for the alt conf when you add it back in, which is
neat).
I'd be extremely grateful for any help to resolve this!
Thanks in advance
Isaac Westwood
I find that the superposition in CCP4MG is the most flexible and easy to
use implementation of any program I've used. There are multiple
superposition methods each with the ability to select residues or atoms.
It's very powerful.
CCP4MG also happens to produce very pretty pictures!
Isaac
On 5 Feb
In addition to the previous suggestions, if you have a metal-binding
protein, beware of acidic compounds chelating the metal and stripping it
out of the protein, as this often lead to the effect you observed as well.
Isaac
On 5 Feb 2015 13:45, Monica Mittal monica.mitta...@gmail.com wrote:
Hi
Dear Lu Zuokun,
There are several methods you can use to locate these problem residues.
Here are 3:
a) manually step through your PDB file in coot (good practice anyway, this
is fundamentally what we as crystallographers should be doing when we are
model building)
b) identify waters with close
Dear Shanti Pal,
did you use ethylene glycol as cryoprotectant? It may even be there in
small amounts in your PEG400 solution. As Nicholas and Tony have said, this
could be noise (or could be distorted due to noise) as it's on a 2-fold
axis. From those pictures, it looks to me like one molecule
(or protein) atom has been modeled
into a region with no density.
Best,
Isaac Westwood
On 13 June 2014 11:35, Robbie Joosten robbie_joos...@hotmail.com wrote:
Hi Tim,
The problem with missing atoms in ligands is that you cannot use the
coordinates for any follow-up calculation that requires ligand
mentioned!
Isaac
--
Dr Isaac Westwood
Department of Pharmacology
University of Oxford
Mansfield Road
Oxford
OX1 3QT
tel: 01865 271595
email: [EMAIL PROTECTED]
_
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Rajan
Pillai
Sent: 15 January 2008 21:40
Also VOIDOO is an excellent program for this.
HYPERLINK
http://xray.bmc.uu.se/~gerard/manuals/voidoo.htmlhttp://xray.bmc.uu.se/~ge
rard/manuals/voidoo.html
Isaac
_
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Rajan
Pillai
Sent: 13 December 2007 22:45
To:
I'm a fairly inexperienced crystallographer, but I have worked on a few
cases very recently (from separate protein systems) in which the ligand was
not clear in the electron density until quite a long way through
refinement: in the latest case, it wasn't possible to be too confident of
the