Oh dear - Yes you are right
There is an old program called compar
See http://www.ccp4.ac.uk/dist/html/compar.html
Here is the example script. You need the same residue numbering in each,
so if the sequence of the 2 coordinate files is different you will need
to run CHAINSAW to renumber one pdb to match the other.
Then use the LSQKAB output PDB moved to fit the first 100 residues, and
you will get a list for all the residues present
Eleanor
#!/bin/sh
set -e
# Tabulates differences between 2 or 3 sets of coordinates,
# against atom type and B value and residue number.
# COMPARISON OF COORDINATES - ON XYZIN1 XYZIN2 AND PROVISIONALLY XYZIN3.
#CARD 1 - TITLE
#CARD 2 - NSETS - NUMBER OF CORD SETS FOR COMPARISON (2 OR 3.)
#CARD 3 - DELXYZ DELB FOR MONITORING
# RMSTAB is written out - useful for SQUID
# A temporary file called TMPOUT is written.
compar \
XYZIN1 $CEXAM/rnase/rnase.pdb \
XYZIN2 $CCP4_SCR/rnase_out.pdb \
RMSTAB $CCP4_SCR/rnase.rms \
<< END-compar
comparing rnase coordinates before and after refinement
2
3.0 16
END-compar
#
On 11/24/2010 05:54 PM, Huiying Li wrote:
Thanks for your reply, Eleanor.
The problem I had with LSQKAB is that it ONLY outputs the RMSD for the
residue range the superpose calculation based upon. What I wanted is to
superpose the two structures with the N-terminal 100 residues, but
calculate the RMSD for the entire structure (400 residues). Can LSQKAB
do that?
Best regards,
Huiying
Huiying Li, Ph. D
Department of Molecular Biology and Biochemistry
Natural Sciences I, Rm 2443
University of California at Irvine
Irvine, CA 92697, USA
Tel: 949-824-4322(or -1953); Fax: 949-824-3280
email: [email protected]
On Wed, 24 Nov 2010, Eleanor Dodson wrote:
Yes - I think there is a button on the GUI to click?
Eleanor
On 11/24/2010 01:58 AM, Huiying Li wrote:
Another question on RMSD:
I have two structures of the same protein superposed with the LSQ
Superpose in Coot by matching the first ~100 residues of the N-terminal
domain. Now I'd like to calculate the pair-wise RMSD for the entire
pre-superposed structures (~400 residues). Can LSQKAB output RMSTAB for
the two input PDB files without doing its own FIT/MATCH calculation?
Thanks,
Huiying
___
Huiying Li, Ph. D
Department of Molecular Biology and Biochemistry
Natural Sciences I, Rm 2443
University of California at Irvine
Irvine, CA 92697, USA
Tel: 949-824-4322(or -1953); Fax: 949-824-3280
email: [email protected]
