pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] troubles to display delphi surface in Pymol

[elena.papaleo <ele...@un...>]

Hi!!!
I am trying to display an electrostatic potential surface=20
calculated by Delphi in Pymol.

I used the following instruction:
> load delphi.phi
> ramp_new map, delphi
> load structure.pdb
> set surface_color map, structure
> show surface

I adopted this procedure in the past on some protein=20
systems and it worked well but now when I use it on other=20
proteins structure it gave me troubles. The problems is=20
that the surface is completely blue (positive) whereas=20
using other visualization programs it appears completely=20
different.
My Pymol version is 0.98, and I also tried a different=20
scale  for the color surface but the results are always=20
the same.

Do you have some suggestions?
Thanks a lot in advance

Elena

Re: [PyMOL] using 1 button mouse with MacPyMol

[<an...@bi...>]

Andrew,

Just get a mouse and plug it into the USB port.  (If it has one button,
it's not a mouse, it's a pain.)


Andreas


> Great job with MacPyMol 0.99.
>
> I've been using version 0.98 on my ibook for a while and I was able to
> manipulate views fairly well with the 1 button laptop mouse.  In
> version 0.99 I can't seem to zoom in and out with just a one button
> mouse.  Is it possible, or is there some sort of hack that can be
> applied such as reassigned mouse commands?
>
> Andrew Wollacott, PhD
> Baker Research Lab
> University of Washington
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep through log
> files
> for problems?  Stop!  Download the new AJAX search engine that makes
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2
> _______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/pymol-users
>


--=20
   -->       Andreas F=F6rster       <--
 8 rue Doudart de Lagr=E9e, 38000 Grenoble
++33.(0)438.866201 and ++33.(0)456.452000
   b5foan at skype and yahoo messenger
         docandreas.blogspot.com

[PyMOL] installation problem on XP laptop

[<dr...@li...>]

Dear all

I just tried to install the latest version of Pymol on a XP laptop.  The
installation completes but when I try to launch the program I get

pymol.exe - Unable to Locate Component

This application has failed to start because MSVCR71.dll was not found.

It says that re-installing might help but it doesn't.  I can't google anything
about this.  Has anyone any ideas?

Thanks in advance

Daniel

[PyMOL] using 1 button mouse with MacPyMol

[Andrew W. <sen...@gm...>]

Great job with MacPyMol 0.99.

I've been using version 0.98 on my ibook for a while and I was able to
manipulate views fairly well with the 1 button laptop mouse.  In
version 0.99 I can't seem to zoom in and out with just a one button
mouse.  Is it possible, or is there some sort of hack that can be
applied such as reassigned mouse commands?

Andrew Wollacott, PhD
Baker Research Lab
University of Washington

[PyMOL] ObjectMapLoadDXFile-Error: Unable to open file!

[Alexei K. <avk...@uc...>]

Hello everybody,

I just started using APBS under WinXP with PyMOL 0.99.

I have used a similar combination under Linux with no problems before, 
but under Windows,
I get ObjectMapLoadDXFile-Error: Unable to open file!
message when I try to run APBS.I tried both, PyMOL and server generated 
pqr with little success.
Anyone has been able to run APBS under WinXP?

Thanks a ton,
Alexei.

[PyMOL] Como School: 21-25 May 2006

[Anastassis P. <a.p...@nk...>]

Dear all,

On behalf of the organizing committee I would like to draw your 
attention to the

8th International School on the Crystallography of Biological 
Macromolecules

For more information please visit:

http://www.crystallographyschool.org

The 'Como meeting' as it is commonly known, is unique in combining a 
series of methods talks that cover all aspect of crystallographic 
structure determination, with talks about exciting research in 
Structural Biology and lively and well-attended poster sessions  - some 
of which are selected for oral presentations' and all these in the 
unique atmosphere and great hospitality offered in the lake-side city 
of Como. Don't miss the opportunity to register - we hope to see as 
many of you as possible to what we hope will be an excellent meeting, 
worthy of the history of the series !

Tassos

Re: [PyMOL] A suggestion

[Ramesh S. <sis...@gm...>]

On 2/2/06, S. Frank Yan <SY...@gn...> wrote:
>
> Hi,
>
> I was wondering if PyMOL (with some plugin) has the capability to
> visualize a series of small molecules that are associated with a protein
> in a seamless way, e.g. poses from a docking exercise.  Right now, what
> we can do is to combine all the structures into a single file and open
> with PyMOL.  It would be a great tool to further advance PyMOL as a
> visualization tool.
>
>
Hi Frank,

I am not sure if I followed your question. But from what I understand, .sdf
file is the perfect answer. Save the docked poses as .sdf file. Load the
.sdf file along with the receptor structure. Then you can cycle through the
small molecules in the .sdf file. What is more, even there is a wizard
called filter, here you can save the good poses, reject the ugly ones and
defer some if you arem't sure. I feel this is quite seamless.

Only hitch (and that is not the right word) is that if you want to effect a
bond rotation or something on a pose, you can't do it since this is a
multi-state object. Hope this helps. Do let me know if you have problem wit=
h
this.

best wishes


Ramesh Sistla

RE: [PyMOL] Re: [ccp4bb]: Mac Intel Benchmarks

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

Ulrich,

Not as far as I know.  I suppose there is a chance it could drive
full-screen stereo 3D on an external CRT monitor, but it definitely
won't do stereo-3d-in-a-window.

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
> Ulrich Baumann
> Sent: Monday, February 06, 2006 12:27 AM
> To: Warren DeLano; pym...@li...
> Subject: [PyMOL] Re: [ccp4bb]: Mac Intel Benchmarks
>=20
> Hi Warren,
>=20
> is this a stereo system? This would be very cheap, a quadro=20
> card costst usually more.
>=20
> Cheers,
>=20
> Ulrich
>=20
> ----- Original Message -----
> From: "Warren DeLano" <wa...@de...>
> To: <pym...@li...>; "CCL Subscribers"=20
> <che...@cc...>; "CCP4BB" <cc...@dl...>; <vm...@ks...>
> Sent: Sunday, February 05, 2006 10:42 PM
> Subject: [ccp4bb]: Mac Intel Benchmarks
>=20
>=20
> > ***  For details on how to be removed from this list visit the  ***
> > ***          CCP4 home page http://www.ccp4.ac.uk         ***
> >
> >
> > Performance enthusiasts:
> >
> > Having finished the MacPyMOL universal binary=20
> (http://delsci.com/pre), I
> > couldn't resist running some benchmarks in order see whether Apple's
> > performance claims hold up with respect to PyMOL.
> >
> > It seems they do:  At equal Ghz, the iMac Core Duo provides 170% the
> > graphics performance of the old iMac G5, 141% of the=20
> single-threaded CPU
> > performance, and 239% of the multi-threaded rendering performance.
> >
> > Even more impressive is how well this $1,300 all-in-one=20
> system performs
> > in comparison to a traditional $5,000 Linux Opteron=20
> workstation.  The
> > iMac Core Duo provides 30% greater graphics performance=20
> than my Quadro
> > FX 3000-equipped dual Opteron and is within 10% in terms of=20
> raw PyMOL
> > number crunching power (surface calculation and ray tracing).
> >
> > Wow.
> >
> > So with respect to PyMOL, Intel-based Macs have at least a=20
> 2-3X better
> > price/performance ratio over dual-CPU Opteron workstations (at least
> > from a commercial vendor like Sun).  If you don't need=20
> 64-bit computing,
> > these new iMacs are a solid choice for molecular visualization with
> > PyMOL.
> >
> > Raw data here:  http://delsci.com/bench
> >
> > Machine tested on left:
> >=20
> <http://store.apple.com/1-800-MY-APPLE/WebObjects/AppleStore?f
> amily=3DiMac
> >>
> >
> > 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...
> >
> >=20
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep=20
> through log files
> for problems?  Stop!  Download the new AJAX search engine that makes
> searching your log files as easy as surfing the  web. =20
> DOWNLOAD SPLUNK!
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D103432&bid=3D230486&
> dat=3D121642
> _______________________________________________
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> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

[PyMOL] Re: [ccp4bb]: Mac Intel Benchmarks

[Ulrich B. <ulr...@ib...>]

Hi Warren,

is this a stereo system? This would be very cheap, a quadro card costst 
usually more.

Cheers,

Ulrich

----- Original Message ----- 
From: "Warren DeLano" <wa...@de...>
To: <pym...@li...>; "CCL Subscribers" 
<che...@cc...>; "CCP4BB" <cc...@dl...>; <vm...@ks...>
Sent: Sunday, February 05, 2006 10:42 PM
Subject: [ccp4bb]: Mac Intel Benchmarks


> ***  For details on how to be removed from this list visit the  ***
> ***          CCP4 home page http://www.ccp4.ac.uk         ***
>
>
> Performance enthusiasts:
>
> Having finished the MacPyMOL universal binary (http://delsci.com/pre), I
> couldn't resist running some benchmarks in order see whether Apple's
> performance claims hold up with respect to PyMOL.
>
> It seems they do:  At equal Ghz, the iMac Core Duo provides 170% the
> graphics performance of the old iMac G5, 141% of the single-threaded CPU
> performance, and 239% of the multi-threaded rendering performance.
>
> Even more impressive is how well this $1,300 all-in-one system performs
> in comparison to a traditional $5,000 Linux Opteron workstation.  The
> iMac Core Duo provides 30% greater graphics performance than my Quadro
> FX 3000-equipped dual Opteron and is within 10% in terms of raw PyMOL
> number crunching power (surface calculation and ray tracing).
>
> Wow.
>
> So with respect to PyMOL, Intel-based Macs have at least a 2-3X better
> price/performance ratio over dual-CPU Opteron workstations (at least
> from a commercial vendor like Sun).  If you don't need 64-bit computing,
> these new iMacs are a solid choice for molecular visualization with
> PyMOL.
>
> Raw data here:  http://delsci.com/bench
>
> Machine tested on left:
> <http://store.apple.com/1-800-MY-APPLE/WebObjects/AppleStore?family=iMac
>>
>
> 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...
>
> 

RE: [PyMOL] cartoon weight/scale

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

Stephen,

you need to adjust the *_width and *_length values individually.

e.g.

get cartoon_rect_length

set cartoon_rect_length, 2

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
> Stephen Kaiser
> Sent: Sunday, February 05, 2006 10:10 PM
> To: pym...@li...
> Subject: [PyMOL] cartoon weight/scale
>=20
> Hi,
>=20
> Can anybody suggest a way to increase the overall=20
> scale/weight of an entire cartoon in a way that's analagous=20
> to the command
>=20
> set cartoon_loop_radius
>=20
> and scales up the entire cartoon together?  it isn't obvious=20
> how to increase scale of a helix or sheet...
>=20
> thanks for your help,
> steve
>=20
>=20
> --
> Steve Kaiser
> Kopito Lab
> Stanford University
> 650-723-7588
>=20
>=20
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep=20
> through log files
> for problems?  Stop!  Download the new AJAX search engine that makes
> searching your log files as easy as surfing the  web. =20
> DOWNLOAD SPLUNK!
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D103432&bid=3D230486&
> dat=3D121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

[PyMOL] cartoon weight/scale

[Stephen K. <ka...@sl...>]

Hi,

Can anybody suggest a way to increase the overall scale/weight of 
an entire cartoon in a way that's analagous to the command

set cartoon_loop_radius

and scales up the entire cartoon together?  it isn't obvious how to 
increase scale of a helix or sheet...

thanks for your help,
steve


-- 
Steve Kaiser
Kopito Lab
Stanford University
650-723-7588

[PyMOL] Re: [o-info] RE: [ccp4bb]: Current Stereo 3D Display Info

[Morten K. <mo...@bi...>]

> these displays for a rainy day.  I've just given up on stereo and  
> switched
> to using higher-end LCD displays.  Less energy, less heat, and less  
> eye
> fatigue for me.

Let me quote myself from a posting to o-info from September 1994:

 > Real men don't Use Stereo

A few hours later, Eleanor replied:

 > Morten - you are getting old! 15 years ago:
 > Real Men Don't Use Colour.
 >  Eleanor

You can add another 10 years to the 15...

Boy, I hate to be right! In fact, I am actually considering giving up  
on colour... ;-)

/Morten

-- 
Morten Kjeldgaard, asc. professor, MSc, PhD
Department of Molecular Biology, Aarhus University
Gustav Wieds Vej 10 C, DK-8000 Aarhus C, Denmark.
Lab +45 89425026 * Mobile +45 51860147 * Fax +45 86123178
Home +45 86188180 * http://www.bioxray.dk/~mok

Re: [PyMOL] Can't figure out APBS

[Brian K. <bk...@it...>]

In addition to the stipulations listed below, I have also noticed 
that apbs can't handle a pdb file that has coordinate columns that 
touch each other such as this example:

				      this column
					V
ATOM     78  N   GLY A  38      66.914  66.219-103.497  1.00 18.01      A  
ATOM     79  CA  GLY A  38      66.309  66.763-104.698  1.00 20.04      A  
ATOM     80  C   GLY A  38      65.598  68.007-104.199  1.00 20.96      A  
ATOM     81  O   GLY A  38      64.432  68.267-104.508  1.00 23.61      A  

I've needed to transform the coordinates of my molecule so that this 
kind of thing doesn't happen.
(realspace_transform.inp in CNS works.)

Hope this helps.
BK

>Hi!
>
>You have to see if you are getting the .dx file. The default of  the 
>program is to put it at the same directory where it was installed, 
>along with the other temporary files: .in, .pqr and .pdb. In case of 
>not, I got the same problem and the solution was: the PDB that you 
>load can`t have chain ID, the aminoacids can`t have alternate 
>conformations and the program only accepts the standard residues. If 
>everything is all right with your PBD, after run the APBS you gotta 
>have the .dx at this directory. Once you got the .dx (the pymol will 
>show the apbs.map) click at the update (on Visualization) and then 
>show.
>Hope this help!
>sandra
>
>
>-------------------------------------------------------
>This SF.net email is sponsored by: Splunk Inc. Do you grep through log files
>for problems?  Stop!  Download the new AJAX search engine that makes
>searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
>http://sel.as-us.falkag.net/sel?cmd=lnk&kid=103432&bid=230486&dat=121642
>_______________________________________________
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>PyM...@li...
>https://lists.sourceforge.net/lists/listinfo/pymol-users

Re: [PyMOL] Can't figure out APBS

[Sandra MG D. <sa...@if...>]

Hi!

You have to see if you are getting the .dx file. The default of  the 
program is to put it at the same directory where it was installed, along 
with the other temporary files: .in, .pqr and .pdb. In case of not, I 
got the same problem and the solution was: the PDB that you load can`t 
have chain ID, the aminoacids can`t have alternate conformations and the 
program only accepts the standard residues. If everything is all right 
with your PBD, after run the APBS you gotta have the .dx at this 
directory. Once you got the .dx (the pymol will show the apbs.map) click 
at the update (on Visualization) and then show.
Hope this help!
sandra

[PyMOL] manual docking problem

[Vincent C. <ch...@le...>]

Hi,

I have a little problem with manual docking.

I load 2 pdb as 2 different objects.
I define the mouse in editing mode and shift+left-click to turn and 
shift+middle-button tu drag.

unfortunatly, the molecule splits in two and loops and helices streches to 
follow one piece of the protein.

any ideas to keep the protein as one single piece?
I am using version 0.98 on windows xp.

thanks
vincent

Vincent Chaptal
CNRS, LEBS-bat 34
1 Av de la terrasse
91 198 gif sur Yvette
tel: 01 69 82 42 04
fax: 01 69 82 31 29
http://www.lebs.cnrs-gif.fr/

[PyMOL] Unix launch script "./pymol.com" becoming "./pymol"

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

Some advanced warning...

For those keeping current via CVS, building from source, or installing
precompiled unix binaries, here is a quick "heads up!" intended to save
you some minor grief:

For the last six years, the PyMOL launch script has been called
"pymol.com" instead of simply "pymol".  I can't remember why I did
things that way, but PyMOL's ".com" convention is different from the
most everything else and for no good reason.  The launch script should
just be the name of the program.

Therefore, as of 0.99rc1, the launch script will simply be "pymol".  No
big deal right?  Well, not so fast:  symbolic links, shell aliases,
external scripts, package builders, and end-user habits may all need to
be adjusted after installing this next version.  That is why I haven't
changed this before now -- but we should clean this up before 1.0.

So, remember: if you update to PyMOL 0.99rc1 (when it's released) and
suddenly can't launch PyMOL, that is likely what is going on.  Either
reset your pointers to "./pymol", or symlink "./pymol" to "./pymol.com"
to preserve the status quo.

Cheers,
Warren

PS. If you're on Linux and want to dispatch this chore right now,
http://delsci.com/pre has a suitable build.

--
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

[PyMOL] A suggestion

[S. F. Y. <SY...@gn...>]

Hi,

I was wondering if PyMOL (with some plugin) has the capability to
visualize a series of small molecules that are associated with a protein
in a seamless way, e.g. poses from a docking exercise.  Right now, what
we can do is to combine all the structures into a single file and open
with PyMOL.  It would be a great tool to further advance PyMOL as a
visualization tool.

Thanks,
Frank

[PyMOL] Can't figure out APBS

[mynameis n. <pin...@ho...>]

For some reason I just can't get APBS to render an electrostatic surface for 
me.
I have installed pymol 0.99 beta37 and APBS 4.0 on Windows XP

Here are the steps I currently take:
1) I load my PDB molecule into Pymol
2) go to Plug-ins and click on APBS tools
3) click on APBS location and give locations for binary (installed in 
C:\program files\APBS) and psize.py (located in C:\program 
files\APBS\tools\manip)
4) click on set grid ---> output:
Maximum number of grid points exceeded.  Old grid dimensions were [129, 129, 
129]
Fine grid points rounded down from [107, 107, 107]
New grid dimensions are [97, 97, 97]
APBS Tools: coarse grid: (82.470,90.545,97.723)
APBS Tools: fine grid: (68.512,73.262,77.484)
APBS Tools: center: (29.733,20.940,40.031)
APBS Tools: fine grid points (97,97,97)

5) click on Run APBS --> output:
ObjectMapLoadDXFile-Error: Unable to open file!

6) click on Visualization tab and click update --> nothing happens.

Can someone please tell me what I am doing wrong?

Thank you so much for any assistance.

_________________________________________________________________
On the road to retirement? Check out MSN Life Events for advice on how to 
get there! http://lifeevents.msn.com/category.aspx?cid=Retirement

[PyMOL] conformation change

[Bingding H. <bh...@bi...>]

Hi,
I want to generate a figure that shows clearly the conformation change 
upon ligand-binding in 3tga(unbound) and 1mtw (ligand bound).
The ligand-binding site is a small pocket in the 3tga and is bigger 
pocket in bound structure. The loops of resi 190-195 strech to allow 
ligand binds.
I want a figure that can show the conformation change of the loops of 
resi 190-195 and also the change of the pocket.
Can anyone  give me a hint?

Thanks

Bingding

[PyMOL] Re: [ccp4bb]: Current Stereo 3D Display Info

[Philippe B. <phi...@un...>]

Hi Stuart,

Well, 20,000 =A3 (ex VAT) for a 20" UXGA is probably not something a lab=20=

can afford as easily as a CRT + graphic board... unless you would like=20=

to ship some free for advertisement (-;

Best regards,
Philippe

Le 31 janv. 06, =E0 14:25, Stuart McKay a =E9crit :

> Anastassis,
> =A0
> Interesting to read about the demise of the CRT and your problems with=20=

> flickering screens.
> =A0
> You (and the other BB members) may be interested to learn of an=20
> alternative technology from IRIS-3D in the UK.=A0Historically=20
> targeted=A0at the=A0Oil and Gas Sector for subsurface imaging,=A0it is =
now=20
> being evaluated in the Life Sciences. This product does not suffer=20
> from the flickering issues mentioned in this thread, being based=20
> around dual projection LCD technology and not requiring special=20
> glasses to view:
> =A0
> The IRIS=A0solution is a glasses-free 3D display system that enables =
you=20
> to work at up to UXGA resolution in stereo mode, is 2D/3D compatible,=20=

> can be used in a normal office environment,=A0does not suffer from=20
> stereo cross-talk (this means no more ghosting, eye-strain or=20
> headaches - enabling you=A0to concentrate on your data=A0rather than =
be=20
> distracted by the display technology) and is compatible with all=20
> stereo enabled software on a wide range of=A0SW/HW platforms.
> =A0
> More information is available from the company website or by=20
> contacting me directly.
> =A0
> Regards,
> =A0
> Stuart
> ...........................
> Stuart McKay, PhD
> CEO
> IRIS-3D Ltd
> James Weir Building
> 75 Montrose St
> Glasgow G1 1XJ
> Scotland, UK
> =A0
> (T) +44-141-548-2423
> (F) +44-141-552-5105
> (M) +44 7786 073663
> =A0
> http://www.iris3d.com
> =A0
> =A0
>> ----- Original Message -----
>> From: Anastassis Perrakis
>> To: Warren DeLano
>> Cc: pym...@li... ; CCP4 Board ; ono ; Albert =
Pauw
>> Sent: Tuesday, January 31, 2006 11:08 AM
>> Subject: Re: [ccp4bb]: Current Stereo 3D Display Info
>>
>> Hi all -
>>
>> While on the subject and after thanking Warren for providing the=20
>> excellent resource ...:
>>
>> We have some nice 3D monitors and Nvidia cards in Linux PC's we do=20
>> stereo with.
>>
>> Warren correctly points out that you need:
>>
>> =A0 =A01280x960=A0 @ 120 Hz requires H-sync of 123 kHz=A0
>> =A0 =A0 =A0 1344x1008 @ 120 Hz requires H-sync of 130 kHz=A0
>> =A0 =A0 =A0 1400x1050 @ 120 Hz requires H-sync of 136 kHz =A0
>>
>> (In fact you need your monitor to switch to these refresh rates only=20=

>> when in stereo, but thats a detail)
>>
>> However, I am totally unable to convince the NVidia drivers we have=20=

>> for Linux to
>> operate at the sync rates I want them to and Warren advices! Thus, we=20=

>> have noticeable flicker at stereo
>> mode (in the non-stereo windows only) which is a shame, given our=20
>> excellent monitors.
>> Is that expected or can be corrected ?
>>
>> Could anyone please advice me how to set the Nvidia Linux drivers to=20=

>> operate at the proper sync rates then ?
>>
>> Tassos
>>
>> PS=A0- Iiyama Vision Master Pro 514 / HM204DT (H-sync: 142 kHz) is=20
>> still available by some European vendors new and is great, we have=20
>> two, plus an old trusty EIZO T966 which is also cool. (Warren, I=20
>> could not find that on your list,its a good machine, does 136 and you=20=

>> might be able to find one still)
>>
>>
>> On Jan 28, 2006, at 20:59, Warren DeLano wrote:
>>
>>> ***=A0 For details on how to be removed from this list visit the=A0 =
***
>>> ***=A0 =A0 =A0 =A0 =A0 CCP4 home page http://www.ccp4.ac.uk =A0 =A0 =
=A0 =A0 ***
>>>
>>>
>>> Folks,
>>>
>>> Whether you favor Macintosh, Linux, or Windows for stereo 3D
>>> visualization, you're going to need some specific (and increasingly
>>> rare) hardware. =A0
>>>
>>> To help you find it, we've just updated our information page on
>>> stereo-3D-capable displays, cards, emitters, and glasses:
>>>
>>> http://pymol.sf.net/stereo3d.html
>>>
>>> Remarkably, we can now only find one company selling a brand new CRT
>>> monitor suitable for stereo 3D.=A0 If you find any others, please do=20=

>>> let
>>> us know!
>>>
>>> Cheers,
>>> Warren
>>>
>>> --
>>> Warren L. DeLano, Ph.D.=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0
>>> Principal Scientist
>>>
>>> . DeLano Scientific LLC =A0
>>> . 400 Oyster Point Blvd., Suite 213=A0 =A0 =A0 =A0 =A0 =A0
>>> . South San Francisco, CA 94080 USA=A0 =A0
>>> . Biz:(650)-872-0942=A0 Tech:(650)-872-0834=A0 =A0 =A0
>>> . Fax:(650)-872-0273=A0 Cell:(650)-346-1154
>>> . mailto:wa...@de... =A0 =A0 =A0
>>>
>>>

Re: [PyMOL] Re: [ccp4bb]: Current Stereo 3D Display Info

[Stephen G. <ste...@us...>]

Hi there,

Most modern monitors are very clever and tell the X server their
preferred sync rates (which never exceed 85 Hz).  You can override
this functionality by adding
    Option    "UseEdidFreqs"    "0"
to the "Device" section of your Xorg (or XFree86) config file.

You will also need to specify your own Modeline to control the monitor
timings.  The program 'gtf', which should come standard in most linux
distros, will help you do this.  Typing 'gtf' without args will give
you a short blurb on how to use the program.  Shove the modeline
output by gtf into the "Monitor" section of your Xorg config file, set
this new modeline as the default timing in the "Screen" section of the
config file, and you should be in business.

HTH,

Stephen

P.S. See http://o-info.bioxray.dk/pipermail/o-info/2003-April/006676.html
for more details.

On 1/31/06, Anastassis Perrakis <a.p...@nk...> wrote:
> Hi all -
>
> While on the subject and after thanking Warren for providing the excellen=
t
> resource ...:
>
> We have some nice 3D monitors and Nvidia cards in Linux PC's we do stereo
> with.
>
> Warren correctly points out that you need:
>
>     1280x960  @ 120 Hz requires H-sync of 123 kHz
>       1344x1008 @ 120 Hz requires H-sync of 130 kHz
>       1400x1050 @ 120 Hz requires H-sync of 136 kHz
> (In fact you need your monitor to switch to these refresh rates only when=
 in
> stereo, but thats a detail)
>
> However, I am totally unable to convince the NVidia drivers we have for
> Linux to
> operate at the sync rates I want them to and Warren advices! Thus, we hav=
e
> noticeable flicker at stereo
> mode (in the non-stereo windows only) which is a shame, given our excelle=
nt
> monitors.
> Is that expected or can be corrected ?
>
> Could anyone please advice me how to set the Nvidia Linux drivers to oper=
ate
> at the proper sync rates then ?
>
>  Tassos
>
> PS - Iiyama Vision Master Pro 514 / HM204DT (H-sync: 142 kHz) is still
> available by some European vendors new and is great, we have two, plus an
> old trusty EIZO T966 which is also cool. (Warren, I could not find that o=
n
> your list,its a good machine, does 136 and you might be able to find one
> still)
>
>
>
>
> On Jan 28, 2006, at 20:59, Warren DeLano wrote:
>
> ***  For details on how to be removed from this list visit the  ***
> ***          CCP4 home page http://www.ccp4.ac.uk         ***
>
>
> Folks,
>
> Whether you favor Macintosh, Linux, or Windows for stereo 3D
> visualization, you're going to need some specific (and increasingly
> rare) hardware.
>
> To help you find it, we've just updated our information page on
> stereo-3D-capable displays, cards, emitters, and glasses:
>
> http://pymol.sf.net/stereo3d.html
>
> Remarkably, we can now only find one company selling a brand new CRT
> monitor suitable for stereo 3D.  If you find any others, please do let
> us know!
>
> 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...
>
>
>
>


--
Stephen Graham
Crystallography Group
School of Molecular and Microbial Biosciences
University of Sydney

[PyMOL] Re: [ccp4bb]: Current Stereo 3D Display Info

[Anastassis P. <a.p...@nk...>]

Hi all -

While on the subject and after thanking Warren for providing the  
excellent resource ...:

We have some nice 3D monitors and Nvidia cards in Linux PC's we do  
stereo with.

Warren correctly points out that you need:

	   1280x960  @ 120 Hz requires H-sync of 123 kHz
       1344x1008 @ 120 Hz requires H-sync of 130 kHz
       1400x1050 @ 120 Hz requires H-sync of 136 kHz

(In fact you need your monitor to switch to these refresh rates only  
when in stereo, but thats a detail)

However, I am totally unable to convince the NVidia drivers we have  
for Linux to
operate at the sync rates I want them to and Warren advices! Thus, we  
have noticeable flicker at stereo
mode (in the non-stereo windows only) which is a shame, given our  
excellent monitors.
Is that expected or can be corrected ?

Could anyone please advice me how to set the Nvidia Linux drivers to  
operate at the proper sync rates then ?

	Tassos

PS - Iiyama Vision Master Pro 514 / HM204DT (H-sync: 142 kHz) is  
still available by some European vendors new and is great, we have  
two, plus an old trusty EIZO T966 which is also cool. (Warren, I  
could not find that on your list,its a good machine, does 136 and you  
might be able to find one still)


On Jan 28, 2006, at 20:59, Warren DeLano wrote:

> ***  For details on how to be removed from this list visit the  ***
> ***          CCP4 home page http://www.ccp4.ac.uk         ***
>
>
> Folks,
>
> Whether you favor Macintosh, Linux, or Windows for stereo 3D
> visualization, you're going to need some specific (and increasingly
> rare) hardware.
>
> To help you find it, we've just updated our information page on
> stereo-3D-capable displays, cards, emitters, and glasses:
>
> http://pymol.sf.net/stereo3d.html
>
> Remarkably, we can now only find one company selling a brand new CRT
> monitor suitable for stereo 3D.  If you find any others, please do let
> us know!
>
> 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...
>
>

[PyMOL] RE: [ccp4bb]: Current Stereo 3D Display Info

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

I believe that even the large Phillips (22") that you list is no longer
being made and that what is in stock at places is just old inventory (could
be wrong though).  It is hard to believe, but these monitors just aren't
being made anymore.  We literally have people in our modeling group hording
these displays for a rainy day.  I've just given up on stereo and switched
to using higher-end LCD displays.  Less energy, less heat, and less eye
fatigue for me.

Steve

-----Original Message-----
From: own...@dl... [mailto:own...@dl...] On Behalf Of
Warren DeLano
Sent: Saturday, January 28, 2006 2:59 PM
To: pym...@li...
Cc: cc...@dl...; vm...@ks...; pd...@sd...;
o-...@o-...; CCL Subscribers
Subject: [ccp4bb]: Current Stereo 3D Display Info


***  For details on how to be removed from this list visit the  ***
***          CCP4 home page http://www.ccp4.ac.uk         ***


Folks,

Whether you favor Macintosh, Linux, or Windows for stereo 3D
visualization, you're going to need some specific (and increasingly
rare) hardware.  

To help you find it, we've just updated our information page on
stereo-3D-capable displays, cards, emitters, and glasses:

http://pymol.sf.net/stereo3d.html

Remarkably, we can now only find one company selling a brand new CRT
monitor suitable for stereo 3D.  If you find any others, please do let
us know!

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...      




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RE: [PyMOL] Menu Bar viewed in stereo on Geowall

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

Matthew,

Could you be thinking of the "-j" launch option?  This can also be
accessed with

stereo on
set stereo_mode, 4

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
> Matthew Bowler
> Sent: Thursday, January 26, 2006 5:04 AM
> To: pym...@li...
> Subject: [PyMOL] Menu Bar viewed in stereo on Geowall
>=20
> Dear All,
> 	I am sure that around 3 months ago I found a command=20
> that would allow the menu bar in pymol to be seen and used=20
> while viewing a session in stereo on a geowall.  However, try=20
> as I might I cannot find the command now, any ideas?  Many=20
> thanks in advance, Matt.
>=20
>=20
>=20
> Matthew Bowler
> MRC Dunn Human Nutrition Unit
> Wellcome Trust / MRC Building
> Hills Road
> Cambridge CB2 2XY
> Tel: 0044 (0) 1223 252826
> Fax: 0044 (0) 1223 252825
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep=20
> through log files for problems?  Stop!  Download the new AJAX=20
> search engine that makes searching your log files as easy as=20
> surfing the  web.  DOWNLOAD SPLUNK!
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D103432&bid=3D230486&
> dat=3D121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

RE: [PyMOL] Cutaway surface

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

Stephen,

set ray_interior_color, color-name
ray

or

set ray_interior_color, -5
ray

to get an an effect like in that figure where the interiors are
different colors (on a per-object basis, or simply recolor afterwards in
Photoshop).

Note that the entire interior needs to be within the clip slab in order
for this to work.

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
> Stephen Graham
> Sent: Friday, January 27, 2006 5:32 AM
> To: pym...@li...
> Subject: [PyMOL] Cutaway surface
>=20
> Hi all,
>=20
> Is there any way good way in pymol of displaying a slice=20
> through a surface and block colouring the 'inner' face of the=20
> surface.=20
> Basically, I would like to generate a figure that looks like=20
> part (b) of=20
> http://www.nature.com/nature/journal/v432/n7014/fig_tab/nature
> 02988_F3.html
> using pymol.  I have tried playing with the lighting models=20
> and backpace culling (a-la set ambient=3D0; set direct=3D0.7; set=20
> reflect=3D0.0; set backface_cull=3D0) but they are not quite what=20
> I am after.
>=20
> Can anyone recommend a good way to achieve this effect?
>=20
> Thanks,
>=20
> Stephen
>=20
> --
> Stephen Graham
> Crystallography Group
> School of Molecular and Microbial Biosciences University of Sydney
>=20
>=20
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep=20
> through log files for problems?  Stop!  Download the new AJAX=20
> search engine that makes searching your log files as easy as=20
> surfing the  web.  DOWNLOAD SPLUNK!
> http://sel.as-us.falkag.net/sel?cmd=3Dk&kid=103432&bid#0486&dat=121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20