On 02/15/2011 04:36 PM, vineet joshi wrote:
Dear CCP4ers,
Is there any specific way that can help me locate the interactions between
ligand (GTP) to any other residue in the protein(GTPase) using CONTACT. And
how do I run CONTACT for a number of .pdb files(around 650) in one single
step and separate them based on their interactions without running it
individually for each of the .pdb file. The latter method is too time
consuming so I need something quicker. Also, I am unable to get access to
the script file for contact. Can someone please help me in this regard.
Regards,
Vineet Joshi
Have you looked at the PISA files held at the EBI for every structure.
These should include the ligand-protein interfaces already calculated.
Or if you look at the GUI and call up contact for one pdb
You will get a script like this:
ncont XYZIN
"/y/people/ccp4/projects/sinRbit/SinR-C_rem-inf-pk-shel-nat_buccaneer3-sym1-coot-3_lsq2.pdb"
source "A/*"
target "B/*"
mindist 0.0
maxdist 5.0
cells OFF
END
That would give contacts between chains A & B
I can see no automatic way of identifying how ligand and protein are
labelled in your 600 GTPases though..
Eleanor
