Hi Everyone,

Could someone tell me how to perform superimposition of two or more ligands from different PDBs?

Thanks in advance.

Feng.


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Today's Topics:

1. Re: Pymol cone shape? (William Scott)
2. Re: New plugin and Doubt with APBS Tools (Michael Lerner)
3. Re: Pymol cone shape? (Terry Jones)
4. Re: change the sphere size of a chosen atom ? (Tsjerk Wassenaar)
5. Re: Pymol cone shape? (Tsjerk Wassenaar)
6. Re: distance atom-protein surface (Praedor Atrebates)
7. Sequence view size (aaron bryden)


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

Message: 1
Date: Wed, 10 Jan 2007 12:24:46 -0800
From: William Scott
Subject: Re: [PyMOL] Pymol cone shape?
To: "Martin.Laurberg"
Cc: pymol-users@lists.sourceforge.net
Message-ID: <664A00E2-CD76-4664-95E9-10AA98EA12F9@chemistry.ucsc.edu>
Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed

Let's ask on the pymol mailing list...

On Jan 10, 2007, at 11:02 AM, Martin.Laurberg wrote:

> Damn, I can convert my 1969 CNS base pair restraints into what they
> call
> CGO drawn lines, and thereby display enforced hydrogen bonds, but I
> wish
> to draw cones for the base pair ladder as ribbons can do it. Oh
> well, ..
>
>
>
> On Wed, 10 Jan 2007, William Scott wrote:
>
>>
>> I think it is possible, but I don't know how.
>>
>>
>>
>> On Jan 10, 2007, at 9:24 AM, Martin.Laurberg wrote:
>>
>>> Hi Bill, is it possible to draw a cone-shape in pymol?
>>>
>>




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

Message: 2
Date: Wed, 10 Jan 2007 15:49:47 -0500
From: "Michael Lerner"
Subject: Re: [PyMOL] New plugin and Doubt with APBS Tools
To: pymol-users@lists.sourceforge.net
Message-ID:

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

We discussed this a bit off-list, and it looks like this was the answer:

The potentials are assigned to points in space. That's why the
isosurfaces don't change, and also why the surface coloring changes
when you change the shape of the surface.

Hope that helps anyone else who might have this question,

-michael

On 1/9/07, Michael Lerner wrote:
> 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
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> > _______________________________________________
> > PyMOL-users mailing list
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> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >
>
>
> --
> Biophysics Graduate Student
> Carlson Lab, University of Michigan
> http://www.umich.edu/~mlerner http://lernerclan.net
>


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



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

Message: 3
Date: Wed, 10 Jan 2007 22:56:30 +0100
From: Terry Jones
Subject: Re: [PyMOL] Pymol cone shape?
To: William Scott
Cc: "Martin.Laurberg" ,
pymol-users@lists.sourceforge.net
Message-ID: <17829.24846.423655.550648@terry-jones-computer.local>
Content-Type: text/plain; charset=us-ascii

Hi William

You can do it, or something that's as close to a cone as you could wish
for, by using a triangle fan. The apex of the fan is the top of the cone
and then you just add points around the base of the cone at whatever
granularity you like.

That would take some programming though, but it's not too difficult if you
know some Python, as the CGO interface is very simple. I wrote a pymol
plugin to do something similar: it takes an input specification file,
parses it, and draws many CGO objects as a result. It works just fine.
Making the resulting cones smoothly colored or transparent would be more,
and harder, work though. Without doing that, your cones may not play
nicely with the rest of the stuff drawn by pymol (which in my case is
nothing at all :-)).

Terry

| Let's ask on the pymol mailing list...
|
| On Jan 10, 2007, at 11:02 AM, Martin.Laurberg wrote:
|
| > Damn, I can convert my 1969 CNS base pair restraints into what they call
| > CGO drawn lines, and thereby display enforced hydrogen bonds, but I wish
| > to draw cones for the base pair ladder as ribbons can do it. Oh well, ..
| >
| > On Wed, 10 Jan 2007, William Scott wrote:
| >>
| >> I think it is possible, but I don't know how.
| >>
| >> On Jan 10, 2007, at 9:24 AM, Martin.Laurberg wrote:
| >>> Hi Bill, is it possible to draw a cone-shape in pymol?



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

Message: 4
Date: Thu, 11 Jan 2007 09:16:23 +0100
From: "Tsjerk Wassenaar"
Subject: Re: [PyMOL] change the sphere size of a chosen atom ?
To: mcfgao@yahoo.com, feng.gao@mail.mcgill.ca
Cc: pymol-users@lists.sourceforge.net
Message-ID:
<8ff898150701110016w2326a770id43f7aa79b39b2a8@mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Ni Hao Feng,

First of all, please do not include an complete daily digest in a
question (or reply) on this or any user list. If required, cut out
only that part which connects to your question or reply.

Then, in addition to Bobs comments, you can also use the terminal or a
script, using the command:

set sphere_scale, 0.3 (or another value)

This will do what it says and scale your atoms sphere radius with the
factor given. Another possibility is to assign a different atomic
radius to your atom:

alter e. s, vdw=newradius_float_argument

maybe like:

alter e. s, vdw=vdw*0.9

Note that you may have to "rebuild" your scene, if you were already
using a sphere representation.

Best,

Tsjerk
--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623



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

Message: 5
Date: Thu, 11 Jan 2007 09:24:05 +0100
From: "Tsjerk Wassenaar"
Subject: Re: [PyMOL] Pymol cone shape?
To: "William Scott"
Cc: "Martin.Laurberg" ,
pymol-users@lists.sourceforge.net
Message-ID:
<8ff898150701110024y4b111ab2ic195813792c4b8d@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Hi William,

Maybe the attached python script will be of some use. It contains a
function (and some helper functions) to draw a CGO arrow in PyMOL. It
contains code for drawing a cone for the head of the arrow.

Hope it helps,

Tsjerk

On 1/10/07, William Scott wrote:
> Let's ask on the pymol mailing list...
>
> On Jan 10, 2007, at 11:02 AM, Martin.Laurberg wrote:
>
> > Damn, I can convert my 1969 CNS base pair restraints into what they
> > call
> > CGO drawn lines, and thereby display enforced hydrogen bonds, but I
> > wish
> > to draw cones for the base pair ladder as ribbons can do it. Oh
> > well, ..
> >
> >
> >
> > On Wed, 10 Jan 2007, William Scott wrote:
> >
> >>
> >> I think it is possible, but I don't know how.
> >>
> >>
> >>
> >> On Jan 10, 2007, at 9:24 AM, Martin.Laurberg wrote:
> >>
> >>> Hi Bill, is it possible to draw a cone-shape in pymol?
> >>>
> >>
>
>
> -------------------------------------------------------------------------
> 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
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> _______________________________________________
> PyMOL-users mailing list
> PyMOL-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>


--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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------------------------------

Message: 6
Date: Thu, 11 Jan 2007 08:36:04 -0500
From: Praedor Atrebates
Subject: Re: [PyMOL] distance atom-protein surface
To: pymol-users@lists.sourceforge.net
Message-ID: <200701110836.04641.praedor@yahoo.com>
Content-Type: text/plain; charset="iso-8859-1"

I needed to have a measurement of the "actual" physical long dimension of a
protein model to compare with x-ray scattering data. I activated the surface
mesh feature and at the extreme ends of the longest axis, right at the
surface boundary, created a carbon atom at each position, then simply used
the distance measurement wizard to measure the distance between the too
points.

praedor

On Wednesday 10 January 2007 11:29, Andreas Henschel wrote:
> Hi Giacomo,
>
> you can either create an atom at that position
> (see eg. http://www.rubor.de/bioinf/tips_python.html#chempy) and than
> use the distance command (or wizard).
[...]
> Giacomo Bastianelli wrote:
> >Dear Pymol users,
> >
> >I would like to measure the distance between an atom and
> >a specific point (not another atom) in the surface of the protein.
> >Is it possible with pymol?
> >do I need additional scripts?
> >
> >Thanks in advance,

--
Reichstag fire is to Hitler as 9/11 is to Bush



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

Message: 7
Date: Thu, 11 Jan 2007 13:02:45 -0600
From: "aaron bryden"
Subject: [PyMOL] Sequence view size
To: pymol-users@lists.sourceforge.net
Message-ID:
<977df0960701111102x11b9f53al82c0be78a8675789@mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Is their any way to get the size in pixels of the sequence view like
their is of the internal gui, or the size in pixels of the space
actually used for drawing? I know that glGetDouble(GL_VIEWPORT) but
this doesn't take into account the internal gui or the sequence view.
I can find a way to get the size of the internal gui but not the
sequence view.

thanks,

Aaron



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

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