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.
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.
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
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
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
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
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
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,
===
*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
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
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
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