Re: [PyMOL] Symmetry Expansion
Thomas,
Thanks for clue. The mapping was broken for all proteins in the "R 3
2" space group. I've fixed it and pushed the update to the
open-source. If anyone finds more bugs along this line, please let me
know.
Cheers,
-- Jason
On Sat, Apr 17, 2010 at 5:42 AM, Thomas Holder
wrote:
> Hi Jason,
>
> about the bug with 2bop, it's just the spacegroup which is mapped wrong I
> think. If the PDB file is assigned correct, then 'R 3 2' should map to the
> matrices which are stored for 'R 3 2 :R' within pymol (xray.py).
>
> Hack to get correct result:
>
> fetch 2bop
> sym = cmd.get_symmetry('2bop')
> sym[-1] = 'R 3 2 :R'
> cmd.set_symmetry('2bop', *sym)
> symexp mates, 2bop, 2bop, 6.0
>
> Cheers,
> Thomas
>
> Jason Vertrees wrote, On 04/16/10 05:39:
>>
>> PyMOLers,
>>
>> A bug was brought to my attention to day in the symmetry expansion
>> command (try it on 2bop). If you have issues with the symexp command
>> in your work, please check out the hastily-written and really-slow,
>> but correct (for my test cases), manual symmetry expansion script:
>> http://pymolwiki.org/index.php/ManualSymExp.
>>
>> I am working on a fix.
>>
>> Last, PyMOLers wrote three other cool scripts and deposited them on
>> the wiki this week--check those out, too.
>>
>> Cheers,
>>
>> -- Jason
>
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
--
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Re: [PyMOL] Symmetry Expansion
Hi Jason,
about the bug with 2bop, it's just the spacegroup which is mapped wrong
I think. If the PDB file is assigned correct, then 'R 3 2' should map to
the matrices which are stored for 'R 3 2 :R' within pymol (xray.py).
Hack to get correct result:
fetch 2bop
sym = cmd.get_symmetry('2bop')
sym[-1] = 'R 3 2 :R'
cmd.set_symmetry('2bop', *sym)
symexp mates, 2bop, 2bop, 6.0
Cheers,
Thomas
Jason Vertrees wrote, On 04/16/10 05:39:
> PyMOLers,
>
> A bug was brought to my attention to day in the symmetry expansion
> command (try it on 2bop). If you have issues with the symexp command
> in your work, please check out the hastily-written and really-slow,
> but correct (for my test cases), manual symmetry expansion script:
> http://pymolwiki.org/index.php/ManualSymExp.
>
> I am working on a fix.
>
> Last, PyMOLers wrote three other cool scripts and deposited them on
> the wiki this week--check those out, too.
>
> Cheers,
>
> -- Jason
--
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
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Re: [PyMOL] Symmetry Expansion
Thomas, You're right--thanks for the correction. The script is now called BiologicalUnit. -- Jason On Fri, Apr 16, 2010 at 7:34 AM, Thomas Holder wrote: > Hi Jason, > > the result of "symexp" is not supposed to be the biological unit, right? > It produces any symmetry mate, whereas your ManualSymExp reads the > REMARK 350 which is the annotated biological unit. It is a very useful > script, but has a bug: If there is more then one biomolecule annotated, > for example if the asymetric unit has multiple copies of the biological > unit, you should only generate the first biomolecule I think. Try 2x1g > (has 2 biomolecules in asymetric unit). > > Cheers, > Thomas > > On Thu, 2010-04-15 at 23:39 -0400, Jason Vertrees wrote: >> PyMOLers, >> >> A bug was brought to my attention to day in the symmetry expansion >> command (try it on 2bop). If you have issues with the symexp command >> in your work, please check out the hastily-written and really-slow, >> but correct (for my test cases), manual symmetry expansion script: >> http://pymolwiki.org/index.php/ManualSymExp. >> >> I am working on a fix. >> >> Last, PyMOLers wrote three other cool scripts and deposited them on >> the wiki this week--check those out, too. >> >> Cheers, >> >> -- Jason >> > > > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Symmetry Expansion
Hi Jason, the result of "symexp" is not supposed to be the biological unit, right? It produces any symmetry mate, whereas your ManualSymExp reads the REMARK 350 which is the annotated biological unit. It is a very useful script, but has a bug: If there is more then one biomolecule annotated, for example if the asymetric unit has multiple copies of the biological unit, you should only generate the first biomolecule I think. Try 2x1g (has 2 biomolecules in asymetric unit). Cheers, Thomas On Thu, 2010-04-15 at 23:39 -0400, Jason Vertrees wrote: > PyMOLers, > > A bug was brought to my attention to day in the symmetry expansion > command (try it on 2bop). If you have issues with the symexp command > in your work, please check out the hastily-written and really-slow, > but correct (for my test cases), manual symmetry expansion script: > http://pymolwiki.org/index.php/ManualSymExp. > > I am working on a fix. > > Last, PyMOLers wrote three other cool scripts and deposited them on > the wiki this week--check those out, too. > > Cheers, > > -- Jason > -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Symmetry Expansion
PyMOLers, A bug was brought to my attention to day in the symmetry expansion command (try it on 2bop). If you have issues with the symexp command in your work, please check out the hastily-written and really-slow, but correct (for my test cases), manual symmetry expansion script: http://pymolwiki.org/index.php/ManualSymExp. I am working on a fix. Last, PyMOLers wrote three other cool scripts and deposited them on the wiki this week--check those out, too. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
