[PyMOL] GTX980Ti for Pymol 3D?

[Albert]

Hello:

Does anybody know whether Nvidia GTX980Ti support Pymol active stereo 
3D? I saw someone said that some GTX graphic card may also work, but I 
am not sure for this one.

Thx a lot

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Re: [PyMOL] Common atoms in two selections (and their indices)

[Thomas Holder]

Hi Tsjerk, Spencer, Osvaldo,

cmd.get_raw_alignment() might be what you are looking for.

http://pymolwiki.org/index.php/Get_raw_alignment

Cheers,
  Thomas

On 27 Oct 2015, at 12:49, Spencer Bliven  wrote:

> Tsjerk–
> 
> You might be able to extract the ids of the aligned residues from an 
> alignment object:
> 
> cmd.align(sele1,sele2copy,object="aln")
> [a.id for a in cmd.get_model('aln').atom]
> 
> Since the alignment is sequential, I think this should contain all the 
> aligned atoms from sele1 concatenated with the aligned atoms from sele2. 
> However, as far as I know the internals of the alignment objects aren't 
> documented, so I'm not sure if this can be relied upon.
> 
> -Spencer
> 
> 
> On Tue, Oct 27, 2015 at 12:22 PM, Tsjerk Wassenaar  wrote:
> Hi Osvaldo,
> 
> Probably that's the trick, although I'd need the indices, but that's simple 
> enough.
> The 'equivalence' one is still standing though :)
> 
> Thanks,
> 
> Tsjerk
> 
> On Tue, Oct 27, 2015 at 11:44 AM, Osvaldo Martin  
> wrote:
> So, you want to know the best way to do this?
> 
> Z = [at_x for at_x in X for at_y in Y if at_x.id == at_y.id
> ]
> 
> Or am I still not getting it right?
> 
> Cheers,
> Osvaldo.
> 
> On Tue, Oct 27, 2015 at 10:56 AM, Tsjerk Wassenaar  wrote:
> 
> 
> 
> Hi Osvaldo,
> 
> I could have been more clear I guess. First of all, let's say I have obtained 
> the atom list of a selection:
> 
> X = cmd.get_model(selection1).atom
> 
> I'm doing stuff with that (PCA, to be exact), but now I want to display the 
> result only for a subselection. Probably getting the intersection of the 
> selections and then check which atoms there match with the original selection 
> is an approach. The question there is what the best way is for checking 
> identity of the atoms.
> 
> The second issue is when there is no intersection of the selections, but 
> there may be correspondence, as in alignment.
> 
> Thanks for thinking along,
> 
> Tsjerk
> 
> On Tue, Oct 27, 2015 at 10:44 AM, Osvaldo Martin  
> wrote:
> Hi Tsjerk,
> 
> Do you mean something like this?
> 
> cmd.index("sel_1 and sel_2")
> 
> I do not get the differences between your two cases. Whats the difference 
> between “atoms which are both in selection 1 and 2” and “matching atoms in 
> the two selections”
> 
> Cheers,
> 
> Osvaldo.
> 
> On Mon, Oct 26, 2015 at 10:33 AM, Tsjerk Wassenaar  wrote:
> 
> 
> 
> 
> Hi Thomas e.a.,
> 
> Given two selections, would there be an easy way to 
> 
> 1. find the atoms which are both in selection 1 and 2, and the indices of 
> those in the selections
> 
> and 
> 
> 2. find the matching atoms in the two selections, like align does, and the 
> indices of those in the selections
> 
> Thanks,
> 
> Tsjerk
> 
> -- 
> Tsjerk A. Wassenaar, Ph.D.

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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[PyMOL] coloring based on alignment

[Oganesyan, Vaheh]

Colleagues,

Was wondering if there is a functionality built  in PyMOL for coloring of the 
molecule based on sequence identity/similarity? This topic was discussed 
briefly in 2007 and the answer was from Robert Campbell suggesting using his 
scripts. Seems to be a good tool to have for anyone.


Regards,

Vaheh Oganesyan
MedImmune, ADPE
www.medimmune.com



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Re: [PyMOL] coloring based on alignment

[Jed Goldstone]

Vaheh,
You can modify the b-factor column, and color by b-factor. I have used
various value-to-bfactor scripts, with different measures of alignment
similarity.

The one problem I've had is extending the Ca color to the rest of the
residue in stick mode.
Jed
On Oct 28, 2015 3:34 PM, "Oganesyan, Vaheh" 
wrote:

> Colleagues,
>
> Was wondering if there is a functionality built  in PyMOL for coloring of
> the molecule based on sequence identity/similarity? This topic was
> discussed briefly in 2007 and the answer was from Robert Campbell
> suggesting using his scripts. Seems to be a good tool to have for anyone.
>
>
> Regards,
>
> Vaheh Oganesyan
> MedImmune, ADPE
> www.medimmune.com
>
>
>
> To the extent this electronic communication or any of its attachments
> contain information that is not in the public domain, such information is
> considered by MedImmune to be confidential and proprietary. This
> communication is expected to be read and/or used only by the individual(s)
> for whom it is intended. If you have received this electronic communication
> in error, please reply to the sender advising of the error in transmission
> and delete the original message and any accompanying documents from your
> system immediately, without copying, reviewing or otherwise using them for
> any purpose. Thank you for your cooperation.
>
>
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