[Chimera-users] concatenate

Elaine Meng meng at cgl.ucsf.edu
Wed Mar 4 07:34:05 PST 2015


Dear Yeping Sun,

How you can refer to one chain or the other depends on how they are described in the input coordinate file (usually a PDB file).  If they are chains A and B you could use commands like:

color red :.A
color gold :.B

Or, maybe they are not different chains but different residue numbers, in which case you would have to use the residue numbers, something like:

color red :1-30
color gold :31-60

If you open one copy of the helical atomic structure, Chimera’s “sym” command can open more copies to make a longer helix, but you would have to somehow tell it the correct symmetry information.  This can be done with the “group” option of that command.  You can give helical symmetry directly (see the example in the manual page, link below) or, if your density map has the symmetry already assigned to it, you can just give its model number, e.g. “group #1” if the map is model 1:

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

It might be hard to figure out the symmetry yourself.  You could try having Chimera guess the symmetry of the map with “measure symmetry” command, but because it is more difficult for helical symmetry, you would still have to specify approximate parameters as input to that command:

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#symmetry>

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 Mar 3, 2015, at 11:14 PM, sunyeping <sunyeping at aliyun.com> wrote:

> Dear all,
> 
> I am dealing with a EM map which is a double helical filament and composed of two protein chains winding each other. Each of the two chains is composed of multiple same protein subunits. Now I am trying to color one chain of the map with one color, and the other chain with another color. How should I do that?
> 
> Besides, it is known that multiple such double helixes can constitute a longer helix by a head-to-tail way.  I can open several helixes in chimera, but how to concatenate they correctly into a long helix?
> 
> Could you help me with these questions?
> 
> With many thanks!  
> 
> Yeping Sun
> 
> Institute of Microbiology, Chinese Academy of Sciences




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