You can go to settings > edit all > sphere scale. Default is set to one, I have found that 0.3-0.4 works best.

 

Bob

 


From: pymol-users-bounces@lists.sourceforge.net [mailto:pymol-users-bounces@lists.sourceforge.net] On Behalf Of GAO FENG
Sent: Wednesday, January 10, 2007 12:00 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] change the sphere size of a chosen atom ?

 

Hi All:

A quick question. When I select one particular atom, say, a sulfur atom, and represented with sphere. Does any know how to resize the sphere? It appears too big to reflect the "real" sense in the space.

Thanks and Happy New Year!

Feng.


pymol-users-request@lists.sourceforge.net wrote:

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Today's Topics:

1. Kabsch & CE Align (Jason Vertrees)
2. New plugin and Doubt with APBS Tools (Ra?l Mera)
3. red-blue, red-cyan stereo (Evan Kantrowitz)
4. Re: New plugin and Doubt with APBS Tools (Michael Lerner)
5. protein peptide interaction (Jamaine Saydu C. Davis)
6. Selecting nearby atoms (Jonathan Arthur)


----------------------------------------------------------------------

Message: 1
Date: Thu, 4 Jan 2007 00:37:46 -0600
From: Jason Vertrees
Subject: [PyMOL] Kabsch & CE Align
To: pymol-users@lists.sourceforge.net
Message-ID: <200701040037.47002.javertre@utmb.edu>
Content-Type: text/plain; charset="iso-8859-1"

Howdy,

Just a quick note to those who used my implementation of the Kabsch algorithm
for alignments: I have uploaded another version to the wiki
http://www.pymolwiki.org/index.php/Kabsch
that uses, what I consider, an elegant solution to the problem --- SVD. Also,
the new code fixes a small bug I had in the last code and you'll need Numpy
for it.

Lastly, I've implemented the CE (structure-based) alignment algorithm as a
plugin for PyMol. Details can also be found on the wiki at
http://www.pymolwiki.org/index.php/Cealign
I'll release the code if I can make the Python code fast or whenever I get the
C/C++ code properly plugged into PyMol. (The C++ code on my machine aligns
two 400+ residue proteins in about 0.250 seconds; the Python code for 167
residue proteins, 35 seconds!)

Please forward bugs/comments to me, address below.

Cheers,

-- Jason

--
Jason Vertrees
javertre@utmb.edu



------------------------------

Message: 2
Date: Sun, 7 Jan 2007 12:17:53 -0600 (CST)
From: Ra?l Mera
Subject: [PyMOL] New plugin and Doubt with APBS Tools
To: pymol-users@lists.sourceforge.net
Message-ID: <802526.3909.qm@web52401.mail.yahoo.com>
Content-Type: text/plain; charset=iso-8859-1

Dear all,

Two things.
First, I just written a small plugin that uses the
program "reduce" to add hydrogens to a molecule or to
a trajectory loaded in Pymol.(since each frame of the
trajectory is hydrogenated by reduce, I think that
protonation states could vary between frames) This
allow us to have a reliable protonation method in
PyMOL, without having to save the structure as PDB and
hydrogenate with another app, and using an open-source
(as far as I know) and easy to install application.

Since I don't have any website right now, I will try
to make it available from the Pymol Wiki. If you want
the plugin right now, just e-mail me.

The other thing is a doubt in using the APBS Tools.
When I use it to calculate electrostatics potentialsof
a trajectory (but the PQR is made by PDB2PQR from a
PDB made with PyMOL, i.e, only from the first
snapshot)
I get a .dx map that I think has the potentials only
for the first frame. When I display the potential
surface in the trajectory, the potentials seems to
change between frames, which I wouldn't expect since I
think that the calculation was performed only for the
first frame.
My doubt is: Are these changes alleatory due to a
change
of the structure's position changes on the grid, or
they have some significance?, if the latter, what
significance? (maybe the changes are produced by the
motion of polar groups?)

Thanks in advance,

Raul

__________________________________________________
Correo Yahoo!
Espacio para todos tus mensajes, antivirus y antispam ?gratis!
Reg?strate ya - http://correo.espanol.yahoo.com/



------------------------------

Message: 3
Date: Tue, 9 Jan 2007 10:01:09 -0500
From: Evan Kantrowitz
Subject: [PyMOL] red-blue, red-cyan stereo
To: pymol-users@lists.sourceforge.net
Message-ID: <81B9F413-ED06-4C29-91F2-052174D39121@bc.edu>
Content-Type: text/plain; charset="us-ascii"

Anyone have an idea about how to write a script to do red-blue or red-
cyan stereo with pymol
-------------------------------------------------------------------
Evan R. Kantrowitz,
Ph.D e
van.kantrowitz@bc.edu
Boston
College

Tel.617-552-4558
Department of
Chemistry
FAX 617-552-2705
Merkert Chemistry Center, Rm 239
Chestnut Hill, MA 02467
-------------------------------------------------------------------


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Message: 4
Date: Tue, 9 Jan 2007 11:53:18 -0500
From: "Michael Lerner"
Subject: Re: [PyMOL] New plugin and Doubt with APBS Tools
To: " Ra?l Mera "
Cc: pymol-users@lists.sourceforge.net
Message-ID:

Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Ra?l,

I don't have time to look at this in detail right now, but .. what
exactly do you mean that the potentials change between frames? What
happens if you draw isosurfaces? Do they change?

-michael

On 1/7/07, Ra?l Mera wrote:
> Dear all,
>
> Two things.
> First, I just written a small plugin that uses the
> program "reduce" to add hydrogens to a molecule or to
> a trajectory loaded in Pymol.(since each frame of the
> trajectory is hydrogenated by reduce, I think that
> protonation states could vary between frames) This
> allow us to have a reliable protonation method in
> PyMOL, without having to save the structure as PDB and
> hydrogenate with another app, and using an open-source
> (as far as I know) and easy to install application.
>
> Since I don't have any website right now, I will try
> to make it available from the Pymol Wiki. If you want
> the plugin right now, just e-mail me.
>
> The other thing is a doubt in using the APBS Tools.
> When I use it to calculate electrostatics potentialsof
> a trajectory (but the PQR is made by PDB2PQR from a
> PDB made with PyMOL, i.e, only from the first
> snapshot)
> I get a .dx map that I think has the potentials only
> for the first frame. When I display the potential
> surface in the trajectory, the potentials seems to
> change between frames, which I wouldn't expect since I
> think that the calculation was performed only for the
> first frame.
> My doubt is: Are these changes alleatory due to a
> change
> of the structure's position changes on the grid, or
> they have some significance?, if the latter, what
> significance? (maybe the changes are produced by the
> motion of polar groups?)
>
> Thanks in advance,
>
> Raul
>
> __________________________________________________
> Correo Yahoo!
> Espacio para todos tus mensajes, antivirus y antispam ?gratis!
> Reg?strate ya - http://correo.espanol.yahoo.com/
>
> -------------------------------------------------------------------------
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to share your
> opinions on IT & business topics through brief surveys - and earn cash
> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
> _______________________________________________
> PyMOL-users mailing list
> PyMOL-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>


--
Biophysics Graduate Student
Carlson Lab, University of Michigan
http://www.umich.edu/~mlerner http://lernerclan.net



------------------------------

Message: 5
Date: Tue, 9 Jan 2007 12:16:05 -0500
From: "Jamaine Saydu C. Davis"
Subject: [PyMOL] protein peptide interaction
To:
Message-ID: <001801c73411$d953e1b0$501b5b80@JSD>
Content-Type: text/plain; charset="us-ascii"

I would like to compare interactions between a protein and two peptides with
different charges. Is there a way to do this in pymol? Once I build the
peptide, I can not dock into the protein binding site.



Best,

JSD

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Message: 6
Date: Wed, 10 Jan 2007 14:32:09 +1100
From: Jonathan Arthur
Subject: [PyMOL] Selecting nearby atoms
To: pymol-users@lists.sourceforge.net
Message-ID: <45A45E39.50500@med.usyd.edu.au>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hello all,

I am trying to select all atoms with 4 Angstroms from a particular atom,
in this case the O of the OH group in a tyrosine residue. I executed the
following commands

select oh, id 341
select close, all within 4 of oh

where the first command creates a named selection for the particular
atom I am interested in and the second selects the nearby atoms. My
problem is, there seems to be too many atoms selected and, when I check
a few bond distances, I definitely have atoms selected further than 4
Angstroms away.

What am I doing wrong?

Also, once the selection is correct, is there any easy way to get a text
list of all of these nearby atoms?

Thanks for your help.

Regards,

Jonathan

--
Dr Jonathan Arthur
Sydney Bioinformatics
Medical Foundation Building, K25
University of Sydney NSW 2006
Phone: +61 2 9036 3132
Fax: +61 2 9036 3233
Email: jarthur@med.usyd.edu.au





------------------------------

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