You are absolutely right, Bernhard! I did indeed have another object in the
session that contains a resi 131. I increased the cutoff until symmetry
mates were indeed generated.
Thanks!
On Tue, Feb 7, 2017 at 4:54 PM, Bernhard Lechtenberg <
blechtenb...@sbpdiscovery.org> wrote:
> Hi Emilia
>
> I just tried your example but could not reproduce your observations. For
> me it did not matter whether I use your first or second example, PyMOL
> never created symmetry mates. I did create the 5DEN-Phe131 using: select
> 5DEN-Phe131, resi 131
>
> Looking into it a bit more I found that if cut-off probably is not large
> enough. There simply is no symmetry molecule within 1 Angstrom of Phe131.
> If you change your command to:
>
> symexp sym5den, 5DEN, resi 131, 8
>
> it should work
>
> Your 2nd line might have worked because you might have selected some other
> residue 131 from a different molecule in your current pymol session?
>
> Hope that helps.
>
> Bernhard
>
>
>
>
> *Bernhard C. Lechtenberg, Ph.D. *Postdoctoral Associate
> Riedl Lab
>
> <http://sbpdiscovery.org/>
>
> 10901 N. Torrey Pines Road, La Jolla, CA 92037
> *T *858.646.3100 ext. 4216 <http://sbpdiscovery.org/>
> blechtenb...@sbpdiscovery.org <blechtenb...@sbpdiscovery.org>
>
> *Science Benefiting Patients™*
>
> On Feb 7, 2017, at 12:55 PM, Emilia C. Arturo (Emily) <ecgart...@gmail.com
> <ecgart...@gmail.com>> wrote:
>
> 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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die tomorrow." - Maria Mitchell
"I'm not afraid of storms for I'm learning to sail my ship." - Louisa May
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