Re: [PyMOL] using "bymol" in combination with "within"

2015-12-03 Thread Sampson, Jared M. 
Hi Andrew -

If you're just looking to expand the selection from atoms in water molecules to 
entire water molecules, I would actually use `byres` instead of `bymol`.  The 
`bymolecule` selector is apparently dependent on how PyMOL sees the bonds (e.g. 
try `fetch 3ghe, async=0; select test, bymol chain H and resi 30` -- you only 
select up to the gap at resi 127).  `Byres` should get the entire HOH residue 
as defined by the residue name and number, as long as they are unique for each 
of your water molecules.

So, in short, this should work:

select closewats, byres (wats within 3 of solute)

Or as Spencer mentioned, using the built-in keywords:

select closewats, byres (solvent within 3 of organic)

Or, if you have multiple organic components and only one of them is your 
ligand, which has the residue name DRG:

select closewats, byres (solvent within 3 of resn DRG)

Hope that helps.

Cheers,
Jared

—
Jared Sampson
Graduate Student
Department of Biochemistry and Molecular Biophysics
Columbia University

On Dec 2, 2015, at 2:57 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 
> 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
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--
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"

2015-12-03 Thread Andrew Kalenkiewicz 
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=/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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[PyMOL] RMSD calculations for a group of structures

2015-12-03 Thread Daniel Munoz Escudero 
Hi!

I have a group of structures (168 in total) and I want to align all of them
to the first one in order to know the RMSD calculation. For that purpose I
use the following:

f=open('rmsd.txt','w')
rms2=cmd.align('structure_0002 and name ca','structure_0001 and name ca')
.
. (NOTE: I got all of these structures by the command split_states somename)
.
rms9=cmd.align('structure_0009 and name ca','structure_0001 and name ca')

How do I get the output with the *number* of each RMSD into the text
file rmsd.txt? What other way can I use to do so?

Thanks in advance,

D.
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Re: [PyMOL] MacPymol

2015-12-03 Thread Thomas Holder 
Hi Young-Jin,

The latest MacPyMOL works fine on El Capitan. XQuartz is not required, unless 
you use the "MacPyMOLX11Hybrid" interface.

Which version do you have installed? In my tests, all MacPyMOL versions newer 
than 1.4 work on El Capitan (not heavily tested, but they open and render 
something). Some of them only open if you select "Allow apps downloaded from: 
Anywhere" in the Security & Privacy System Preferences. Some older versions 
also might have problems with multiple or external displays.

Cheers,
  Thomas

On 02 Dec 2015, at 18:01, Young-Jin Cho  wrote:

> 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

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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