Shane
Atwell
From: Judith Murray-Rust [mailto:[EMAIL PROTECTED]
Sent: Thursday, September 07, 2006 3:54 PM
To: Shane Atwell
Subject: RE: [ccp4bb]: Getting MR solutions that have the molecule in the same spot as an existing structure
Havr you tried ccp4 (unsupported program) reforigin ?
Probably not in the GUI....
J
-------------------
Judith Murray-Rust
Structural Biology Lab
Cancer Research UK
-----Original Message-----
From: [EMAIL PROTECTED] on behalf of Shane Atwell
Sent: Thu 07-Sep-06 10:08 PM
To: James Irving
Cc: ccp4bb@dl.ac.uk
Subject: RE: [ccp4bb]: Getting MR solutions that have the molecule in the same spot as an existing structure
I don't mind doing MR, its just much more convenient for downstream
manipulation to have the solution in the same symmetry position in the
unit cell in the case that it is the same crystal form. So I'm looking
for a way of either not doing MR, or doing MR and then automatically
moving the solution to the equivalent position as the parent using
symmetry operators.
If such a tool exists it would be nice for manipulating deposited
structures as well, since I have run across structures in the pdb of the
same protein in the same crystal form with different bound compounds but
with the molecules in different symmetry positions, forcing you to do an
lsqfit or symgen to compare them.
Shane
________________________________
From: James Irving [mailto:[EMAIL PROTECTED]]
Sent: Thursday, September 07, 2006 1:38 PM
To: Shane Atwell
Cc: ccp4bb@dl.ac.uk
Subject: Re: [ccp4bb]: Getting MR solutions that have the
molecule in the same spot as an existing structure
Dear Shane,
Why do you want to avoid performing an MR step with the new
crystal? If you are having trouble applying a solution from one crystal
to another it may be that the two datasets haven't been indexed
equivalently, depending on the space group of course. Try alternative
indexing schemes using the REINDEX program in ccp4i. Also I've seen a
couple of situations where subtle differences in unit cell dimensions
have reflected the fact that the two crystals really aren't isomorphous.
In my opinion (which may not be echoed by more learned
crystallographers) it is best to let each crystal "speak for itself"
rather than trying to force a solution by restricting the search space.
Cheers,
James
On 07/09/06, Shane Atwell <[EMAIL PROTECTED]> wrote:
When solving structures that are the same crystal form
as a parent, what's the best way of getting or moving the solution to
the same position as the parent? This is for cases where a typical rigid
body refinement isn't sufficient to pull out the solution.
It is not very convenient to look at the parent and the
solution and then fix the solution using pdbset symgen, at least for
dozens or hundreds of structures.
I've tried using beast to do the MR in a small box
around the parent solution, and it works, but takes a long time even for
a 'small' search area (e.g. 10 degrees and 2 Angstroms).
Its possible that doing the rigid body refinement w/
lower res data could pull in solutions that are further off, but I doubt
it would be very robust..
It also seems possible to use contact or a similar
program to find which symmetry molecule of the solution 'clashes' with
the parent solution. I'm toying with this, but haven't gotten it to work
yet.
Short of custom modification of the MR program, is there
something available that I'm missing?
Shane Atwell
--
Dr. James Irving
NH&MRC C.J. Martin Fellow
Division of Structural Biology
Wellcome Trust Centre for Human Genetics
Oxford University
Roosevelt Drive
Headington,
Oxford OX3 7BN
UK
email: [EMAIL PROTECTED]
phone: +44 1865 287 550
