pymol-users — Collaborative support and tips for PyMOL users

Re: [MMTK] [PyMOL] improving interoperability between python molecule toolkits (fwd)

[Richard M. <rp...@wa...>]

On Thursday, December 12, 2002, at 11:31  PM, Konrad Hinsen wrote:
>
>> The question is whether the will exists to do this? Many of the 
>> toolkits
>
> On my side, yes.

As well as on mine (PyQuante).

Rick Muller
rp...@wa...
http://wag.caltech.edu/home/rpm

Re: [MMTK] [PyMOL] improving interoperability between python molecule toolkits (fwd)

[Konrad H. <hi...@cn...>]

Gustavo Mercier <gam...@ya...> writes:

> to the chemistry of a problem. In advanced undergraduate course, an
> instructor may wish to breakthrough the "black box". The scripting

*Should* wish to do so. Understanding what one is doing is the
difference between a scientist and a lab technician.

> this effort. Unfortunately, the issue is one of leadership to
> initiate such a project. May be those who mantain MMTK, PyQuante,
> PyMol, etc. may be willing to take the initiative.

This issue has been addressed at a meeting on OpenSource software for
atomistic simulations (which includes physics and chemistry) this
year. The result is the formation of an informal organization called
"FSAtom": http://www.fsatom.org/ Among the goals of this organizations
is the design of common interfaces to ensure the interoperability of
OpenSource codes. There will be more meetings (not committee style,
but scientific workshops) as well as mailing list discussions.
Everybody is welcome to join.

> may go along way to make development not only easier but useful. It
> would be best not to rediscover the wheel.

And come up with a hexagon ;-)

> As a suggestion, let's consider the chemistry implementation of XML
> -- CML. Whatever the details of the object "molecule", it would be
> beneficial to input and output to/from CML. A specification of

I don't agree. I looked at CML a while ago, thought about implementing
it in MMTK, but quickly found out that almost none of the information
I needed to store about molecules could be represented in CML, except
by adding "conventions" of my own - but then I could just as well
define my own XML format. CML is based on the right intentions, but is
too weak as an implementation.

BTW, common file formats are another goal of the FSAtom organization.

Konrad.
-- 
-------------------------------------------------------------------------------
Konrad Hinsen                            | E-Mail: hi...@cn...
Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.56.24
Rue Charles Sadron                       | Fax:  +33-2.38.63.15.17
45071 Orleans Cedex 2                    | Deutsch/Esperanto/English/
France                                   | Nederlands/Francais
-------------------------------------------------------------------------------

Re: [MMTK] Re: [PyMOL] improving interoperability between python moleculetoolkits (fwd)

[Konrad H. <hi...@cn...>]

> One of the reasons I have stuck with OpenDX (www.opendx.org) for
> visualization for so long is the general (object-oriented) data
> model. It has its limitations, but it has proven very powerful.
> Users can define a wide variety of data in hierarchical forms.

Indeed. But this illustrates nicely a frequent problem faced by
software designers: Software like OpenDX is powerful and flexible, but
also huge and difficult to learn. A small specialized tool is easier
to use for the specialized user. Of course those users then find
themselves in a mess of specialized tools a few years later, but it is
rather hopeless to try to warn them about this in advance.

> future system should put a great deal of work into developing a
> strong underlying general data model, not just for molecules, but
> for all kinds of scientific data: grids, vector fields, polygonal
> surfaces, trees etc. Just leaving things open to general objects is

Although that is desirable in principle, too ambitious projects often
end up in either an unfinished or an unmanageable state. Take CORBA,
for example. A great concept, very general but implementations are few
in number, often slow, sometimes expensive, and always come with a
steep learning curve. Or take SGML: the general of the general, but
people started looking at it only when its slim brother XML was there.

It is not easy to find the right equilibrium between simplicity and
generality. For the specific case of scientific computing, I think
simplicity is more important in most cases. Scientists need to
understand and be able to modify code that is the basis for their
research. And they are usually not well-trained software developers.

> Anyone ever checked out the Object Management Group (OMG)? I went to
> one of their meetings (Objects ion Bio- & Chem-Informatics 2001) a
> while back and was impressed with the concept. They are basically a
> non-profit consortium that sets open industry standards for objects

Well... It's a design by committee approach that has rarely produced
useful results in spite of an enormous effort. Moreover, which
scientist can afford to participate in their meetings? That's a
full-time job.

Konrad.
-- 
-------------------------------------------------------------------------------
Konrad Hinsen                            | E-Mail: hi...@cn...
Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.56.24
Rue Charles Sadron                       | Fax:  +33-2.38.63.15.17
45071 Orleans Cedex 2                    | Deutsch/Esperanto/English/
France                                   | Nederlands/Francais
-------------------------------------------------------------------------------

Re: [MMTK] [PyMOL] improving interoperability between python molecule toolkits (fwd)

[Konrad H. <hi...@cn...>]

Eugen Leitl <eu...@le...> writes:

> It seems to be in everyone's interest to allow easy interoperation
> between the toolkits. However, in my experience it is a frustrating and
> difficult task, even for relatively simple tasks. 

True.

> I believe that a common set of core modules is required. The most

Not necessarily, although it might be the most practical approach. The
minimum requirement in Python is a common core interface,
implementations could be different.

> and optimised for specialised work. If a common molecule definition can
> be agreed upon by the major authors of the toolkits concerned,
> interoperability will be made MUCH easier. Other multipurpose molecular

Definitely. The problem is that this is a major effort, first for
defining a sufficiently universal set of classes, and then for
adapting all the codes to it, plus eventually providing a
compatibility layer to keep old client code working. It won't happen
overnight.

> The question is whether the will exists to do this? Many of the toolkits

On my side, yes.

Konrad.
-- 
-------------------------------------------------------------------------------
Konrad Hinsen                            | E-Mail: hi...@cn...
Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.56.24
Rue Charles Sadron                       | Fax:  +33-2.38.63.15.17
45071 Orleans Cedex 2                    | Deutsch/Esperanto/English/
France                                   | Nederlands/Francais
-------------------------------------------------------------------------------

RE: [PyMOL] Lighting questions: round 2

[Schubert, C. <Car...@3d...>]

Kelley,

syntax is something like this:

    set light, [ 0.0, 0.0, -1.0 ]

If you want to shine light directly from above I would give

    set light, [ 0.0, -1.0, 0.0 ]

a shot. i.e. with a vector from [0,0,0] to [ 0.0, -1.0, 0.0 ], but that is
just a guess. I have not seen any documentation on how the direction of
light is defined in Pymol. Alternatively you can write out the scene for
PovRay and try to play around with the settings there.

Happy Pymoling

	Carsten

-----Original Message-----
From: Kelley Moremen [mailto:mo...@ar...]
Sent: Thursday, December 12, 2002 17:07
To: pym...@li...
Subject: [PyMOL] Lighting questions: round 2


Dear Pymolers,

After my last round question on lighting it became clear that the relevant
setting for positing the light source for the ray traced image was "light".
There are three parameters to be set with the "light" setting, but it is not
clear what each value refers to (is it X,Y,Z for the position of the light
source?).  More importantly, what is the syntax for the alteration of the
light setting from the command line? I am running Pymol in OS X and do not
have access to the GUI panel for changing settings. I have tried numerous
variations on the theme of:
set light=-0.4, -0.4, -1.0
Any clues as to the appropriate syntax for altering the lighting to
originate from straight above the object in the image window?

Thanks,
Kelley



Dr. Kelley Moremen 
Associate Professor 
Complex Carbohydrate Research Center
Department of Biochemistry and Molecular Biology 
University of Georgia, Athens, GA 30602-7229 
Office (706) 542-1705    Fax: (706) 542-1759
Email: mo...@ar...
(send email with large attachments to: mo...@bm...)
Website: http://bmbiris.bmb.uga.edu/moremen/lab/ 

[PyMOL] Lighting questions: round 2

[Kelley M. <mo...@ar...>]

Dear Pymolers,

After my last round question on lighting it became clear that the relevant
setting for positing the light source for the ray traced image was =B3light=B2.
There are three parameters to be set with the =B3light=B2 setting, but it is no=
t
clear what each value refers to (is it X,Y,Z for the position of the light
source?).  More importantly, what is the syntax for the alteration of the
light setting from the command line? I am running Pymol in OS X and do not
have access to the GUI panel for changing settings. I have tried numerous
variations on the theme of:
set light=3D-0.4, -0.4, -1.0
Any clues as to the appropriate syntax for altering the lighting to
originate from straight above the object in the image window?

Thanks,
Kelley


Dr. Kelley Moremen=20
Associate Professor
Complex Carbohydrate Research Center
Department of Biochemistry and Molecular Biology
University of Georgia, Athens, GA 30602-7229
Office (706) 542-1705    Fax: (706) 542-1759
Email: mo...@ar...
(send email with large attachments to: mo...@bm...)
Website: http://bmbiris.bmb.uga.edu/moremen/lab/

Re: [PyMOL] Setting light direction in ray traced images

[Kristl A. <kr...@ph...>]

You can go to Settings - Edit all and change the vetor of the light ...
you may also want to increase direct -- light coming from camera shot or
ambient light.
Check out pg 32 and 33 in the online manual (Ray-Tracing section).

Do you know if I can add an additional light and how to do that?

Thanks and Good Luck!
Kristl


On Thu, 12 Dec 2002, Kelley Moremen wrote:

> Dear Pymolers,
>
> I am sure this has been discussed previously but I can=B9t find the respo=
nse
> anywhere.  How do you alter the light settings to allow you to change the
> direction of incoming light (and corresponding shadows).  I am generating
> images of a deep active site pocket in a slab view and I need the light t=
o
> come from above rather than the front/side in order to illuminate the dee=
p
> pocket. Alternatively, is there another way to illuminate the recesses of
> the pocket and maintain the shadow effects at the surface?
>
> Thanks,
>
> Kelley
>
> Dr. Kelley Moremen
> Associate Professor
> Complex Carbohydrate Research Center
> Department of Biochemistry and Molecular Biology
> University of Georgia, Athens, GA 30602-7229
> Office (706) 542-1705    Fax: (706) 542-1759
> Email: mo...@ar...
> (send email with large attachments to: mo...@bm...)
> Website: http://bmbiris.bmb.uga.edu/moremen/lab/
>
>
>

Re: [MMTK] [PyMOL] improving interoperability between python molecule toolkits (fwd)

[Gustavo M. <gam...@ya...>]

Hi!
I think the comments below are right on the money.
I believe that a molecular modeling package powered by Python is a great idea, particularly for those who would like to teach computational chemistry.
For example, many popular modeling packages allow the students to perform simulations using a black box approach. This is fine for introductory courses where the focus is on the end results relevant to the chemistry of a problem. In advanced undergraduate course, an instructor may wish to breakthrough the "black box". The scripting power of Python together with a set of modules would be the best tool for such a course. The students could program simulations using objects available through the modules. Each layer of the black box can be peeled by programming with lower level objects.
Although I've been a bit away from Python (my last heavy use was with version 1.5x!), I certainly will support and even contribute to this effort. Unfortunately, the issue is one of leadership to initiate such a project. May be those who mantain MMTK,  PyQuante, PyMol, etc. may be willing to take the initiative.
The definition of a common object/data structure for the "molecule" is a first step. This is a critical step and a little bit of thought may go along way to make development not only easier but useful. It would be best not to rediscover the wheel.
As a suggestion, let's consider the chemistry implementation of XML -- CML. Whatever the details of the object "molecule", it would be beneficial to input and output to/from CML. A specification of "molecule" based on CML would make it easier to interface with other technologies. I recognize that there are problems with CML, but this should not stop the community from considering this "standard".
Gustavo
 Eugen Leitl <eu...@le...> wrote:


-- 
-- Eugen* Leitl leitl
______________________________________________________________
ICBMTO: N48 04'14.8'' E11 36'41.2'' http://eugen.leitl.org
83E5CA02: EDE4 7193 0833 A96B 07A7 1A88 AA58 0E89 83E5 CA02
http://moleculardevices.org http://nanomachines.net

---------- Forwarded message ----------
Date: Thu, 12 Dec 2002 16:58:47 +1030
From: Michael Sorich 
To: pym...@li...
Subject: [PyMOL] improving interoperability between python molecule toolkits

Hello all,

I share in Warren's vision of extending PyMol into a "complete platform
for crystallography, computational chemistry, modeling, and
informatics". However, I believe this can only come about by cooperation
and integration with other python based molecule toolkits. 

<cut stuff ...> 

It seems to be in everyone's interest to allow easy interoperation
between the toolkits. However, in my experience it is a frustrating and
difficult task, even for relatively simple tasks. 

Does anyone else feel the same frustration? And if so, does anyone have
a solution?

I believe that a common set of core modules is required. The most
important feature is the molecule. 

<cut stuff ...>

 


--
Gustavo A. Mercier, Jr., MD,PhD
Seattle Nuclear Medicine & U/S Associates
1229 Madison, Suite 1150
Seattle, WA 98104-1377
voice: 206-386-6300; fax: 206-386-6312
gam...@ya... 


---------------------------------
Do you Yahoo!?
New DSL Internet Access from SBC & Yahoo!

[PyMOL] Setting light direction in ray traced images

[Kelley M. <mo...@ar...>]

Dear Pymolers,

I am sure this has been discussed previously but I can=B9t find the response
anywhere.  How do you alter the light settings to allow you to change the
direction of incoming light (and corresponding shadows).  I am generating
images of a deep active site pocket in a slab view and I need the light to
come from above rather than the front/side in order to illuminate the deep
pocket. Alternatively, is there another way to illuminate the recesses of
the pocket and maintain the shadow effects at the surface?

Thanks,

Kelley =20

Dr. Kelley Moremen=20
Associate Professor
Complex Carbohydrate Research Center
Department of Biochemistry and Molecular Biology
University of Georgia, Athens, GA 30602-7229
Office (706) 542-1705    Fax: (706) 542-1759
Email: mo...@ar...
(send email with large attachments to: mo...@bm...)
Website: http://bmbiris.bmb.uga.edu/moremen/lab/

Re: [PyMOL] Poyray / windows

[Virgile A. <ka...@wa...>]

Hi Kristl,

Use "ray renderer=1" instead of a simple "ray".
The raytracing will use Povray if well installed and create a pov file.

Hope that it helps

Cheers

Virgile

[PyMOL] Poyray / windows

[Kristl A. <kr...@ph...>]

Is it possible to output a Pymol file that Povray can read using windows?

Also is it possible to add lights into a Pymol file?

Thanks,
Kristl

Re: [PyMOL] improving interoperability between python molecule toolkits

[Michael B. <mb...@gm...>]

Hi again,

Ok, so the license is available at

http://www.bio.cam.ac.uk/nmr/ccp/project/about_ccpn/licensing/licensing.html


Unfortunately, this looks quite incompatible to the GPL:

 (2) Conditions for DISTRIBUTION of SOFTWARE to MEMBERS

 (2.1) An individual or ORGANISATION must be a MEMBER  of
CCPN in order to receive any SOFTWARE from CCPN, and must
adhere    to    the    MEMBERSHIP,    DISTRIBUTION    and
RE-DISTRIBUTION  rules.  Under   these  conditions,   any
previously DISTRIBUTED SOFTWARE  may be used  in for  the
lifetime of  the  SOFTWARE  even if  MEMBERSHIP  of  CCPN
lapses.

 (4) Conditions for MEMBERSHIP of CCPN

 MEMBERSHIP for an  individual or  ORGANISATION shall  be
based on  registration  and  payment  of  annual  fee  as
required and  detailed  below.  The  annual  fee  may  be
reviewed from time to time. The current scale of fees are
as follows:
 a. individuals and not for profit ORGANISATIONs
   - nil
 b. ORGANISATIONs with annual  turnover less than  200000
pounds Sterling
   - nil
 c. ORGANISATIONs  with  annual turnover  between  200000
pounds Sterling and 1 million pounds Sterling
   - 1000 pounds Sterling
 d. ORGANISATIONs with  annual turnover  larger than  one
million pounds Sterling
   - 7000 pounds Sterling

This makes the software not freely distributable, IMHO

Furthermore, it violates one of the definitions of Open-Source Software,
namely 'No Discrimination Against Persons or Groups', see
http://www.opensource.org/docs/definition.php.

Please correct me if I'm wrong.

thanks,

Michael

Re: [PyMOL] improving interoperability between python moleculetoolkits

[Richard G. <re...@co...>]

Jules Jacobsen wrote:
> 
... stuff deleted
> The core of this program is the data model in which each atom in a
> molecule is defined. The next layer are the conversion scripts which take
> the molecule data from the model and pipe them out to whatever format is
> needed for the various data manipulation programs (Aqua, XPLOR and the
> like). Seeing as this model is in existance and will be tightly integrated
> with the PDB databank for their structural checking procedures prior to
> accepting a model it would make sense that this be used as an industrial
> standard.

My two cents:

One of the reasons I have stuck with OpenDX (www.opendx.org) for visualization for so 
long is the general (object-oriented) data model. It has its limitations,
but it has proven very powerful. Users can define a wide variety of data in 
hierarchical forms. Modules can be quite smart about the data structures they
recieve: for example the isosurface module can accept groups of 2D and 3D grids
and will produce corresponding groups of lines and surfaces. It was also easy
for me to create a RenderMan/BlueMoon module that allowed OpenDX users to seamlessly
access almost all the features of the renderer without modifying any OpenDX code.
Same was true of the MatLab module a student and I created.
This was all possible because of the general data model (which, by the
way, was designed with parallelism in mind from the start).

I'm not neccessarily trying to plug the OpenDX model (though I strongly
enourage folks to take careful look), but I think that any future system 
should put a great deal of work into developing a strong underlying
general data model, not just for molecules, but for all kinds of scientific data:
grids, vector fields, polygonal surfaces, trees etc. Just leaving things open to 
general objects is not a good idea ... there needs to be some structure and standardization
so that 3rd-party modules can be intelligent and interoperable.

Anyone ever checked out the Object Management Group (OMG)? I went to one of their
meetings (Objects ion Bio- & Chem-Informatics 2001) a while back and was impressed
with the concept. They are basically a non-profit consortium that sets open industry 
standards for objects across all different languages. CORBA is one of their babies. 
The PDB is also involved with OMG as are a number of bio/macromolecule groups (Michel
Sanner of Scripps gave a nice talk on his Python-based modeling system). Worth looking 
into.


Richard Gillilan
MacCHESS, Cornell

Re: [PyMOL] improving interoperability between python molecule toolkits

[Michael B. <mb...@gm...>]

On Thu, Dec 12, 2002 at 10:33:47AM +0000, Jules Jacobsen wrote:
> I completely agree here, an integrated total platform would be immensely
> useful.
> I think that the problem is not necessarily all that far from a solution-
> currently there is a collaborative computing project for NMR (CCPN)
> 
> http://www.bio.cam.ac.uk/nmr/ccp/
 
Looks interesting, but I couldn't find a License. What's the License for
CCPN, please?

thanks,

Michael

Re: [PyMOL] improving interoperability between python molecule toolkits

[Jules J. <jo...@he...>]

I completely agree here, an integrated total platform would be immensely
useful.
I think that the problem is not necessarily all that far from a solution-
currently there is a collaborative computing project for NMR (CCPN)

http://www.bio.cam.ac.uk/nmr/ccp/

The core of this program is the data model in which each atom in a
molecule is defined. The next layer are the conversion scripts which take
the molecule data from the model and pipe them out to whatever format is
needed for the various data manipulation programs (Aqua, XPLOR and the
like). Seeing as this model is in existance and will be tightly integrated
with the PDB databank for their structural checking procedures prior to
accepting a model it would make sense that this be used as an industrial
standard.


Jules


Jules Jacobsen
MRC Centre for Protein Engineering
Cambridge Laboratory of Molecular Biology



On Thu, 12 Dec 2002, Michael Sorich wrote:

> Hello all,
>
> I share in Warren's vision of extending PyMol into a "complete platform
> for crystallography, computational chemistry, modeling, and
> informatics". However, I believe this can only come about by cooperation
> and integration with other python based molecule toolkits. MMTK has code
> which may be expanded into a general molecular mechanics engine. Frowns
> toolkit allows for detailed chemical analysis based on topology,
> including useful tools such as substructure searching (required for
> forcefield atom typing). PyQuante allows for Quantum Chemical
> calculations.
>
> It seems to be in everyone's interest to allow easy interoperation
> between the toolkits. However, in my experience it is a frustrating and
> difficult task, even for relatively simple tasks.
>
> Does anyone else feel the same frustration? And if so, does anyone have
> a solution?
>
> I believe that a common set of core modules is required. The most
> important feature is the molecule. Each toolkit uses a different
> molecule, each with a different interface, holding different information
> and optimised for specialised work. If a common molecule definition can
> be agreed upon by the major authors of the toolkits concerned,
> interoperability will be made MUCH easier. Other multipurpose molecular
> modelling programs (MOE, Sybyl) seem to get by using a common molecule
> definition, so I believe that it is theoretically possible. The aim
> would be to define a molecule that contains all the functionality
> required for the multiple toolkits and to maintain the interfaces used
> by the toolkits as much as possible.
>
> The question is whether the will exists to do this? Many of the toolkits
> are relatively young. I feel that the longer the problem is ignored, the
> less likely that it will be possible to combine features from various
> toolkits.
>
> I am interested in other people's thoughts on this matter.
>
>
> Michael Sorich
> PhD Student
> School of Pharmaceutical, Molecular and Biomedical Sciences
> University of South Australia
> Email: mic...@po...
>            mik...@ho...
>
>
>
> ---
> Outgoing mail is certified Virus Free.
> Checked by AVG anti-virus system (http://www.grisoft.com).
> Version: 6.0.408 / Virus Database: 230 - Release Date: 24/10/2002
>
>
>
> -------------------------------------------------------
> This sf.net email is sponsored by:
> With Great Power, Comes Great Responsibility
> Learn to use your power at OSDN's High Performance Computing Channel
> http://hpc.devchannel.org/
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>

[PyMOL] Re: molecular surfaces

[Kristian R. <kri...@ch...>]

Dear Rajarshi Guha,

You could at least try to reconfigure Robert Campbell's Color-by-B-factor=
=20
script. It assigns each atom its own color according to another value.

http://www.rubor.de/bioinf/pymol_tips.html#bfac

Kristian

[PyMOL] improving interoperability between python molecule toolkits

[Michael S. <mik...@ho...>]

Hello all,

I share in Warren's vision of extending PyMol into a "complete platform
for crystallography, computational chemistry, modeling, and
informatics". However, I believe this can only come about by cooperation
and integration with other python based molecule toolkits. MMTK has code
which may be expanded into a general molecular mechanics engine. Frowns
toolkit allows for detailed chemical analysis based on topology,
including useful tools such as substructure searching (required for
forcefield atom typing). PyQuante allows for Quantum Chemical
calculations.

It seems to be in everyone's interest to allow easy interoperation
between the toolkits. However, in my experience it is a frustrating and
difficult task, even for relatively simple tasks. 

Does anyone else feel the same frustration? And if so, does anyone have
a solution?

I believe that a common set of core modules is required. The most
important feature is the molecule. Each toolkit uses a different
molecule, each with a different interface, holding different information
and optimised for specialised work. If a common molecule definition can
be agreed upon by the major authors of the toolkits concerned,
interoperability will be made MUCH easier. Other multipurpose molecular
modelling programs (MOE, Sybyl) seem to get by using a common molecule
definition, so I believe that it is theoretically possible. The aim
would be to define a molecule that contains all the functionality
required for the multiple toolkits and to maintain the interfaces used
by the toolkits as much as possible.

The question is whether the will exists to do this? Many of the toolkits
are relatively young. I feel that the longer the problem is ignored, the
less likely that it will be possible to combine features from various
toolkits. 

I am interested in other people's thoughts on this matter.


Michael Sorich
PhD Student
School of Pharmaceutical, Molecular and Biomedical Sciences
University of South Australia
Email: mic...@po...
           mik...@ho...



---
Outgoing mail is certified Virus Free.
Checked by AVG anti-virus system (http://www.grisoft.com).
Version: 6.0.408 / Virus Database: 230 - Release Date: 24/10/2002
 

[PyMOL] molecular surfaces

[Rajarshi G. <raj...@pr...>]

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Hi,
  I'm a first time user of PyMol and I was wondering whether it's possible to 
do the following:

I have a program which uses Hyperchem HIN files to calculate hydrophobicity 
data for each atom in the molecule. Essentially it gives the follwoing info:

  Atom Num.   Atom Type.   Value.

for each atom in the molecule. I would like to plot the value for each atom as 
an intrerpolated surface. Essentially its the same as a electrostatic 
potential plot - except that the values are actually hydrophobicity values.

Is this at all possible in PyMol? I'd appreciate any pointers or suggestions



- -- 
- -------------------------------------------------------------------
Rajarshi Guha  <raj...@pr...> <http://jijo.cjb.net>
GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04  06F7 1BB9 E634 9B87 56EE
- -------------------------------------------------------------------
A memorandum is written not to inform the reader, but to protect the writer.
		-- Dean Acheson

-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.0.7 (GNU/Linux)

iD8DBQE992/OG7nmNJuHVu4RAmrhAJ458FXZPFHZFUQh0z1YWd2VVJdfxgCfUrKn
TvA4y13QqeqVi5YFbcEJqsM=
=3HQq
-----END PGP SIGNATURE-----

Re: [PyMOL] multiple objects

[Jules J. <jo...@he...>]

Hi Michael,

If I understand you right you already can do this- make sure that no atoms
are selected first then click on the mouse menu so that when you press
'shift' RotF and MovF are implemented. Then all you have to do is move the
mouse over the molecule you want to move/rotate whilst holding down the
shift key and that molecule will move. To move all just release the shift
key. Finally ensure the molecules are displayed in stick/line form or else
they won't move.

Jules

On Mon, 9 Dec 2002, Michael Ford wrote:

> So I know how to manipulate objects individually using the rotate and
> translate commands.  But what would be really useful is to be able to
> control which objects are controlled by the mouse (probably a critical
> function that will be implemented in the next release??).  Insight
> handles this with the ability to 'clip' to an object or manipulate the
> 'world' (meaning all objects).
>
> Just wondering and eagerly anticipating the new version!
>
>
> Michael Ford
>
>
> -------------------------------------------------------
> This sf.net email is sponsored by:ThinkGeek
> Welcome to geek heaven.
> http://thinkgeek.com/sf
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>

[PyMOL] multiple objects

[Michael F. <mf...@cc...>]

So I know how to manipulate objects individually using the rotate and
translate commands.  But what would be really useful is to be able to
control which objects are controlled by the mouse (probably a critical
function that will be implemented in the next release??).  Insight
handles this with the ability to 'clip' to an object or manipulate the
'world' (meaning all objects).  

Just wondering and eagerly anticipating the new version!


Michael Ford

Re: [PyMOL] double bonds

[Michael G. L. <ml...@um...>]

On Mon, 9 Dec 2002, John Duperon wrote:

> Hello everyone,
>
> hopefully this is a question which is not answered in some FAQ that I
> missed...is it possible to have PyMol show double bonds in a simple
> manner not unlike what would be found in a high school text book?  Just
> a black and white stick diagram?  Or perhaps the same, but using the
> dotted notation?

you can try going into lines mode and turning on the valence display:

hide
show lines
set valence, 0.1

a higher value for valence spreads things out more.
i don't know of a way to get the dotted notation.

cheers,

-michael

--
This isn't a democracy;|                        _  |Michael Lerner
 it's a cheer-ocracy.  | ASCII ribbon campaign ( ) |   Michigan
-Torrence,  Bring It On|  - against HTML email  X  |  Biophysics
                       |                       / \ | mlerner@umich

[PyMOL] double bonds

[John D. <du...@mp...>]

Hello everyone,

hopefully this is a question which is not answered in some FAQ that I 
missed...is it possible to have PyMol show double bonds in a simple 
manner not unlike what would be found in a high school text book?  Just 
a black and white stick diagram?  Or perhaps the same, but using the 
dotted notation?

Thanks in advance,

John

Re: [PyMOL] how to show both ligand and surface

[Jules J. <jo...@he...>]

Hi Eric,

Try:

set transparency=0.5
show sticks

transparency values from 0-1

hope this helps

Jules


On Sun, 8 Dec 2002, eric hu wrote:

> Hi, I am kinda new to pymol. I wonder if I can show
> both ligand and the surface around it. In other word,
> can I increase the transparency of the surface so that
> I can still see the ligand in line representation.
> Thanks!
>
> Eric
>
> __________________________________________________
> Do you Yahoo!?
> Yahoo! Mail Plus - Powerful. Affordable. Sign up now.
> http://mailplus.yahoo.com
>
>
> -------------------------------------------------------
> This sf.net email is sponsored by:ThinkGeek
> Welcome to geek heaven.
> http://thinkgeek.com/sf
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>

[PyMOL] how to show both ligand and surface

[eric hu <eri...@ya...>]

Hi, I am kinda new to pymol. I wonder if I can show
both ligand and the surface around it. In other word,
can I increase the transparency of the surface so that
I can still see the ligand in line representation.
Thanks!

Eric

__________________________________________________
Do you Yahoo!?
Yahoo! Mail Plus - Powerful. Affordable. Sign up now.
http://mailplus.yahoo.com

[PyMOL] pai-pai stacking

[eric hu <eri...@ya...>]

Is there anyway to indicate a pai-pai stacking similar
like hydrogen bond?

Eric

__________________________________________________
Do you Yahoo!?
Yahoo! Mail Plus - Powerful. Affordable. Sign up now.
http://mailplus.yahoo.com