[Chimera-users] Problems with binding site representation

vigneshwari subramanian vignesh.bioinfo at gmail.com
Mon Nov 11 05:48:39 PST 2013


Hi Elaine,
Sorry to bother you again.

I tried to generate a similar figure for the PDB id: 1U19. I am interested
in showing the surface around the ligand Retinal which is covalently bound
to rhodopsin.

The surface shown here looks a bit weird. Kindly check the attachment. Only
part of the surface around the ligand is shown. Moreover the cavity remains
closed.

I don't know how to adjust the parameters. I tried many options. But I
couldn't extend the contact area so that it covers the whole ligand.

Are there any options to do the same for apo structures?

Thanks,
vigneshwari




On Sat, Nov 9, 2013 at 6:09 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Vigneshwari,
> You can see the manual page by using command "help measure" or you can see
> it on our website here:
>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html>
> <
> http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#contactArea
> >
>
> Best,
> 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 9, 2013, at 3:31 AM, vigneshwari subramanian wrote:
>
> > Hi Elaine,
> >
> > Thank you so much for your timely help. I could actually make the same
> figure. I need to do the same for our dataset.
> >
> > It would be really helpful if you can tell me what each of these
> parameters mean. I think you gave an overview. But I would like to know
> what each of these mean.
> >
> > 3 slab -.1,0
> >
> >  measure contactArea #0.2 #0.1 3 slab -.1,0 color tan
> > measure contactArea #0.2 #0.1 2.99 slab -.11,-.01 color cornflowerblue
> >
> > I checked the manual. But I couldn't find any information about measure
> contactArea.
> >
> > I am there in the chimera list.
> >
> > regards,
> > vigneshwari
>
>
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