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@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