[Chimera-users] surfaces and

Elaine Meng meng at cgl.ucsf.edu
Wed Jun 3 16:06:04 PDT 2015


Dear Prof. Szabo,
I believe that even though you had hidden the other parts, Chimera was still trying to make a surface of the whole thing.  

I see from the RCSB PDB information that chain 7 is the signal sequence, chain 8 is the SRP RNA, and chain 9 is the SRP 54 protein.   Here are some example commands to show just the surface around the SRP 54 protein (you can show the command line using menu: Favorites… Command Line):

open 2j28
~ribb
~disp
disp :.7-9
focus
surfcat srp :.9
surf srp

… those commands open the PDB file, hide ribbon, hide atoms, show atoms of chains 7-9 only, define a set named “srp” of atoms you want to group into one surface, then show the surface for that “srp” set (you could have named it something else).  If you didn’t want to show the RNA and signal sequence, you would just “disp :.9” (show chain 9 only) instead of “disp :.7-9” (show chains 7-9).

This will probably work on your computer.  If the surface still fails, however, there are different kinds of surfaces you could use instead.  Several workarounds for surface failures are listed in this manual page:

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html>

I already described method #1 from that page, but if that didn’t work, the others I had in mind are mentioned as method #3. 

Method 3A: use “molmap” command, for example commands to do this for chain 9 if you already opened 2j28:

molmap :.9  4  gridSpacing  0.5

You could try different values of the parameters to adjust the appearance of the surface, and adjust the “contour level” of the isosurface by dragging the vertical bar in the histogram in the Volume Viewer dialog that will appear when you use the command.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html>

Method 3B:  use Multiscale Models (in menu under Tools… Higher-Order Structure) to make a separate low-resolution surface for each chain.  Start the tool, click Make Models, then use the dialog to show just the surfaces you want, change coloring, surface resolution, etc.  
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemulti.html>

When I tried this on 2j28, chain 9  was the green blob, but I’m not sure it always picks the same set of initial colors.
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 Jun 3, 2015, at 1:17 PM, A G Szabo <agszabo at bell.net> wrote:

> I have been working with a very large structure of many subunits, the E.Coli Ribosome particle with the Signal Recognition Particle attached (PDB 2J28)
> 
> 
> I was able to create an image of the SRP part of the complex. I selected that subunit. And was able to hide all the other subunits. So with the subunit selected I tried to visualize only that image as a surface. Wouldn’t let me, getting an error message that it was too large and I should somehow split it.  Don’t know how to do that. I know the whole dataset is very large, but the SRP portion is only 400 amino acids.
> 
> A work around would be if I could somehow select the SRP subunit and have it as a dataset to reload as that subunit alone. Then not so big.  Don’t know how to do that either.
> 
> 
> Your suggestions. I couldn’t find anything in the tutorials that might help.
> 
> I was able to show the surface of another PDB file that was much smaller.
> 
> Arthur G. Szabo
> 
> Professor Emeritus
> 
> Chemistry
> 
> Wilfrid Laurier University
> 
> Waterloo Ontario Canada.
> 
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> Chimera-users at cgl.ucsf.edu
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