I suppose you mean residue-residue contact maps. Some possible tools are:
- Chimera (
https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/rrdistmaps/rrdistmaps.html
)
- CMView (http://bioinformatics.org/cmview/)
- CoCo maps, web based (https://www.molnac.unisa.it/BioTools/cocomaps/)
- CMweb, web based (http://cmweb.enzim.hu/)
Hope it helps
Jose
On Thu, Sep 22, 2016 at 7:05 AM, Martyn Symmons <[log in to unmask]>
wrote:
> 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
> >>
> >>
> >
> >
>
