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if you have the cctbx installed, you could use iotbx.emma.
iotbx.emma is designed to compare heavy atom solutions and if you would
supply a full protein, things tend to get a bit slowish
Nothing however stands in your way of selecting manually a small sub set
of CA atoms (say 10 sequence equivalent or so in both structures) and
run emma.
It will provide you with the operators needed to shift your structure.
It is space group general (doesn't depend on setting and takes care of
the continuous set of translations along certain axis in certain
spacegroups)
HTH
Peter
Shane Atwell wrote:
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:* [email protected]
*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]
<mailto:[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] <mailto:[EMAIL PROTECTED]>
phone: +44 1865 287 550
