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?

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

http://www.cgl.ucsf.edu