[Chimera-users] putting multiple structures together in Chimera

A G Szabo agszabo at bell.net
Tue Jul 7 11:54:56 PDT 2015


Elaine

Thank you very much for your prompt reply. The time difference between the west coast and here helps me.  Thanks

I think have it figured out but if I run into any snags I'll get back to you.

art

-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Sent: July-07-15 2:50 PM
To: A G Szabo
Cc: chimera-users at cgl.ucsf.edu
Subject: putting multiple structures together in Chimera

Dear Prof. Szabo,
I’m glad you’ve been able to make at least some of the images you wanted!

You can just open both structure files at the same time in Chimera … there is no need to merge or combine them into a single model. The tricky part is getting the desired relative positioning of the structures.  

Sometimes when there are overlapping sets of atoms, you can do it by simply superimposing those sets of atoms, say with the “match” command, and then hiding (undisplaying) one set of the duplicate parts.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html>

If there aren’t overlapping parts to match, you could just try to put the structures into the correct relative position by hand, that is, by moving one structure at a time with the mouse. When a structure is movable with the mouse, we call it “active” and by default, everything is active.  You can control deactivation/activation, i.e. freezing and unfreezing structures so that only the unfrozen ones will move, using the “A” or “Active” checkboxes in the Model Panel, or with the checkboxes under the Command Line.  You can open the Model Panel and/or show the Command Line from the Favorites menu.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef>

It sounds like you might know enough about the complex structure to use this manual approach.  Of course, the result will be approximate, only as good as your ability to place the structures by hand.  If you meant you wanted some calculation to automatically position one structure relative to the other, sorry, you would need to use some other program outside of Chimera.

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 Jul 7, 2015, at 9:46 AM, A G Szabo <agszabo at bell.net> wrote:
> 
> I am pleased to inform you that I have been using aspects of Chimera that permit me to prepare images of proteins deposited in the pdb.  It was a pleasant surprise to find that the learning curve was not as steep as I thought it might be.  Mind you, there are many aspects of Chimera that I have not yet attempted to use.
> Now I wish to do something that may not be possible to do with Chimera. And I  am not sure where to look in the tutorials.
> I have a ribbon diagram of a protein-RNA complex, PDB 4p3e, two proteins, SRP 19 and SRP68, bound to  a segment of 7SL RNA.
> I can also obtain the structure of another protein SRP54 which also bind to this complex. However, the structure of pdb 4p3e with SRP54 is not available.
> I know where SRP54 should bind to the RNA, and I know which domain of SRP54 binds to the RNA.
> How can I somehow combine the two files, one for SRP54 and the other 4p3e and locate SRP54 onto the 4p3e structure? (not sure it is possible) Of course crystallographers know how to achieve this structural combination. I don’t have a clue.
> I checked the tutorial list and the closest I seemed to come was the Merge  command.  However, the tutorial did not seem to deal  with what I wanted to do.
> Thank you in advance for your assistance.
> Arthur G. Szabo Ph.D.
> Professor Emeritus, Chemistry
> Wilfrid Laurier University
> Waterloo, Canada.





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