function similar to that found in GRASP, to quickly draw the border of a surface selection (or subset) and calculate or display local features of the molecular surface? I have no access to SGIs now. I have a memory

Re: [ccp4bb] Any programs other than GRASP have a surface scribing function?

I have used CCP4MG to produce a molecular surface of the model that i have been working on. There is an example in the online documentation to produce a molecular surface for the entire molecule or for a subset of atoms, and color it by solvent accessibility or other properties. It produces

Re: [ccp4bb] Any programs other than GRASP have a surface scribing function?

You can use APBS plugin in PyMol. See installation instruction at http://www-personal.umich.edu/~mlerner/PyMOL/ or http://www.pymolwiki.org/index.php/APBS Holly Date: Tue, 8 Jan 2008 14:01:02 -0600 From: [EMAIL PROTECTED] Subject: [ccp4bb] Any programs other

Re: [ccp4bb] DNA contamination post-Talon?

DNA carry-through in protein purification is quite common, especially if you are working with basic proteins. A Talon step certainly doesn't guarantee the removal of nucleic acid, and large fragments will certainly run in the void volume of your gel-filtration column. You can try washing the

Re: [ccp4bb] Any programs other than GRASP have a surface scribing function?

Just to add to that, on OS X, if you install the apbs and pymol packages via fink, everything will be set up for you. I think this is also true of at least Ubuntu and other debian linux varieties. As far as I am aware, the plugin is not compatible with the non-X-windows PyMOL on OS X. On Tue,

[ccp4bb] nCNS - neutron diffraction patch for CNSsolve 1.1 has been released.

=== *nCNS* 1.0.0 software Release === Software *nCNS* version 1.0.0 has just been released. *nCNS* is a patch for CNSsolve V1.1 http://cns.csb.yale.edu/v1.1/, combining for the

[ccp4bb] Drug target crystallography and virtual discovery course, PSP Jan 21-22 2008

Dear All, we still have a few places open for a 2-day pre-conference training course ahead of the Advances in Protein Crystallography 2008 conference. Palm Springs is nice in winter and the APC is right before the Lab Automation 2008 meeting. I teach the crystallography part and Katherine

Re: [ccp4bb] how to model this density?

Thank you all. I have build a (NAG)2MAN core sugar chain into the density. It seems more MAN can be fit into the density. On Jan 9, 2008 5:07 AM, Li Zhijie [EMAIL PROTECTED] wrote: Hi Jiamu, I think you can safely say that it is an N-linked glycan. To model the sugar, check COOT's get