*** For details on how to be removed from this list visit the ***
*** CCP4 home page http://www.ccp4.ac.uk ***
OK, here's a program that does roughly what you want:
symsup 1.pdb 2.pdb
takes each chain from the second pdb (or mmCIF) and moves it so that the
COM of the chain is as close as possible to the COM of the first pdb.
The result is written out as symsup.pdb
This usually gives the right answer, but occasionally a chain will be
misplaced for very extended molecules. A better solution would be to
look for the RMS difference from the atoms of the moving chain to the
nearest corresponding atoms of the stationary molecule.
To compile this you need clipper 2.0. Alternatively I've put Linux and
OSX binaries here:
http://www.ysbl.york.ac.uk/~cowtan/ftp/symsup.tar.gz
Kevin
P.R. Evans wrote:
*** For details on how to be removed from this list visit the ***
*** CCP4 home page http://www.ccp4.ac.uk ***
This is a useful function if you are trying to compare different models
from wherever, eg molecular replacement (indeed I think it's sort of
buried in Phaser, probably using EMMA)
O, coot & ccp4mg have some of the functionality, but not quite.
I've just used a combination of manual testing in ccp4mg & pdbset, but
also tried Eleanor's distang/pdbset method which also works
Phil
--On 15 May 2006 12:29:52 +0100 Kevin Cowtan <[EMAIL PROTECTED]>
wrote:
IIRC Paul wrote a globularise function in coot which will do what you
want - you give it a position in real space where you want the thing
positioned, and it will shift everything. This probably doesn't involve
writing out symmetry coordinates, so should still work if the code exists
in the current version. But you'd have to check with Paul.
Failing that, I already have code in buccaneer to do per-chain flipping
about crystal space. It would take an hour or so to write a utility to do
exactly what you are asking for automatically. If anyone else is
interested in such a utility, speak now and I'll do it.
Kevin
Phil Evans wrote:
*** For details on how to be removed from this list visit the ***
*** CCP4 home page http://www.ccp4.ac.uk ***
Is there a program somewhere which will give me the best symmetry
operation to superimpose two molecules? I'm trying to compare
different autobuilds where the different programs have built different
asymmetric units (sometimes for different fragments). The residues
numbering is random of course.
I've tried
Coot, but the writing out of symmetry-related coordinates
is currently broken,
ccp4mg but I don't seem to be able to get symmetry-related neighbours
of molecule 1 (say) around the position of molecule 2, only around its
own position
any suggestions?
Phil
