[Chimera-users] Problems with binding site representation

Elaine Meng meng at cgl.ucsf.edu
Fri Nov 8 13:05:42 PST 2013


Aha, here's the correct command to remove the smaller blobs.  I had omitted the "metric" option:

sop hideDust #1,2 size 1 metric sizeRank

Elaine

On Nov 8, 2013, at 11:14 AM, Elaine Meng wrote:

> Hi Vigneshwari,
> I'm guessing you want to have different colors for the inside and outside of the surface.
> 
> The probe radius and vertex density only affect the shape and smoothness of the surface. To show different inside/outside colors you have to do some trickery that includes making two surfaces, one offset from the other, and coloring the two surfaces differently.  If you click the Image Gallery entry to see the larger image,
> 
> <http://www.cgl.ucsf.edu/chimera/ImageGallery/entries/pocket/pocket_2zcp.html>
> 
> ... it says a little more about how the image was made.  It mentions commands "measure contactArea" to make the offset surface patches and "sop hideDust" to get rid of disconnected bits of surface. The details aren't given (and I didn't make the image myself), but here is a series of commands from my attempt to reverse-engineer the image:
> 
> open 2zcp
> delete :.b
> split atoms :fps
> surface
> 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
> ~surf #0
> show :fps | ions
> ~ribbon
> color white,a C
> back solid dim gray
> set silhouette
> 
> The split command splits the ligand FPS residues into model #0.1, the remaining atoms into #0.2  Then I show surfaces for both of those and then use "measure contactArea" to create new surfaces #1 and #2 that are just the contact patches from the original surfaces.  Then I hide the original surfaces (#0), hide ribbons, show only the FPS and ion atoms, etc.
> 
> The main limitation of this whole process is that you need a binding partner that can be split from the other atoms and used to define the pocket region.
> 
> Also, one remaining problem in reproducing the image is that there are disconnected extra blobs of surface that I thought should be removed by the following command, but aren't.  We may need to get back to you about that step.
> 
> sop hideDust #1,2 size 1
> 
> Well, there is one other minor problem.  The splitting removed the purple dashed lines between the ligand and ions because now they are in different models from each other (#0.1 and #0.2).  You could fake their presence by opening another copy of the whole structure and hiding all of it except its FPS and ions:
> 
> open 2zcp
> delete #3:.b
> ~ribbon #3
> show #3:fps,mg
> rep wire #3
> 
> Resulting image with only the extra-blobs problem remaining is attached below.
> 
> You can see the manual pages for the individual commands with more details of what they do and their options by using the help command (for example, "help split") or clicking the respective links from here:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html>
> 
> 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 8, 2013, at 5:05 AM, vigneshwari subramanian wrote:
> 
>> Dear all,
>> I have been trying hard to make a figure similar to the one shown in this web page.
>> 
>> http://www.cgl.ucsf.edu/chimera/ImageGallery/
>> 
>> I would like to have 2 different colours to represent the inner and outer surfaces of binding site. I opened 2 different structures of the same protein and adjusted the surface parameters (probe radius and vertex density) . But that doesn't seem to work.
>> 
>> I would be really happy if someone can help me to sort out this issue.
>> thanks,
>> vigneshwari
> 
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