pymol-users — Collaborative support and tips for PyMOL users

RE: [PyMOL] pymol-specific dri problems

[Soisson, S. M. <ste...@me...>]

Peter,

I am running SuSE linux on a machine with a Radeon7500 card and it does run
OK.  I noticed the error in your radeon glxinfo about a read error of some
sort on radeon_dri.so.  Good chance this is a problem.  The bad thing here
is that Radeon does not distribute linux drivers for the 7500 card (last I
checked), so you are a bit on your own.  My best guess is to try tracking
down the dri error - perhaps downloading the latest versions of everything
(XFree86, openGL, etc) and reinstalling.  Sorry I couldn't be of more
specific help.

Good luck,

Steve

 

-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of Peter C. Lai
Sent: Wednesday, March 22, 2006 7:34 PM
To: pym...@li...
Subject: Re: [PyMOL] pymol-specific dri problems


On 3/20/06, Soisson, Stephen Michael <ste...@me...> wrote:
> Can you post your output from glxinfo?  This will have some information
> about the DRI modules.
>
> What OS and graphics card?  Without knowing any of the details, the best
> place to start is by downloading a driver from radeon, and following the
> installation procedure exactly.  It is sometimes very, very tricky.

OS: FreeBSD 6-RELEASE
Card: Radeon 7500 RV250. I have also machines with a Radeon R200 card
and a Matrox G200 that haven't worked either with otherwise the exact
same software setups. Again, all of my softtware is built from source
(the FreeBSD ports tree from Feb. 2006).

I am using the DRI drivers that come with Mesa 6.4.1. I have tested
this on all of my machines with different cards, same software, and
they all have the same issue, with pymol only (well I have only tested
with the mesa-demos and VMD but those should be fairly representative
of working OpenGL applications).

Attached are the glxinfo outputs for the radeon and mga cards (with
LIBGL_DEBUG=verbose, as usual).

>
> Cheers,
>
> Steve
>
> -----Original Message-----
> From: pym...@li...
> [mailto:pym...@li...] On Behalf Of Peter C. Lai
> Sent: Sunday, March 19, 2006 9:21 PM
> To: pym...@li...
> Subject: [PyMOL] pymol-specific dri problems
>
>
> Setup: X.org 6.9.0; dri/libglut-6.4.1,  built from freebsd-ports
>
> I am getting this libGL error causing pymol to fall back to software
> rendering:
>
> libGL: XF86DRIGetClientDriverName: 5.0.3 radeon (screen 0)
> libGL: OpenDriver: trying /usr/X11R6/lib/modules/dri/radeon_dri.so
> libGL error: dlopen /usr/X11R6/lib/modules/dri/radeon_dri.so failed
> (/usr/X11R6/lib/modules/dri/radeon_dri.so: Undefined symbol
> "_glapi_Dispatch")
> libGL error: unable to find driver: radeon_dri.so
>
> Direct Rendering is enabled.
> Other applications (i.e. the mesa demos) that rely on both libglut and
> libGL work fine and are direct rendering enabled. VMD works fine,
> PyMol's UI is way better, which is why I'm trying to get this working
> :)
>
> So obviously, it does not appear to be a problem with my DRI
> installation. Perhaps one of the coders can shed some light on this?
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by xPML, a groundbreaking scripting
language
> that extends applications into web and mobile media. Attend the live
webcast
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> _______________________________________________
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> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>
>
>
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Re: [PyMOL] pymol-specific dri problems

[Peter C. L. <co...@gm...>]

On 3/20/06, Soisson, Stephen Michael <ste...@me...> wrote:
> Can you post your output from glxinfo?  This will have some information
> about the DRI modules.
>
> What OS and graphics card?  Without knowing any of the details, the best
> place to start is by downloading a driver from radeon, and following the
> installation procedure exactly.  It is sometimes very, very tricky.

OS: FreeBSD 6-RELEASE
Card: Radeon 7500 RV250. I have also machines with a Radeon R200 card
and a Matrox G200 that haven't worked either with otherwise the exact
same software setups. Again, all of my softtware is built from source
(the FreeBSD ports tree from Feb. 2006).

I am using the DRI drivers that come with Mesa 6.4.1. I have tested
this on all of my machines with different cards, same software, and
they all have the same issue, with pymol only (well I have only tested
with the mesa-demos and VMD but those should be fairly representative
of working OpenGL applications).

Attached are the glxinfo outputs for the radeon and mga cards (with
LIBGL_DEBUG=3Dverbose, as usual).

>
> Cheers,
>
> Steve
>
> -----Original Message-----
> From: pym...@li...
> [mailto:pym...@li...] On Behalf Of Peter C. La=
i
> Sent: Sunday, March 19, 2006 9:21 PM
> To: pym...@li...
> Subject: [PyMOL] pymol-specific dri problems
>
>
> Setup: X.org 6.9.0; dri/libglut-6.4.1,  built from freebsd-ports
>
> I am getting this libGL error causing pymol to fall back to software
> rendering:
>
> libGL: XF86DRIGetClientDriverName: 5.0.3 radeon (screen 0)
> libGL: OpenDriver: trying /usr/X11R6/lib/modules/dri/radeon_dri.so
> libGL error: dlopen /usr/X11R6/lib/modules/dri/radeon_dri.so failed
> (/usr/X11R6/lib/modules/dri/radeon_dri.so: Undefined symbol
> "_glapi_Dispatch")
> libGL error: unable to find driver: radeon_dri.so
>
> Direct Rendering is enabled.
> Other applications (i.e. the mesa demos) that rely on both libglut and
> libGL work fine and are direct rendering enabled. VMD works fine,
> PyMol's UI is way better, which is why I'm trying to get this working
> :)
>
> So obviously, it does not appear to be a problem with my DRI
> installation. Perhaps one of the coders can shed some light on this?
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by xPML, a groundbreaking scripting langua=
ge
> that extends applications into web and mobile media. Attend the live webc=
ast
> and join the prime developer group breaking into this new coding territor=
y!
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D110944&bid=3D241720&dat=
=3D121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>
>
> -------------------------------------------------------------------------=
-----
> Notice:  This e-mail message, together with any attachments, contains inf=
ormation of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, New Jer=
sey, USA 08889), and/or its affiliates (which may be known outside the Unit=
ed States as Merck Frosst, Merck Sharp & Dohme or MSD and in Japan, as Bany=
u) that may be confidential, proprietary copyrighted and/or legally privile=
ged. It is intended solely for the use of the individual or entity named on=
 this message.  If you are not the intended recipient, and have received th=
is message in error, please notify us immediately by reply e-mail and then =
delete it from your system.
> -------------------------------------------------------------------------=
-----
>

Re: [PyMOL] pymol-specific dri problems

[Peter C. L. <co...@gm...>]

On 3/20/06, Warren DeLano <wa...@de...> wrote:
> Peter,
>
> Did you compile by source, or is this a problem with one of our
> executables?
Hi Warren,

This is compiled by source. I could install the linux binary with the
appropriate linux libraries to see, but if the native freebsd version
isn't working, it is less likely another layer of emulation will make
things better.

>
> Cheers,
> Warren
>
> --
> Warren L. DeLano, Ph.D.
> Principal Scientist
>
> . DeLano Scientific LLC
> . 400 Oyster Point Blvd., Suite 213
> . South San Francisco, CA 94080 USA
> . Biz:(650)-872-0942  Tech:(650)-872-0834
> . Fax:(650)-872-0273  Cell:(650)-346-1154
> . mailto:wa...@de...
>
>
> > -----Original Message-----
> > From: pym...@li...
> > [mailto:pym...@li...] On Behalf Of
> > Peter C. Lai
> > Sent: Sunday, March 19, 2006 7:15 PM
> > To: pym...@li...
> > Subject: [PyMOL] pymol-specific dri problems
> >
> > Setup: X.org 6.9.0; dri/libglut-6.4.1,  built from freebsd-ports
> >
> > I am getting this libGL error causing pymol to fall back to
> > software rendering:
> >
> > libGL: XF86DRIGetClientDriverName: 5.0.3 radeon (screen 0)
> > libGL: OpenDriver: trying /usr/X11R6/lib/modules/dri/radeon_dri.so
> > libGL error: dlopen /usr/X11R6/lib/modules/dri/radeon_dri.so failed
> > (/usr/X11R6/lib/modules/dri/radeon_dri.so: Undefined symbol
> > "_glapi_Dispatch")
> > libGL error: unable to find driver: radeon_dri.so
> >
> > Direct Rendering is enabled.
> > Other applications (i.e. the mesa demos) that rely on both
> > libglut and libGL work fine and are direct rendering enabled.
> > VMD works fine, PyMol's UI is way better, which is why I'm
> > trying to get this working
> > :)
> >
> > So obviously, it does not appear to be a problem with my DRI
> > installation. Perhaps one of the coders can shed some light on this?
> >
> >
> > -------------------------------------------------------
> > This SF.Net email is sponsored by xPML, a groundbreaking
> > scripting language that extends applications into web and
> > mobile media. Attend the live webcast and join the prime
> > developer group breaking into this new coding territory!
> > http://sel.as-us.falkag.net/sel?cmd=3Dk&kid=110944&bid$1720&dat=121642
> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >
> >
> >
> >
>

[PyMOL] pymol-099rc6 installation problem on am64bit

[Andrea S. <and...@gm...>]

Hi all,
I have downloaded pymol-099rc6 and followed the instructions  to install it=
.
Typing pymol I get back:
pymol.exe not such file or dir
even if the pymol exec is there.  My laptop is an amd64bit hp pavillon

thanks

andrea




--
"La conoscenza libera il genere umano dalla superstizione"
J. Watson

Re: [PyMOL] Producing publication quality images

[Joao R. C. M. <jrc...@if...>]

Or using Gimp (on Linux and window$).

Cheers

Joao Renato.

Mark A Saper wrote:

> You can easily change the resolution (dpi) of an image without  
> changing the number of pixels, by editing the file in Photoshop (in  
> Image Size, change resolution without rescaling) or in  
> GraphicConverter (on Mac).
> _________________________________
>

[PyMOL] labels

[Sabine S. <pa...@no...>]

Hi everyone,

I got a odd problem with labeling:

I used:

label resi 196 and name c, "%s %s" % (resn, resi)
set label_color, black
set label_font_id, 4

To shift the label I "shift-middle-click-drag (in 3-Button-editing-mode)"
but I get a duplication of the label?=20

When I opened another pse-file there was no duplication or if I said "hide =
label" it only removed the one it hasn't moved.=20
But in the case with the more complicated stuff it either showed them doubl=
e or none?

What am I doing wrong?

thanks=20

Sabine



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Re: [PyMOL] Producing publication quality images

[Mark A S. <sa...@um...>]

You can easily change the resolution (dpi) of an image without  
changing the number of pixels, by editing the file in Photoshop (in  
Image Size, change resolution without rescaling) or in  
GraphicConverter (on Mac).
_________________________________
Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry
Biophysics Research Division, University of Michigan
930 N University Ave
Ann Arbor MI 48109-1055       U.S.A.

sa...@um...        (734) 764-3353        fax (734) 764-3323
http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html

RE: [PyMOL] Producing publication quality images

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

It's not pretty, and this is easy enough to do by hand, but I've had 
enough people ask me about this that I hacked up a little rendering plugin 
just now.  Can someone grab it from

http://www-personal.umich.edu/~mlerner/PyMOL/rendering.py

put it in $PYMOL_PATH/modules/pmg_tk/startup/ (or whatever it is you do on 
your OS of choice) and tell me what you think?

-michael

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

On Tue, 21 Mar 2006, Warren DeLano wrote:

> Terry,
>
> The trick is to render large and then reduce.  With recent versions, you
> can do something like this
>
> # To get a 300 dpi PNG file for a 4 inch by 3 inch image...
>
> # Ray-traced:
>
> ray 1200,900
> png hires_ray.pdb, dpi=300
>
> # OpenGL:
>
> draw 1200,900
> png hires_ogl.pdb, dpi=300
>
> Cheers,
> Warren
>
> --
> Warren L. DeLano, Ph.D.
> Principal Scientist
>
> . DeLano Scientific LLC
> . 400 Oyster Point Blvd., Suite 213
> . South San Francisco, CA 94080 USA
> . Biz:(650)-872-0942  Tech:(650)-872-0834
> . Fax:(650)-872-0273  Cell:(650)-346-1154
> . mailto:wa...@de...
>
>
>> -----Original Message-----
>> From: pym...@li...
>> [mailto:pym...@li...] On Behalf Of
>> Terry Jones
>> Sent: Tuesday, March 21, 2006 12:43 PM
>> To: pym...@li...
>> Subject: [PyMOL] Producing publication quality images
>>
>> Hi. I'm wondering if there's a way to make pymol produce
>> high-quality images suitable for publication.
>>
>> I've used ray/png to produce images, but the person I pass
>> them on to tells me they're only 50 to 100 dpi, and they're
>> wanting 300 dpi if possible.
>>
>> Is there a way to do this in pymol? Or can I export image
>> data and use some other tools to get to a 300dpi image?
>>
>> BTW, I'll try to make sure that pymol gets credited in the paper.
>>
>> Thanks,
>> Terry
>>
>>
>> -------------------------------------------------------
>> This SF.Net email is sponsored by xPML, a groundbreaking
>> scripting language that extends applications into web and
>> mobile media. Attend the live webcast and join the prime
>> developer group breaking into this new coding territory!
>> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&
>> dat=121642
>> _______________________________________________
>> PyMOL-users mailing list
>> PyM...@li...
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>
>>
>>
>>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by xPML, a groundbreaking scripting language
> that extends applications into web and mobile media. Attend the live webcast
> and join the prime developer group breaking into this new coding territory!
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>
>

Re: [PyMOL] stereo: should wait for LCD solutions in near future?

[Ricardo A. <apa...@iq...>]

Warren,

Thank you for replying.

Cheers,

Ricardo


Warren DeLano wrote:

>Ricardo,
>
>A 20+" 1600-1920 by 1200 pixel "switchable" stereo LCD display based on
>Parallax Barrier at a $2-3,000 price point would have a good shot at
>displacing shutter glasses -- but I don't know that any such product yet
>exists.  
>
>In my experience:
>
>- Lenticular displays work fine for video but are unsuitable for
>technical graphics where thin lines must be rendered cleanly and without
>artifacts or anisotropy.
>
>- Polarization and/or mirror-based displays are too bulky, complex, and
>expensive.
>
>- Only Parallax Barrier provides both stereo and non-stereo display
>modes in the space of a desktop LCD monitor without unreasonable visual
>artifacts.  But losing 2X in horizontal resolution means one needs to
>start with a very high resolution display (1920 or higher).  The $500
>Sharp 3D autostereoscopic display is a great proof of concept, and if it
>had 3X more pixels, I think it would be a viable option.  
>
>Incidentally, Dimension Technologies has a 19" autostereoscopic display
>for $3,695 with about twice as many pixels as the Sharp 15"
><http://www.dti3d.com/component/page,shop.product_details/flypage,shop.f
>lypage/product_id,7/option,com_virtuemart/Itemid,1/>, but I think it
>will still take 50% more pixels for ~33% less money in order to tap the
>full potential of this market. 
>
>For now, I'd stick with CRTs and shutter glasses.
>
>Cheers,
>Warren
>
>--
>Warren L. DeLano, Ph.D.                     
>Principal Scientist
>
>. DeLano Scientific LLC  
>. 400 Oyster Point Blvd., Suite 213           
>. South San Francisco, CA 94080 USA   
>. Biz:(650)-872-0942  Tech:(650)-872-0834     
>. Fax:(650)-872-0273  Cell:(650)-346-1154
>. mailto:wa...@de...      
> 
>
>  
>
>>-----Original Message-----
>>From: pym...@li... 
>>[mailto:pym...@li...] On Behalf Of 
>>Ricardo Aparicio
>>Sent: Monday, March 20, 2006 2:17 PM
>>To: pym...@li...
>>Subject: [PyMOL] stereo: should wait for LCD solutions in near future?
>>
>>Dear all,
>>
>>After reading many messages from last January, I would like 
>>to have a better idea if the best option for stereo continues 
>>to be the one kindly indicated  at  
>>http://pymol.sourceforge.net/stereo3d.html
>>(some messages mentioned alternatives like those listed bellow).
>>
>>Is there a chance that in near future a technology based on 
>>LCD monitors may become available at reasonable price and 
>>competitive image quality?
>>(intrinsic horizontal low resolution of LCD 3D options seems 
>>to be a problem)
>>
>>Comments are welcomed.
>>
>>Cheers,
>>
>>Ricardo Aparicio
>>
>>
>>http://store.sharpsystems.com/product.asp?sku=2555920
>>http://www.sharp3d.com/technology/howsharp3dworks/
>>
>>http://www.inition.co.uk/inition/open_week_stereoscopic.htm
>>http://www.inition.co.uk/inition/compare.php?SubCatID=1
>>http://www.inition.co.uk/inition/product.php?URL_=product_ster
>>eovis_planar_sd1710&SubCatID_=3
>>
>>
>>http://www.crystalcanyons.net/abouts/3dc9_DualMonitorComplete.shtm
>>
>>
>>
>>
>>
>>
>>    
>>
>
>
>-------------------------------------------------------
>This SF.Net email is sponsored by xPML, a groundbreaking scripting language
>that extends applications into web and mobile media. Attend the live webcast
>and join the prime developer group breaking into this new coding territory!
>http://sel.as-us.falkag.net/sel?cmd=k&kid0944&bid$1720&dat1642
>_______________________________________________
>PyMOL-users mailing list
>PyM...@li...
>https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>.
>
>  
>

RE: [PyMOL] Producing publication quality images

[Terry J. <tc...@ca...>]

Thanks Warren, I'll try that. I got two other replies, neither mentioning
the 300dpi arg to png. If that isn't recognized, I'll upgrade.

Terry

RE: [PyMOL] Producing publication quality images

[Warren D. <wa...@de...>]

Terry,

The trick is to render large and then reduce.  With recent versions, you
can do something like this

# To get a 300 dpi PNG file for a 4 inch by 3 inch image...

# Ray-traced:

ray 1200,900
png hires_ray.pdb, dpi=3D300

# OpenGL:

draw 1200,900
png hires_ogl.pdb, dpi=3D300

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Terry Jones
> Sent: Tuesday, March 21, 2006 12:43 PM
> To: pym...@li...
> Subject: [PyMOL] Producing publication quality images
>=20
> Hi. I'm wondering if there's a way to make pymol produce=20
> high-quality images suitable for publication.
>=20
> I've used ray/png to produce images, but the person I pass=20
> them on to tells me they're only 50 to 100 dpi, and they're=20
> wanting 300 dpi if possible.
>=20
> Is there a way to do this in pymol? Or can I export image=20
> data and use some other tools to get to a 300dpi image?
>=20
> BTW, I'll try to make sure that pymol gets credited in the paper.
>=20
> Thanks,
> Terry
>=20
>=20
> -------------------------------------------------------
> This SF.Net email is sponsored by xPML, a groundbreaking=20
> scripting language that extends applications into web and=20
> mobile media. Attend the live webcast and join the prime=20
> developer group breaking into this new coding territory!
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D110944&bid=3D241720&
> dat=3D121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

[PyMOL] Producing publication quality images

[Terry J. <tc...@ca...>]

Hi. I'm wondering if there's a way to make pymol produce high-quality
images suitable for publication.

I've used ray/png to produce images, but the person I pass them on to tells
me they're only 50 to 100 dpi, and they're wanting 300 dpi if possible.

Is there a way to do this in pymol? Or can I export image data and use some
other tools to get to a 300dpi image?

BTW, I'll try to make sure that pymol gets credited in the paper.

Thanks,
Terry

[PyMOL] Red-Blue anaglyph in Pymol

[Jean-Christophe A. <am...@es...>]

Hello,

I was wondering if it is possible to produce Red-Blue Anaglyph using =20
pymol either in "live" or static. I saw a demo site of pymol where it =20=

seems to be possible (http://www.sciencesoft.at/index.jsp?=20
link=3Dpymol&lang=3Den), but how ? Or is it planned for a next version =
of =20
Pymol.
Thanks.
Jean-Christophe

________________________
Jean-Christophe Am=E9, PhD
D=E9partement Int=E9grit=E9 du G=E9nome, UMR 7175-LC1 du CNRS
=C9cole Sup=E9rieure de Biotechnologie de Strasbourg
P=F4le API
Parc d'innovation, Boulevard S=E9bastien Brant
BP 10413
67412 ILLKIRCH CEDEX
France

tel.: +33 (0)3 90 24 47 05
Fax.: +33 (0)3 90 24 46 86

http://parplink.u-strasbg.fr
http://idg.u-strasbg.fr/

=AB Science sans conscience n'est que ruine de l'=E2me ...=BB (Fran=E7ois =
=20
Rabelais, 1483-1553)

RE: [PyMOL] stereo: should wait for LCD solutions in near future?

[Warren D. <wa...@de...>]

Ricardo,

A 20+" 1600-1920 by 1200 pixel "switchable" stereo LCD display based on
Parallax Barrier at a $2-3,000 price point would have a good shot at
displacing shutter glasses -- but I don't know that any such product yet
exists. =20

In my experience:

- Lenticular displays work fine for video but are unsuitable for
technical graphics where thin lines must be rendered cleanly and without
artifacts or anisotropy.

- Polarization and/or mirror-based displays are too bulky, complex, and
expensive.

- Only Parallax Barrier provides both stereo and non-stereo display
modes in the space of a desktop LCD monitor without unreasonable visual
artifacts.  But losing 2X in horizontal resolution means one needs to
start with a very high resolution display (1920 or higher).  The $500
Sharp 3D autostereoscopic display is a great proof of concept, and if it
had 3X more pixels, I think it would be a viable option. =20

Incidentally, Dimension Technologies has a 19" autostereoscopic display
for $3,695 with about twice as many pixels as the Sharp 15"
<http://www.dti3d.com/component/page,shop.product_details/flypage,shop.f
lypage/product_id,7/option,com_virtuemart/Itemid,1/>, but I think it
will still take 50% more pixels for ~33% less money in order to tap the
full potential of this market.=20

For now, I'd stick with CRTs and shutter glasses.

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Ricardo Aparicio
> Sent: Monday, March 20, 2006 2:17 PM
> To: pym...@li...
> Subject: [PyMOL] stereo: should wait for LCD solutions in near future?
>=20
> Dear all,
>=20
> After reading many messages from last January, I would like=20
> to have a better idea if the best option for stereo continues=20
> to be the one kindly indicated  at =20
> http://pymol.sourceforge.net/stereo3d.html
> (some messages mentioned alternatives like those listed bellow).
>=20
> Is there a chance that in near future a technology based on=20
> LCD monitors may become available at reasonable price and=20
> competitive image quality?
> (intrinsic horizontal low resolution of LCD 3D options seems=20
> to be a problem)
>=20
> Comments are welcomed.
>=20
> Cheers,
>=20
> Ricardo Aparicio
>=20
>=20
> http://store.sharpsystems.com/product.asp?sku=3D2555920
> http://www.sharp3d.com/technology/howsharp3dworks/
>=20
> http://www.inition.co.uk/inition/open_week_stereoscopic.htm
> http://www.inition.co.uk/inition/compare.php?SubCatID=3D1
> http://www.inition.co.uk/inition/product.php?URL_=3Dproduct_ster
> eovis_planar_sd1710&SubCatID_=3D3
>=20
>=20
> http://www.crystalcanyons.net/abouts/3dc9_DualMonitorComplete.shtm
>=20
>=20
>=20
>=20
>=20
>=20

[PyMOL] stereo: should wait for LCD solutions in near future?

[Ricardo A. <apa...@iq...>]

Dear all,

After reading many messages from last January, I would like to have a 
better idea if the best option
for stereo continues to be the one kindly indicated  at  
http://pymol.sourceforge.net/stereo3d.html
(some messages mentioned alternatives like those listed bellow).

Is there a chance that in near future a technology based on LCD monitors 
may become available at reasonable price and competitive image quality?
(intrinsic horizontal low resolution of LCD 3D options seems to be a 
problem)

Comments are welcomed.

Cheers,

Ricardo Aparicio


http://store.sharpsystems.com/product.asp?sku=2555920
http://www.sharp3d.com/technology/howsharp3dworks/

http://www.inition.co.uk/inition/open_week_stereoscopic.htm
http://www.inition.co.uk/inition/compare.php?SubCatID=1
http://www.inition.co.uk/inition/product.php?URL_=product_stereovis_planar_sd1710&SubCatID_=3


http://www.crystalcanyons.net/abouts/3dc9_DualMonitorComplete.shtm

Re: [PyMOL] Saving PDB with CONECT information

[Alan <ala...@gm...>]

Thanks a lot Warren.

If you allow me, my script to build sequences of 3 peptides is almost
done. I could even use sculpt to improve my molecules structures.

For the moment I am missing just one thing. I want to make the N-term
and C-term (NH3+ and COO-) automatically for all 20 tripeptide. I know
how to to do it by mouse, but how to 'add hydrogens' and 'make pk1
positive', e. g., by command?

Thanks a lot for PyMol.

Cheers,
Alan

On 20/03/06, Warren DeLano <wa...@de...> wrote:
> Alan,
>
> > Is PyMol able to save the built protein/molecule in a PDB
> > file with CONECT information. If so, how to do it?
>
> Yes,
>
> set pdb_conect_all
>
> before saving the pdb file in order to get a PDB file with explicit
> connectivity and valences for all atoms.
>
> Cheers,
> Warren
>
> --
> Warren L. DeLano, Ph.D.
> Principal Scientist
>
> . DeLano Scientific LLC
> . 400 Oyster Point Blvd., Suite 213
> . South San Francisco, CA 94080 USA
> . Biz:(650)-872-0942  Tech:(650)-872-0834
> . Fax:(650)-872-0273  Cell:(650)-346-1154
> . mailto:wa...@de...
>
>
> > -----Original Message-----
> > From: pym...@li...
> > [mailto:pym...@li...] On Behalf Of Alan
> > Sent: Monday, March 20, 2006 11:39 AM
> > To: Pymol
> > Subject: [PyMOL] Saving PDB with CONECT information
> >
> > Hello List!
> >
> > Is PyMol able to save the built protein/molecule in a PDB
> > file with CONECT information. If so, how to do it?
> >
> > Thanks in advance for any help.
> >
> > Cheers,
> > Alan
> > --
> > Alan Wilter S. da Silva, D.Sc. - Research Associate
> > Department of Biochemistry, University of Cambridge.
> > 80 Tennis Court Road, Cambridge CB2 1GA, UK.
> >
> >
> > -------------------------------------------------------
> > This SF.Net email is sponsored by xPML, a groundbreaking
> > scripting language that extends applications into web and
> > mobile media. Attend the live webcast and join the prime
> > developer group breaking into this new coding territory!
> > http://sel.as-us.falkag.net/sel?cmd=3Dk&kid=110944&bid$1720&dat=121642
> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >
> >
> >
> >
>


--
Alan Wilter S. da Silva, D.Sc. - Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.

RE: [PyMOL] Saving PDB with CONECT information

[Warren D. <wa...@de...>]

Alan,

> Is PyMol able to save the built protein/molecule in a PDB=20
> file with CONECT information. If so, how to do it?

Yes,

set pdb_conect_all

before saving the pdb file in order to get a PDB file with explicit
connectivity and valences for all atoms.

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of Alan
> Sent: Monday, March 20, 2006 11:39 AM
> To: Pymol
> Subject: [PyMOL] Saving PDB with CONECT information
>=20
> Hello List!
>=20
> Is PyMol able to save the built protein/molecule in a PDB=20
> file with CONECT information. If so, how to do it?
>=20
> Thanks in advance for any help.
>=20
> Cheers,
> Alan
> --
> Alan Wilter S. da Silva, D.Sc. - Research Associate=20
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
>=20
>=20
> -------------------------------------------------------
> This SF.Net email is sponsored by xPML, a groundbreaking=20
> scripting language that extends applications into web and=20
> mobile media. Attend the live webcast and join the prime=20
> developer group breaking into this new coding territory!
> http://sel.as-us.falkag.net/sel?cmd=3Dk&kid=110944&bid$1720&dat=121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

[PyMOL] Saving PDB with CONECT information

[Alan <ala...@gm...>]

Hello List!

Is PyMol able to save the built protein/molecule in a PDB file with
CONECT information. If so, how to do it?

Thanks in advance for any help.

Cheers,
Alan
--
Alan Wilter S. da Silva, D.Sc. - Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.

Re: [PyMOL] transparency for nb_spheres

[Robert I. <imm...@gm...>]

Chad,

You can try,

show spheres, resn HOH  (or whatever your waters are called)
set sphere_scale, .2
set sphere_transparency, .5

Good luck,

-bob

On 3/20/06, Chad R. Simmons <cr...@co...> wrote:
> Hello,
>
> I am using "nb_spheres" to represent waters in a figure I am generating b=
ut
> cannot figure out how to make them transparent (i.e. set
> sphere_transparency=3Dx only works for traditional spheres).  Any help wo=
uld
> be greatly appreciated.
>
> Thanks.
>
> Chad
> **********************************************
> Chad R. Simmons
> Cornell University
> Division of Nutritional Sciences
> 235 Kinzelberg Hall
> Ithaca, NY  14853
>
> Email:  cr...@co...
> Phone:  (607)255-2685
> Fax:  (607)255-1033
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by xPML, a groundbreaking scripting langua=
ge
> that extends applications into web and mobile media. Attend the live webc=
ast
> and join the prime developer group breaking into this new coding territor=
y!
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D110944&bid=3D241720&dat=
=3D121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>

[PyMOL] transparency for nb_spheres

[Chad R. S. <cr...@co...>]

Hello,

I am using "nb_spheres" to represent waters in a figure I am generating but 
cannot figure out how to make them transparent (i.e. set 
sphere_transparency=x only works for traditional spheres).  Any help would 
be greatly appreciated.

Thanks.

Chad
**********************************************
Chad R. Simmons
Cornell University
Division of Nutritional Sciences
235 Kinzelberg Hall
Ithaca, NY  14853

Email:  cr...@co...
Phone:  (607)255-2685
Fax:  (607)255-1033

[PyMOL] pymol-specific dri problems

[Peter C. L. <co...@gm...>]

Setup: X.org 6.9.0; dri/libglut-6.4.1,  built from freebsd-ports

I am getting this libGL error causing pymol to fall back to software render=
ing:

libGL: XF86DRIGetClientDriverName: 5.0.3 radeon (screen 0)
libGL: OpenDriver: trying /usr/X11R6/lib/modules/dri/radeon_dri.so
libGL error: dlopen /usr/X11R6/lib/modules/dri/radeon_dri.so failed
(/usr/X11R6/lib/modules/dri/radeon_dri.so: Undefined symbol
"_glapi_Dispatch")
libGL error: unable to find driver: radeon_dri.so

Direct Rendering is enabled.
Other applications (i.e. the mesa demos) that rely on both libglut and
libGL work fine and are direct rendering enabled. VMD works fine,
PyMol's UI is way better, which is why I'm trying to get this working
:)

So obviously, it does not appear to be a problem with my DRI
installation. Perhaps one of the coders can shed some light on this?

[PyMOL] Bug: spheres with negative x-coordinates don't show up

[Tsjerk W. <ts...@gm...>]

Hi Warren,

I just ran into a bug with pymol 0.99 rc1 on SUSE 10 Linux on my Acer
TravelMate 800, which has an ATI Radeon video card. The problem is that for
atoms with negative x-coordinates the spheres don't show up. When I shift
the coordinates using alter_state the spheres show up again. This happens
with different files. I don't know whether the problem is specific to my
laptop. Later I can try it on some other workstations (windows/red hat) if
you want. Raytracing still works fine. If you want I can send you an image
showing the problem or hand you a pdb file which does the trick for me.

Cheers,

Tsjerk

--

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336

RE: : [PyMOL] Surface Vertex Coordinates

[Warren D. <wa...@de...>]

Laurence,

> Does it do all drawing objects or just surfaces ?

All objects except labels.  However, triangle normals aren't current
exported, which means that surfaces and cartoons don't look nearly as
good...I'm not sure if this is something that can be added in VRML2 or
not. =20

> and will it be in MacPyMol ?

Yes, with the next release.

Cheers,
Warren


--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: Laurence Pearl [mailto:Lau...@ic...]=20
> Sent: Friday, March 17, 2006 5:03 AM
> To: Warren DeLano; hi...@ge...
> Cc: pym...@li...
> Subject: RE: : [PyMOL] Surface Vertex Coordinates
>=20
> Does it do all drawing objects or just surfaces ?
>=20
> and will it be in MacPyMol ?
>=20
>=20
> Laurence
>=20
> --------------------------------------------------------------
> ------------------
> Laurence H. Pearl
> Section of Structural Biology, Institute of Cancer Research=20
> Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB,=20
> UK Phone +44-(0)20 7153 5422 : Secretary +44-(0)20 7153 5443 : FAX =20
> +44-(0)20 7153 5457
> --------------------------------------------------------------
> ------------------
> "Live Simply and do Serious Things .. "
> - Dorothy Crowfoot Hodgkin
> --------------------------------------------------------------
> ------------------
> >>> "Warren DeLano" <wa...@de...> 03/17/06 6:56 AM >>>
> > Of course it would be a whole lot easier if PyMol output VRML=20
> > directly  =20
> > ..... Warren ?????
>=20
> Chris Want's latest VRML2 code is now in CVS (with a few=20
> minor tweaks of my own...)
>=20
> save my_vrml.wrl
>=20
> Cheers,
> Warren
>=20
> --
> Warren L. DeLano, Ph.D.                    =20
> Principal Scientist
>=20
> . DeLano Scientific LLC =20
> . 400 Oyster Point Blvd., Suite 213          =20
> . South San Francisco, CA 94080 USA  =20
> . Biz:(650)-872-0942  Tech:(650)-872-0834    =20
> . Fax:(650)-872-0273  Cell:(650)-346-1154
> . mailto:wa...@de...     =20
> =20
>=20
> > -----Original Message-----
> > From: pym...@li...
> > [mailto:pym...@li...] On Behalf=20
> Of Laurence=20
> > Pearl
> > Sent: Wednesday, March 15, 2006 9:35 AM
> > To: Benjamin Hitz
> > Cc: pym...@li...
> > Subject: Re: : [PyMOL] Surface Vertex Coordinates
> >=20
> > The Povray intermediate file generated when you do 'ray=20
> renderer =3D 1'
> > contains all vertices, normals and colouring information=20
> for cartoon=20
> > and surface object types. However you do need to produce a parsing=20
> > script to extract these in to a useful form for importing=20
> into other=20
> > programs. Have a look at the front cover of Mol Cell vol 20(4) - I=20
> > generated a cartoon of the protein in PyMol, output it as a povray=20
> > file, and then converted it to VRML using a jiffy produced by Chris=20
> > Richardson, and then used it as an object in the Blender 3D
> > modelling  =20
> > package to generate the picture.
> >=20
> > Of course it would be a whole lot easier if PyMol output VRML=20
> > directly  =20
> > ..... Warren ?????
> >=20
> > Laurence Pearl
> >=20
> >=20
> > On 15 Mar 2006, at 17:01, Benjamin Hitz wrote:
> >=20
> > >>
> > >> I am interested in the coordinates of the vertices of the mesh=20
> > >> representation of the molecular surface. Is there any
> > method to read
> > >> them out?
> > >>
> > >> Thanks
> > >>
> > >
> > > Me too.  With coloring and/or other "property"=20
> information as well.
> > >
> > >
> > >
> > > --
> > > Ben Hitz
> > > Senior Scientific Programmer ** Saccharomyces Genome=20
> Database ** GO=20
> > > Consortium Stanford University ** hi...@ge...
> > >
> > >
> > >
> > >
> > >
> > > -------------------------------------------------------
> > > This SF.Net email is sponsored by xPML, a groundbreaking=20
> scripting=20
> > > language that extends applications into web and mobile
> > media. Attend
> > > the live webcast and join the prime developer group
> > breaking into this
> > > new coding territory!
> > > http://sel.as-us.falkag.net/sel?=20
> > > cmd=3Dlnk&kid=3D110944&bid=3D241720&dat=3D121642
> > > _______________________________________________
> > > PyMOL-users mailing list
> > > PyM...@li...
> > > https://lists.sourceforge.net/lists/listinfo/pymol-users
> > >
> > --------------------------------------------------------------
> > ----------
> > --
> >    Laurence H. Pearl
> >=20
> >    Section of Structural Biology, Institute of Cancer Research
> >    Chester Beatty Laboratories,  237 Fulham Road, London SW3 6JB, UK
> >=20
> >    Phone +44-(0)20 7153 5422 : Secretary +44-(0)20 7153 5443
> >    FAX   +44-(0)20 7153 5457 : E-Mail Lau...@ic...
> > --------------------------------------------------------------
> > ----------
> > --
> >    " Live Simply and do Serious Things .. " - Dorothy=20
> Crowfoot Hodgkin
> > --------------------------------------------------------------
> > ----------
> > --
> >=20
> >=20
> >=20
> > -------------------------------------------------------
> > This SF.Net email is sponsored by xPML, a groundbreaking scripting=20
> > language that extends applications into web and mobile=20
> media. Attend=20
> > the live webcast and join the prime developer group=20
> breaking into this=20
> > new coding territory!
> > http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D110944&bid=3D241720&
> > dat=3D121642
> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >=20
> >=20
> >=20
> >=20
>=20
>=20
>=20
>=20
>=20

RE: : [PyMOL] Surface Vertex Coordinates

[Warren D. <wa...@de...>]

> Of course it would be a whole lot easier if PyMol output VRML=20
> directly  =20
> ..... Warren ?????

Chris Want's latest VRML2 code is now in CVS (with a few minor tweaks of
my own...)

save my_vrml.wrl

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Laurence Pearl
> Sent: Wednesday, March 15, 2006 9:35 AM
> To: Benjamin Hitz
> Cc: pym...@li...
> Subject: Re: : [PyMOL] Surface Vertex Coordinates=20
>=20
> The Povray intermediate file generated when you do 'ray=20
> renderer =3D 1' =20
> contains all vertices, normals and colouring information for=20
> cartoon and surface object types. However you do need to=20
> produce a parsing script to extract these in to a useful form=20
> for importing into other programs. Have a look at the front=20
> cover of Mol Cell vol 20(4) - I generated a cartoon of the=20
> protein in PyMol, output it as a povray file, and then=20
> converted it to VRML using a jiffy produced by Chris =20
> Richardson, and then used it as an object in the Blender 3D=20
> modelling  =20
> package to generate the picture.
>=20
> Of course it would be a whole lot easier if PyMol output VRML=20
> directly  =20
> ..... Warren ?????
>=20
> Laurence Pearl
>=20
>=20
> On 15 Mar 2006, at 17:01, Benjamin Hitz wrote:
>=20
> >>
> >> I am interested in the coordinates of the vertices of the mesh=20
> >> representation of the molecular surface. Is there any=20
> method to read=20
> >> them out?
> >>
> >> Thanks
> >>
> >
> > Me too.  With coloring and/or other "property" information as well.
> >
> >
> >
> > --
> > Ben Hitz
> > Senior Scientific Programmer ** Saccharomyces Genome Database ** GO=20
> > Consortium Stanford University ** hi...@ge...
> >
> >
> >
> >
> >
> > -------------------------------------------------------
> > This SF.Net email is sponsored by xPML, a groundbreaking scripting=20
> > language that extends applications into web and mobile=20
> media. Attend=20
> > the live webcast and join the prime developer group=20
> breaking into this=20
> > new coding territory!
> > http://sel.as-us.falkag.net/sel?=20
> > cmd=3Dlnk&kid=3D110944&bid=3D241720&dat=3D121642
> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >
> --------------------------------------------------------------
> ----------
> --
>    Laurence H. Pearl
>=20
>    Section of Structural Biology, Institute of Cancer Research
>    Chester Beatty Laboratories,  237 Fulham Road, London SW3 6JB, UK
>=20
>    Phone +44-(0)20 7153 5422 : Secretary +44-(0)20 7153 5443
>    FAX   +44-(0)20 7153 5457 : E-Mail Lau...@ic...
> --------------------------------------------------------------
> ----------
> --
>    " Live Simply and do Serious Things .. " - Dorothy Crowfoot Hodgkin
> --------------------------------------------------------------
> ----------
> --
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.Net email is sponsored by xPML, a groundbreaking=20
> scripting language that extends applications into web and=20
> mobile media. Attend the live webcast and join the prime=20
> developer group breaking into this new coding territory!
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D110944&bid=3D241720&
> dat=3D121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

RE: [PyMOL] disulfide bonds

[Warren D. <wa...@de...>]

Marilyn,

You've got to show the actual lines or sticks:

show sticks, (cys/ca+cb+sg) and byres (cys/sg and bound_to cys/sg)

Cheers,
Warren


--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Yoder, Marilyn
> Sent: Thursday, March 16, 2006 7:23 AM
> To: pym...@li...
> Subject: [PyMOL] disulfide bonds
>=20
> Hi,
> =20
> I apologize because I suspect this question has been asked=20
> before, but I don't see it in the FAQ, Wiki, and can't figure=20
> how to efficiently search the maillist archive.
> =20
> How does one draw a disulfide bond?  My preference is the=20
> classical 'thunderbolt', from CA-S-S-CA atoms.
> =20
> Thanks,
> Marilyn
> =20
> Marilyn D. Yoder
> Division of Cell Biology and Biophysics
> University of Missouri-Kansas City
> 5007 Rockhill Rd.
> Kansas City, MO  64110-2499
> phone: 816-235-1986
> fax: 816-235-1503
> =20
>=20