Hello All,
I have two questions about refinement with Refmac5.
1. I have a protein structure that is C-terminally amidated. What is
the best way to handle this?
I was trying to use the sketcher to create my own library definition for
the modifed amino acid, but then I had issues with the mo
On Saturday 21 July 2007 11:12, Joe Krahn wrote:
> we all use in our daily research. They don't even want to keep the PDB
> format at all. It's primary purpose now is for structural biologists.
That is inevitable. The PDB format is simply not capable of representing
the complexities of current cr
On Sat, Jul 21, 2007 at 05:22:42PM +0100, Winter, G (Graeme) wrote:
> ... or alternatively just start something on wikipedia?
Wikipedia actually has a policy against articles that are too technical in
nature, so it might not be the appropriate place for this kind of content.
http://en.wikipedia.o
The new PDB format (version 3) has a lot of very useful improvements,
and an update is long overdue. However, I am irate that RCSB chose NOT
to use the ACA meeting to discuss the changes. Instead, the format is
being put into production at the same time as the ACA meeting. It is
essentially stating
I would happily contribute to this, and migrate anything relevant from my
own stuff. I think this could be a very valuable resource. The PyMOL
wiki is a good example of what could be done. The main requirement for
success I think is having a few dedicated users who want to see it
succeed. We shou
Hi!
A crystallography wiki was discussed at the last CCP4 developers
meeting, and I've been looking into it.
Setting up a wiki is not hard, but keeping it up-to-date and secure is.
(We've had problems with this at York, where we've been running one for
a few years). Therefore I suggest it is
... or alternatively just start something on wikipedia?
Just MHO - thought a few times something like this would be useful.
Cheers,
Graeme
From: CCP4 bulletin board on behalf of Kay Diederichs
Sent: Sat 21/07/2007 3:23 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [
So - rather than repeat things that are obvious to some people, would it
not be good to have a crystallography-FAQ that one could point people
to? This should be part of a Wiki where "we crystallographers" could
collect our wisdom. This would be much more systematic, and less
volatile, than the
Sorry for the cliche, but the goal of refinement is not to reduce R
factors, but to produce a good model.
ARP/wARP uses the 'WEIGHT AUTO' option of REFMAC5 to get a good
geometry.
You should set the weight to a value that produces 1-2 and 1-3
distances rms deviations similar to the ARP/wARP
