[chimera-dev] Intersurf QUESTION

[Elaine Meng]

Hi Nicolas,
We're glad you like Chimera!

There isn't an existing option to save the Intersurf histogram, so it would have to be done with Python scripting (beyond my skills, sorry… someone else may need to respond about that). 

However, you could use Find Clashes/Contacts (or command "findclash") instead of Intersurf if your goal is to get a list of contact distances between two sets of atoms.

You can specify the two sets of atoms and then save information to a file.  For example, the following commands would do that for contacts between 1zik chain A (peptide part only, not the water) and chain B (peptide part only, not the water):

open 1zik; preset apply int 2
findclash :.A&protein test :.B&protein overlap -1 hbond 0 saveFile ~/Desktop/contacts.txt

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>
You can do the same things with the GUI, it would just take me more typing to describe.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html>

The information in the text file includes the atom names, their VDW overlap (which can be negative if their VDW surfaces are separated), and the distances between the atom centers.  The lines are ordered by decreasing overlap, and you can get longer and longer distances by specifying a more negative overlap (e.g. overlap -2 instead of the -1 in the example command above).  The output looks like this:

Allowed overlap: -2
H-bond overlap reduction: 0
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True

633 contacts
atom1  atom2  overlap  distance
LEU 5.A CD1   MET 2.B CE    0.769  2.991
MET 2.A CE    MET 2.B CE    0.761  2.999
MET 2.A CA    MET 2.B CE    0.707  3.053
[… etc. …]

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco



On Nov 5, 2013, at 9:46 AM, niko <nicolas.papageorgiou at afmb.univ-mrs.fr> wrote:

> Hello,
> I use CHIMERA since several years. Thank you very much for this excellent program
> MY QUESTION : Is it possible to save the ASCII file of the histogram generated by the "intersurf" calculation between two molecules ?
> Thank you very much  
> Nicolas Papageorgiou.