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And if you want to know what actually contacts what then you can try
CONTACT program in CCP4 which was mentioned a few weeks back.

Or how about the UCSF Chimera command 'findclash' which will print out
contacting atom pairs and show pseudobonds.
https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/findclash.html
For example if you have several chains then the command:

findclash :.o test other overlapCutoff 0.0 hbondAllowance 0.0 saveFile browse

would find contacts of chain o with other chains based on van der
Waals radii (haven't tried it with explicit hydrogens).
('saveFile browse' gives a dialogue to save the results to a file.)

I have been parsing the results from that file, grouping by residue,
and plotting a 2D contact plot: chain 1 residues versus chain 2.

Usually I set overlapCutoff to be negative in case there is something
interesting 'hovering' close but not in actual contact (or maybe
bouncing off given its B-factor....)

All the best
 Martyn

PS Chimera's command line is launched from the menu 'Favorites'

Martyn Symmons
Cambridge


On Thu, Sep 22, 2016 at 2:24 PM, Eleanor Dodson
<[log in to unmask]> wrote:
> Do you mean contacts between molecules. PISA dos that - available at PDBe or
> in CCP4 suite
> Eleanor
>
> On 22 September 2016 at 13:44, Reza Khayat <[log in to unmask]> wrote:
>>
>> Hi,
>>
>>
>>
>> Can someone suggest a program for generating intermolecular contact maps
>> in a PDB file? Thanks.
>>
>>
>>
>> Best wishes,
>> Reza
>>
>>
>>
>> Reza Khayat, PhD
>>
>> Assistant Professor
>>
>> Department of Chemistry
>>
>> City College of New York
>>
>> 85 Saint Nicholas Terrace, CDI 2.318
>>
>> New York, NY 10031
>>
>> http://www.khayatlab.org/
>>
>> 212-650-6070
>>
>>
>
>