[PyMOL] how to separate the complex subunits

[Smith Liu]

Dear All,


Suppose I have a protein complex displayed by pymol, is any way pymol can 
separate its subunits in a fixed and beautiful patten of arrangement in the 
pymol window?


If the subunit contains may alpha helices too dense for display each helix 
visibly by pymol, is any way pymol can extend the full subunit so that each 
helix can be easily visible in pymol, without breaking the whole subunit from 
N-terminal to C-terminal into separated and disjoined parts?


Smith--
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[PyMOL] Brownian motion in movie?

[H. Adam Steinberg]

>

Does anyone know how CompChemist made the Brownian motion in the movie? I would 
really like to duplicate that effect!

H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366

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Re: [PyMOL] Brownian motion in movie?

[Tsjerk Wassenaar]

Hi Adam,

That type of motion is typically the result of MD simulation. Some of the
examples were just showing the motion on very short time scales and others
were over longer times, using a smoothing filter. In addition, there was an
example of structure morphing without dynamics.

If you want, I can probably hand you a few tools and tips to do similar
things without too much effort. The time scales you'd require (read waiting
time) is modest for what you'd need to make movies.

Let me know if you're interested.

Cheers,

Tsjerk

On Sat, Dec 5, 2015 at 1:54 AM, H. Adam Steinberg <
h.adam.steinb...@gmail.com> wrote:

> 
>
> Does anyone know how CompChemist made the Brownian motion in the movie? I
> would really like to duplicate that effect!
>
> H. Adam Steinberg
> 7904 Bowman Rd
> Lodi, WI 53555
> 608/592-2366
>
>
>
> --
> 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
>



-- 
Tsjerk A. Wassenaar, Ph.D.
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Re: [PyMOL] RMSD calculations for a group of structures

[Thomas Holder]

Hi Daniel,

You say you used "split_states", so all your conformations have the same 
topology (are the same molecule). In that case, I suggest to use cmd.rms 
instead of cmd.align, which will be more efficient. You also don't need to 
split the structures, but call the function with the correct "mobile_state" and 
"target_state" arguments. The cmd.rms() function returns the RMSD. Note that it 
by default calculates the all-atom RMSD, vs. cmd.align which does outlier 
rejection.

Example:

python
from pymol import cmd
f=open('rmsd.txt','w')
cmd.fetch('1nmr')
for state in range(2, cmd.count_states() + 1):
r = cmd.rms('1nmr and name CA',
'1nmr and name CA', 1, state)
f.write('State: %3d RMS: %5.2f\n' % (state, r))
f.close()
python end

Hope that helps.

Cheers,
  Thomas

On 03 Dec 2015, at 17:13, Daniel Munoz Escudero  wrote:

> 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.

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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[PyMOL] PyMOL with Python 3

[Thomas Holder]

Hi all,

We have refactored Open-Source PyMOL to work with Python 3. If you are 
interested, the patched code and the patch itself are currently available from 
the sourceforge download page:

https://sf.net/projects/pymol/files/pymol/1.8/
pymol-v1.8.0.0-r4145-py3.tar.bz2 (patched code)
pymol-v1.8.0.0-r4145-py3.patch (diff agains current SVN)

Disclaimer: If you have no particular interest in Python 3, then this is not 
for you. Most currently available PyMOL plugins and Python scripts will not 
work with this version, they will need to be refactored as well.

If you find any bugs or unexpected behavior, please let us know. In Python 3, 
all strings (type "str") are unicode, while in Python 2 "str" is an alias for 
"bytes". This difference is probably the most significant one for PyMOL. Once 
the patch looks rock solid and also proves to still work fine with Python 2, we 
will check it in to SVN.

Cheers,
  Thomas

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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