[Chimera-users] HIV ligands

Eric Pettersen pett at cgl.ucsf.edu
Tue Jan 31 15:29:55 PST 2012

On Jan 30, 2012, at 5:27 PM, Forbes J. Burkowski wrote:

> Hi:
> I think I have found a bug or least a small inconsistency...
> If you fetch 3NDW and do the menu invocation:
> Select... Residue...
> The list in the submenu offerings includes RIT.
> In a command line, I can use:
> sel :RIT
> to get the same selection.
> Now, repeat the above invocations for 2FDE.
> The Select... Residue... leads us to believe that the ligand can be
> accessed as 385.  But when I use:
> sel :385
> I do not get a selection.
> This alternate strategy to do the selection is important for me  
> because I
> am getting the same problem when I put this command into the  
> runCommand
> string within a script.
> The same problem seems to exist for 3SM2 and 3SO9.  Both have the  
> ligand
> designated by a number so I have a suspicion that one must do  
> something
> different in the sel command when a number is used to designate the  
> ligand
> instead of a character triplet (such as RIT).
> Is this a bug or am I missing something in the syntax of the sel  
> command?

Hi Forbes,
	Pedantically speaking, the single-colon (e.g ":532") syntax takes a  
residue sequence number afterward, whereas the lesser-known double- 
colon syntax (e.g. "::ala") takes the residue name.  Now, as a  
convenience, if you type something that is not an integer after the  
single colon, then it assumes you mean the residue name and switches  
over to interpreting it like the double colon does.  But in your case  
you have character strings that you always want interpreted as  
residues names regardless of whether they look like integers, so you  
should just use "::" all the time.


                         Eric Pettersen
                         UCSF Computer Graphics Lab

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