pymol-users Mailing List for PyMOL Molecular Graphics System

Hi! Everyone:
Would you like to tell me what kind of commands I can use to draw a line
in pymol, if I know the exact location of this line in 3D-space?
Happy new year!
Fei Xu

On Tuesday, December 24, 2002, at 12:07 PM, 
pym...@li... wrote:

>    1. Suggestions for manual - nonspecialists perspective (James L. 
> Kilgore)
>
>
> What I'd like to see written in an accessible form for a 
> non-programmer is
>
> 1) A concise-but-ground-up description of what information is in a PDB
> file and other file formats including:

http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html
>
>  2)  How to read the file documentation from within PyMOL:
>
> - Go over the conventions for annotating structure files or at least
> link to something LESS THAN 300 PAGES LONG that explains the salient
> points).

http://pymol.sourceforge.net/html/toc.html

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

http://tofu.tamu.edu/pymol/

http://pymol_tutorial.tripod.com/

> - How to display protein sequence, including disulfide bond positions
> -  conditions for determination (e.g. low pH often used in NMR, could
> affect structure).
>
> 3) Directions on how to select and alter display parameters for 
> entities
> by connection like bound ligands, a selected number of contiguous
> polypeptide residues or one of several subunits, etc.
>
> 4) Instructions on options to selectively visualize interfaces between
> molecules.
>
> 5) Description and display of calculated features like electrostatic
> surfaces, hydrogen bond locations, etc.
>
> One possibility for making the software more user-friendly would be to
> organize a user  "Quick Start" abbreviated file containing links to the
> main document.
>
> -- 
> Jim Kilgore
>
>
>
>
>
>
> --__--__--
>
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>
> End of PyMOL-users Digest
>
>
>
William G. Scott

Associate Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
Sinsheimer Laboratories
University of California at Santa Cruz
Santa Cruz, California 95064
USA

phone:  +1-831-459-5367 (office)
                +1-831-459-5292 (lab)
fax:         +1-831-4593139  (fax)

What I'd like to see written in an accessible form for a non-programmer is

1) A concise-but-ground-up description of what information is in a PDB 
file and other file formats including:

- Number of subunits displayed from multimeric complexes.
- presence and number of bound ligands, number of water molecules, ions, 
etc.
- resolution, literature references,
- specific mention of which PyMOL display commands access which type of data

Those of us who are trying to teach ourselves this stuff are bewildered by

 2)  How to read the file documentation from within PyMOL:

- Go over the conventions for annotating structure files or at least 
link to something LESS THAN 300 PAGES LONG that explains the salient 
points).
- How to display protein sequence, including disulfide bond positions
-  conditions for determination (e.g. low pH often used in NMR, could 
affect structure).

3) Directions on how to select and alter display parameters for entities 
by connection like bound ligands, a selected number of contiguous 
polypeptide residues or one of several subunits, etc.

4) Instructions on options to selectively visualize interfaces between 
molecules.

5) Description and display of calculated features like electrostatic 
surfaces, hydrogen bond locations, etc.

One possibility for making the software more user-friendly would be to 
organize a user  "Quick Start" abbreviated file containing links to the 
main document.  

-- 
Jim Kilgore

Hi David,

try this:

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


Kristian



David wrote:
> Hi,
> 
> How do I access the objects I load from files (e.g. pdb file) directly
> (i.e. in a script)? If I want to print the coordinates of an atom, or
> the value of at a point in the electron density grid?
> 

Hi,

How do I access the objects I load from files (e.g. pdb file) directly
(i.e. in a script)? If I want to print the coordinates of an atom, or
the value of at a point in the electron density grid?
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
sp...@xr...	sp...@gr...   http://zorn.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

Hello:

Stereo ray-tracing is not supported yet.  Ray trace one image and then
rotate around y by 5 degrees and re-trace.

Cheers,
JTM

"We can be sure that if a detailed understanding of the molecular basis of
chemo-therapeutic activity were to be obtained, the advance of medicine
would be greatly accelerated."
  
Linus Pauling, Nobel Laureate 1954
 
"...everything that living things do can be understood in terms of the
jigglings and wigglings of atoms."
  
Richard Feynman
  
*************************
Jason Thomas Maynes
PhD/MD Program
Department of Biochemistry
Faculty of Medicine
University of Alberta
ja...@bi...
*************************



On Fri, 20 Dec 2002, cheom-gil cheong wrote:

> Dear All  :
> 
> I tried to ray trace the cross-eyed stereo figure.
> On the screen, I saw the nice stereo figure.
> However, when I opened the .png file using Adobe Illustrator after ray 
> tracing and saving the file in PyMol, I don't see the stereo figure but only 
> one image.
> Did I do something wrong?
> Did anybody successfully ray trace and make a stereo figures for the 
> publications?
> 
> Thank you very much in advance.
> 
> Sincerely Yours,
> 
> 
> 
> 
> Cheom-Gil Cheong, Ph.D.
> 
> 
> 
> _________________________________________________________________
> MSN 8 limited-time offer: Join now and get 3 months FREE*. 
> http://join.msn.com/?page=dept/dialup&xAPID=42&PS=47575&PI=7324&DI=7474&SU= 
> http://www.hotmail.msn.com/cgi-bin/getmsg&HL=1216hotmailtaglines_newmsn8ishere_3mf
> 
> 
> 
> -------------------------------------------------------
> This SF.NET email is sponsored by:  The Best Geek Holiday Gifts!
> Time is running out!  Thinkgeek.com has the coolest gifts for
> your favorite geek.   Let your fingers do the typing.   Visit Now.
> T H I N K G E E K . C O M        http://www.thinkgeek.com/sf/
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 

"We can be sure that if a detailed understanding of the molecular basis of
chemo-therapeutic activity were to be obtained, the advance of medicine
would be greatly accelerated."

Linus Pauling, Nobel Laureate 1954

"...everything that living things do can be understood in terms of the
jigglings and wigglings of atoms."

Richard Feynman

*************************
Jason Thomas Maynes
PhD/MD Program
Department of Biochemistry
Faculty of Medicine
University of Alberta
ja...@bi...
*************************

Dear All  :

I tried to ray trace the cross-eyed stereo figure.
On the screen, I saw the nice stereo figure.
However, when I opened the .png file using Adobe Illustrator after ray 
tracing and saving the file in PyMol, I don't see the stereo figure but only 
one image.
Did I do something wrong?
Did anybody successfully ray trace and make a stereo figures for the 
publications?

Thank you very much in advance.

Sincerely Yours,




Cheom-Gil Cheong, Ph.D.



_________________________________________________________________
MSN 8 limited-time offer: Join now and get 3 months FREE*. 
http://join.msn.com/?page=dept/dialup&xAPID=42&PS=47575&PI=7324&DI=7474&SU= 
http://www.hotmail.msn.com/cgi-bin/getmsg&HL=1216hotmailtaglines_newmsn8ishere_3mf

Hi have a quick PyMOL question.  I have a large ensemble of 
conformations (1000+) that I would like to look at simultaneously.  
Each conformation is a MODEL in a single PDB file (similar to NMR 
structures, but not derived experimentally).  PyMOL treats my PDB file 
as a trajectory, so I can view the models as a series of frames.  
However, a movie view makes it difficult to visualize the 
conformational space spanned by the models.  Is there any way to view 
all of the models at the same time?

Mark

Mark DePristo
Ph.D. Candidate
Dept. of Biochemistry
Cambridge University
mde...@cr...
http://www-cryst.bioc.cam.ac.uk/~mdepristo/

At 10:41 13/12/2002 +0100, Konrad Hinsen wrote:

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

 >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

> > 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.

CML is designed to be extensible by a variety of mechanisms such as 
external ontologies and we would be delighted to hear from those who find 
it "too weak". We are currently developing a computational chemistry 
implementation (CCML) as previously mentioned on this list. The feature of 
XML languages is that XML requires semantics to be well designed and 
interoperable, *and* to have communally available software tools for 
reading, validating and writing and linking to ontologies.  CML is designed 
for collaborative working and  we shall shortly announce the mailing list.

P.

Unilever Centre for Molecular Informatics
Cambridge University, UK

hi cheom,
you scan try "turn x, 5".
ok?

andre ambrosio
MSc student
CBME/IFSC/USP - Brazil

cheom-gil cheong wrote:

> Dear all  :
>
> I want to make final finest adjustments of the molecule in PyMol.
> Adjusting orientation by mouse is too coarse for the final finest
> adjustments.
> I used command "rotate x 5" but it did not work.
> Does somebody know how to do?
>
> Thanks a lot in advance.
>
> Sincerely Yours,
>
> Cheom-Gil Cheong, Ph.D.
> Research Associate
> Department of Molecular Biology
> The Scripps Research Institute
> che...@ho...
> ch...@sc...
>
> _________________________________________________________________
> Add photos to your e-mail with MSN 8. Get 2 months FREE*.
> http://join.msn.com/?page=features/featuredemail
>
> -------------------------------------------------------
> This SF.NET email is sponsored by: Order your Holiday Geek Presents Now!
> Green Lasers, Hip Geek T-Shirts, Remote Control Tanks, Caffeinated Soap,
> MP3 Players,  XBox Games,  Flying Saucers,  WebCams,  Smart Putty.
> T H I N K G E E K . C O M       http://www.thinkgeek.com/sf/
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Dear all  :

I want to make final finest adjustments of the molecule in PyMol.
Adjusting orientation by mouse is too coarse for the final finest 
adjustments.
I used command "rotate x 5" but it did not work.
Does somebody know how to do?

Thanks a lot in advance.

Sincerely Yours,


Cheom-Gil Cheong, Ph.D.
Research Associate
Department of Molecular Biology
The Scripps Research Institute
che...@ho...
ch...@sc...




_________________________________________________________________
Add photos to your e-mail with MSN 8. Get 2 months FREE*. 
http://join.msn.com/?page=features/featuredemail

Hi,

* xiaofeng qian <xia...@ho...> [2002-12-16 20:47] wrote:

>  Does anybody know how to display the electrondensity map in the wall-side 
> stereo way(not cross-eye way)?

You can switch to wall-eyed, by changing the sign of the stereo angle.
You will need to alter the stereo_shift as well:

  set stereo_angle, -2.1
  set stereo_shift, -2.
  
Cheers,
Robert
-- 
Robert L. Campbell, Ph.D.               http://biophysics.med.jhmi.edu/rlc
rl...@k2...                                    phone: 410-614-6313
Research Specialist/X-ray Facility Manager
HHMI/Dept. of Biophysics & Biophysical Chem., The Johns Hopkins University
    PGP Fingerprint: 9B49 3D3F A489 05DC B35C  8E33 F238 A8F5 F635 C0E2

Hello,
  Does anybody know how to display the electrondensity map in the wall-side 
stereo way(not cross-eye way)?
  Thanks a lot.

Xiaofeng




_________________________________________________________________
The new MSN 8: smart spam protection and 2 months FREE*  
http://join.msn.com/?page=features/junkmail

On Fri, 13 Dec 2002, Richard Gillilan wrote:

> Even XML is very verbose for molecular data, but I haven't seen any
> better way to write general objects to disk.

Apropos CML and verbose, I'd like to cite a recent post from Peter 
Murray-Rust from svg-developers:

Date: Sun, 15 Dec 2002 09:07:44 +0000
From: Peter Murray-Rust <pe...@ur...>
Reply-To: svg...@ya...
To: svg...@ya...
Cc: h....@ic...
Subject: [svg-developers] CML and SVG (definitive and final)

I am not a regular reader of svg-developers but I have been informed that
a flame war arose on it about CML (Chemical Markup Language). I don't want
to continue this - please treat this as a last posting :-)

Firstly I am a great supporter of SVG - I applauded it on XML-DEV 2-3
years ago as the first killer-app for XML-over-the-wire. I am delighted to
see such strong support for it. I hope that it becomes standard in all
modern browsers and we can rely on this - if anyone has good news on this
front let me know (off-list!).

Secondly public thanks for Michael Bierman and colleagues for the CML/SVG
application at adobe.com. This has helped to evangelise CML.

Thirdly modern CML has been informed by the SVG microsyntax and is
reasonably compact. When I saw the path attribute it convinced me that we
didn't have to mark up every tag. The CML portrayed on your list was the
first version when schemas and XSLT did not exist. The current CML (see
http://www.xml-cml.org) is formulated under XML Schema and uses a rich set
of data types to define and verify the fields. An example:
<molecule>
  <atomArray
   elementType="O C N Cl C C C C..."
   atomId="a1 a2 a3 a78 a23 a34..."
   x3="1.2 3.4 4.5 5.6 6.7 7.8..."
   y3="3.4 4.5 5.6 6.7 7.8 ..."
   z3=" 4.5 8.9 1.2 3.4..."
   />
</molecule>

That represents a complete molecule, with dataTyping (through XML Schema)
and fully explicit semantics (apart from the coordinate units). It is no
more verbose than several current formats and produces SVG of
approximately the same size. Personally I find XSLT works well though it
would be useful to have microparsing in XSLT 2.0. I also really like the
ability to transform SVG to FO - this is really a killer app for chemistry
(although most chemists have a complete phobia about all sorts of XML - as
evidenced by some of the discussion). SVG is a really important tool to
convince chemists of the value of XML.

Peter

BTW It is sad but not uncommon to see uninformed and critical discussion
of XML in chemistry. We are delighted to answer emails and this is always
the best way. We have some useful tools and many supporters :-)

Peter Murray-Rust. (CML, VHG and XML-DEV)
CML http://www.xml-cml.org/
Virtual HyperGlossary http://www.vhg.org.uk/ [new website; has XML demos]
Unilever Centre for Molecular Informatics, Cambridge University, UK
pm...@ca...

> Yes, CORBA is complex and has some overhead. I have also read that
> Microsoft's DCOM/OLE is very complex. I don't think either of
> these is a good way to go, though there are some very cool applications
> I have seen. A lab I know at LBL uses CORBA as a device interface. 

You can do nice things with CORBA, but you should be aware that using
CORBA means turning your project into a full-time software development
activity.

> Even XML is very verbose for molecular data, but I haven't seen any
> better way to write general objects to disk.

Being verbose is not really a problem nowadays, it just means bigger
files. But XML is manageable, the rules are simple, which wasn't
the case for SGML.

> options. The mode of operation I have seen for years is that a
> research group hands down mostly undocumented scripts to future
> members, passing on the knowlege of how to use them by one-on-one

Sounds familiar...

> what they want. I agree with Allen Holhub in his book on C/C++
> coding rules: "Don't solve problems that don't exist" and "Solve the
> specific problem not the general case". Too much code is over

Unless you know you will need the general case a month later anyway.
It is a difficult tradeoff that requires much experience.

But this is where high-level languages like Python are a big help.
They reduce the implementation time significantly, so you can afford
to write code for the special case, learn from your mistakes, and then
start from scratch for implementing the general case if and when you
need it.

This is a point that is not well enough appreciated, in my opinion.
Reduced development time means not only getting the job done earlier,
but also reduces the value (expressed in invested time) of code
relative to ideas, algorithms, results, etc. Which is good news for
scientists, for whom implementation is not the main job.

> What can I say? Nobody likes to have to adhere to standards, and it

I do. If there are standards, and they work well, then I am happy
to use them instead of starting from scratch.

> is very hard work to get people to agree on them. Ultimately,

That is the real problem. Especially when adhering to standards means
modifying existing and working code, which is, on a short time scale,
unproductive.

But my criticism about OMG-style design-by-committee is not standards,
it the institutionalization of the process that restricts
participation to big players. This is not a good model for scientific
programming, in which most innovation as well as most code comes from
small research groups who do programming as a side job next to their
research.

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

Hello
I'm trying to prepare lovely images for my thesis and cant seem to get
them just right
I'm using ray 1200, 900 which I thought would be fine however although
it looks lovely on screen, it dosent seem to print properly-ie
resolution goes down and colours change
Do i need to use povray? I thought ray in pymol was to produce lovely
figures?
Thank you in advance
Lauris

> Konrad Hinsen wrote:
> 
> 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. ...

Yes, CORBA is complex and has some overhead. I have also read that
Microsoft's DCOM/OLE is very complex. I don't think either of
these is a good way to go, though there are some very cool applications
I have seen. A lab I know at LBL uses CORBA as a device interface. 

>  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.

Even XML is very verbose for molecular data, but I haven't seen any
better way to write general objects to disk.

> 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.

I agree that simplicity is most important. The vast majority of 
scientific users are non-programmers and have no time or desire to
write and debug code (scripts, visual programs or otherwise). These
folks need a good end-user application with simple configuration
options. The mode of operation I have seen for years is that a research group hands down
mostly undocumented scripts to future members, passing on the knowlege
of how to use them by one-on-one interaction. A few students will delve 
into the code and really modify, but most will just know how to edit
a few parameters to get what they want. I agree with Allen Holhub in his
book on C/C++ coding rules: "Don't solve problems that don't 
exist" and "Solve the specific problem not the general case". Too much code 
is over configurable, which makes installation and use a combinatorial nightmare.

> 
> 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.
> 

What can I say? Nobody likes to have to adhere to standards, and it is very hard work
to get people to agree on them. Ultimately, though, I think that is the way
things will head as information (ge



> Konrad.

Kristl,

	It may not be possible to switch PyMOL over to correctly recognizing =
these bonds by default, but you should be able to use the "bond" command =
after loading to manually create the bonds.

Cheers,
Warren


--
mailto:wa...@su...
Warren L. DeLano, Ph.D.=20
Informatics Manager=20
Sunesis Pharmaceuticals, Inc.=20
341 Oyster Point Blvd.=20
S. San Francisco, CA 94080=20
(650)-266-3606 FAX:(650)-266-3501



> -----Original Message-----
> From: Kristl Adams [mailto:kr...@ph...]
> Sent: Friday, December 13, 2002 12:16 PM
> To: pym...@li...
> Subject: [PyMOL] bond cut-off
>=20
>=20
>=20
> Anyone know how to increase the bond drawing cut-off?  I'm=20
> trying to get
> Pymol to draw bonds from the Fe to the N atoms in a heme group.
>=20
> Thanks in advance,
> Kristl
>=20
> kr...@ph...
>=20
>=20
>=20
> -------------------------------------------------------
> This sf.net email is sponsored by:
> With Great Power, Comes Great Responsibility=20
> 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
>=20

Anyone know how to increase the bond drawing cut-off?  I'm trying to get
Pymol to draw bonds from the Fe to the N atoms in a heme group.

Thanks in advance,
Kristl

kr...@ph...

> Thanks for the reminder about FSAtom. Maybe we should start a 
> discussion somewhere about what needs to be included in either a common 
> file format or a common interface.

That would be a good occasion to start real activity on the
FSAtom mailing list. Anyone can subscribe at

       http://www.tddft.org/mailman/listinfo/fsatom

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

On Friday, December 13, 2002, at 01:41  AM, Konrad Hinsen wrote:
>
>> 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,

Thanks for the reminder about FSAtom. Maybe we should start a 
discussion somewhere about what needs to be included in either a common 
file format or a common interface.

R.

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

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

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

> 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
-------------------------------------------------------------------------------

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