[PyMOL] MacPymol
Hi, By accident(!) I upgraded my Mac OS to El Captain. The problem is now I cannot open my MacPymol that was fine up to previous or lion. I downloaded XQuartz but still somehow doensn't open my old MacPymol. Has some one experienced or solved this problem? Thanks in advance. Young-Jin -- Go from Idea to Many App Stores Faster with Intel(R) XDK Give your users amazing mobile app experiences with Intel(R) XDK. Use one codebase in this all-in-one HTML5 development environment. Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs. http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140___ 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] using "bymol" in combination with "within"
Andrew,
Can you provide an example? In my tests the bymol and within operators work
as expected.
fetch 4FC1 #high-res neutron scattering structure with water hydrogens
select solvent w. 3 of resi 7
stored.i=0; cmd.iterate("sele", "stored.i+=1"); print stored.i #7 atoms
select bymol solvent w. 3 of resi 7
stored.i=0; cmd.iterate("sele", "stored.i+=1"); print stored.i #12 atoms
Is this an MD structure? It's a bit weird that you have hydrogens on your
waters. Some MD programs I've worked with give poorly constructed PDB
files, so I wonder if it could be a problem with your input structure.
-Spencer
On Wed, Dec 2, 2015 at 8:58 PM Andrew Kalenkiewicz
wrote:
> Hi Spencer,
>
> Thanks for your response! I was also originally under the impression that
> my selection #2 should be a superset of selection #1, but that is
> definitely not the case. There are atoms in selection #1 that are not
> included in selection #2.
>
> What I want to do is select all the water molecules that have at least one
> of their atoms within 3 angstroms of my protein-ligand complex (the
> solute). Based on the above discrepancy, I know that selection #2 does not
> give me this. This is corroborated by an independent calculation I did in a
> different program (the Bio3D pacakge in R).
>
> All best,
> Andrew
>
> On Wed, Dec 2, 2015 at 10:53 AM, Spencer Bliven
> wrote:
>
>> Andrew,
>>
>> The 'byres' selector expands the inner selection to include all
>> covalently bonded atoms. Thus, your selection #2 should be a superset of
>> selection #1. Are you sure that's not the case?
>>
>> What do your 'wats' and 'solute' selections refer to? Are you trying to
>> find the water molecules to some selected organic solvent molecule? If so,
>> you might mean
>>
>> select wats within 3 of (bymolecule solute)
>>
>> This would first expand selection 'solute' to encompass any covalently
>> connected atoms, then would return any atoms from selection 'wats' which
>> are within 3Å of the resulting molecule.
>>
>> A more complete explanation of what you're trying to select (and which
>> PDB entry, if applicable) would be helpful.
>>
>> -Spencer
>>
>> P.S. You might also be interested in the predefined keywords 'solvent'
>> (all waters) and 'organic' (ligands, buffers).
>>
>> On Wed, Dec 2, 2015 at 3:32 PM Andrew Kalenkiewicz <
>> ajkalenkiew...@gmail.com> wrote:
>>
>>> Dear PyMOL users,
>>>
>>> I'm wondering if anyone knows how exactly a selection is defined if you
>>> utilize both the "bymol" and "within" commands together. For instance,
>>> consider the following two selections:
>>>
>>> 1. "select closewats, wats within 3 of solute"
>>> 2. "select closewats, bymol (wats within 3 of solute)"
>>>
>>> In the latter case, it seems to me that the distance cutoff imposed by
>>> within is not by "closest atom" for each respective molecule (which is what
>>> I actually want). Visually, I can see that the first selection includes
>>> more total water molecules than the second selection. So what does the
>>> distance cutoff refer to? The geometrical center? Center of mass? I
>>> couldn't find anything on the PyMOL wiki that explains this.
>>>
>>> Thanks,
>>> Andrew
>>>
>>> --
>>> Andrew Kalenkiewicz
>>> Biomedical Engineering M.S.E. '15
>>> Cellular & Molecular Biology B.S. '13
>>> University of Michigan, Ann Arbor
>>> 734-709-0355
>>> aj...@umich.edu
>>>
>>> --
>>> Go from Idea to Many App Stores Faster with Intel(R) XDK
>>> Give your users amazing mobile app experiences with Intel(R) XDK.
>>> Use one codebase in this all-in-one HTML5 development environment.
>>> Design, debug & build mobile apps & 2D/3D high-impact games for multiple
>>> OSs.
>>> http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140
>>> ___
>>> 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
>>
>>
>
>
> --
> Andrew Kalenkiewicz
> Biomedical Engineering M.S.E. '15
> Cellular & Molecular Biology B.S. '13
> University of Michigan, Ann Arbor
> 734-709-0355
> aj...@umich.edu
>
--
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Re: [PyMOL] using "bymol" in combination with "within"
Andrew, The 'byres' selector expands the inner selection to include all covalently bonded atoms. Thus, your selection #2 should be a superset of selection #1. Are you sure that's not the case? What do your 'wats' and 'solute' selections refer to? Are you trying to find the water molecules to some selected organic solvent molecule? If so, you might mean select wats within 3 of (bymolecule solute) This would first expand selection 'solute' to encompass any covalently connected atoms, then would return any atoms from selection 'wats' which are within 3Å of the resulting molecule. A more complete explanation of what you're trying to select (and which PDB entry, if applicable) would be helpful. -Spencer P.S. You might also be interested in the predefined keywords 'solvent' (all waters) and 'organic' (ligands, buffers). On Wed, Dec 2, 2015 at 3:32 PM Andrew Kalenkiewicz wrote: > Dear PyMOL users, > > I'm wondering if anyone knows how exactly a selection is defined if you > utilize both the "bymol" and "within" commands together. For instance, > consider the following two selections: > > 1. "select closewats, wats within 3 of solute" > 2. "select closewats, bymol (wats within 3 of solute)" > > In the latter case, it seems to me that the distance cutoff imposed by > within is not by "closest atom" for each respective molecule (which is what > I actually want). Visually, I can see that the first selection includes > more total water molecules than the second selection. So what does the > distance cutoff refer to? The geometrical center? Center of mass? I > couldn't find anything on the PyMOL wiki that explains this. > > Thanks, > Andrew > > -- > Andrew Kalenkiewicz > Biomedical Engineering M.S.E. '15 > Cellular & Molecular Biology B.S. '13 > University of Michigan, Ann Arbor > 734-709-0355 > aj...@umich.edu > > -- > Go from Idea to Many App Stores Faster with Intel(R) XDK > Give your users amazing mobile app experiences with Intel(R) XDK. > Use one codebase in this all-in-one HTML5 development environment. > Design, debug & build mobile apps & 2D/3D high-impact games for multiple > OSs. > http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140 > ___ > 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 -- Go from Idea to Many App Stores Faster with Intel(R) XDK Give your users amazing mobile app experiences with Intel(R) XDK. Use one codebase in this all-in-one HTML5 development environment. Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs. http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140___ 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] using "bymol" in combination with "within"
Dear PyMOL users, I'm wondering if anyone knows how exactly a selection is defined if you utilize both the "bymol" and "within" commands together. For instance, consider the following two selections: 1. "select closewats, wats within 3 of solute" 2. "select closewats, bymol (wats within 3 of solute)" In the latter case, it seems to me that the distance cutoff imposed by within is not by "closest atom" for each respective molecule (which is what I actually want). Visually, I can see that the first selection includes more total water molecules than the second selection. So what does the distance cutoff refer to? The geometrical center? Center of mass? I couldn't find anything on the PyMOL wiki that explains this. Thanks, Andrew -- Andrew Kalenkiewicz Biomedical Engineering M.S.E. '15 Cellular & Molecular Biology B.S. '13 University of Michigan, Ann Arbor 734-709-0355 aj...@umich.edu -- Go from Idea to Many App Stores Faster with Intel(R) XDK Give your users amazing mobile app experiences with Intel(R) XDK. Use one codebase in this all-in-one HTML5 development environment. Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs. http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140___ 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
