Hmm. I've stumbled on a clue. In case it's a bug in the code or a finding
someone in the future might find useful when stumbling into the same
problem, here is what I've just found:
These two ways of executing symexp give different results - the first does
not generate symmetry mates (again, there is no error in the console, only
a display of " ExecutiveSymExp: Generating symmetry mates... "), but the
second does generate symmetry mates:
1. symexp sym5den, 5DEN, 5DEN-Phe131, 1
2. symexp sym5den, 5DEN, resi 131, 1
The argument in the selection entry (i.e. '5DEN-Phe131') is a selection I'd
made of 'resi 131' from PDB id 5DEN. Clearly the two calls to symexp are
not identical, but I don't (yet) understand why.
Emily.
On Tue, Feb 7, 2017 at 2:29 PM, Emilia C. Arturo (Emily) <
ecgart...@gmail.com> wrote:
> Hello.
>
> I am trying to use symexp to inspect symmetry mates of several structures.
> I'm mystified about why some input structures lead to quick generation of
> symmetry mates, while others seem to lead to apparently never-ending symexp
> execution. All pdb files I've used as input contain a CRYST1 record. For
> some, the PyMOL console displays " ExecutiveSymExp: Generating symmetry
> mates... " but symmetry mates are not generated. My processors don't appear
> to be taxed at all during this time. This 'bug' was reported on this
> mailing list, the most recent was, I think, 2011:
> https://sourceforge.net/p/pymol/mailman/message/27240486/.
>
> Is there any update on this function? Or, does anyone have insight about
> why some pdb files cause this while others do not?
>
> I am using MacPyMOL version 1.7.6.2 on my MacBook Pro that runs OS X
> Yosemite.
>
> Emily.
>
>
>
> --
> "Study as if you were going to live forever; live as if you were going to
> die tomorrow." - Maria Mitchell
>
> "I'm not afraid of storms for I'm learning to sail my ship." - Louisa May
> Alcott
>
>
--
"Study as if you were going to live forever; live as if you were going to
die tomorrow." - Maria Mitchell
"I'm not afraid of storms for I'm learning to sail my ship." - Louisa May
Alcott
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