[Chimera-users] Question

[Eric Pettersen]

On May 19, 2006, at 6:46 AM, szklars2 at tcnj.edu wrote:

> Hello. My name is Anne Szklarski and I am a student at The College  
> of New
> Jersey. I was wondering if there was a way that the python files  
> could be
> modified in notepad. Does it require the Python software? The  
> reason I ask
> is because I have been renaming certain atoms in the .ent files using
> notepad so that I may specifically select them in chimera. The only
> problem with my current method is that I have to start the rendering
> process from the beginning which is quite time consuming. So I was
> wondering if there was a way that I could alter the chimera file  
> directly
> and not lose any of the colors, etc. that I have chosen. I  
> appreciate any
> information on this matter.
>
> Thank you,
> Anne Szklarski

Dear Anne,
	The answer is yes, but it is awkward and many editors will choke on  
the long lines in most session files.  I am thinking there must be a  
better way to accomplish what you want to do without editing the  
session.  Perhaps you could give a little more detail on the context  
in which you are having trouble referring to specific atoms?
	I'm going to guess that we're talking about the command line (and  
let me know if I'm wrong).  In the command line, you can color red  
atom CA of residue 14, chain A in model 0 with:

	color red #0:14.a at ca

if you only have a single model open, then this will do:

	color red :14.a at ca

If the difficulty is that you are having trouble remembering the  
syntax of atom specifiers (the ':14.a at ca' thing), you can use the  
'alias' command to give it a more mnemonic name:

	alias ca14 :14.a at ca

then henceforward the alias can be used in commands:

	color red ca14

Aliases are remembered in session files, so if you open your old  
session, create an alias, and save a new session, the new session  
will have the alias in it.

If the trouble is that you have duplicate atom names in the same  
residue (some small molecules are like that), then you could refer to  
them by serial number (the first number after the ATOM or HETATM),  
like so:

	color red @/serialNumber=525

and you could again use an alias to make that more mnemonic.

If I'm totally whiffing on guessing what the problem is, please fill  
me in!

--Eric