pymol-users Mailing List for PyMOL Molecular Graphics System (Page 2)

Hi,
(replying to my own message)
On Thu, 2012年12月13日 15:52 EST, Robert Campbell
<rob...@qu...> wrote:
> Hi Jon,
> 
> On Thu, 2012年12月13日 16:09 EST, Jonathan Grimes <jon...@st...>
> wrote:
> 
> > Hi All,
> > 
> > I have 2 different states of the same molecule......different
> > conformations generated from MD, so the same number of Calpha atoms,
> > with a direct 1:1 mapping between Calphas with the same residue
> > numbering.
> > 
> > I would like to draw a "bond" between equivalent C-alpha atoms, and I
> > will then ramp colour along the bond, say blue-white-red.
> > 
> > Could I get advice how to draw a bond between 2 Calpha atoms (same
> > resi) from different states
> 
> I have a script for drawing a cylinder (you can specify the radius and the
> beginning and ending colors) between two atoms. The script is at:
> 
> http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/draw_cylinder_cgo.py
> 
> First "run" the script via the "File" menu or via the command line:
> 
> run draw_cylinder_cgo.py
> 
> You will then have two new functions defined "draw_cylinder" and
> "draw_cylinder_cgo". The former allows you to pick two atoms to draw the
> cylinder between:
> 
> draw_cylinder name, atom1, atom2, radius, start_color, end_color
> 
> where each atom is a standard PyMOL selection (defaults to pk1 and
> pk2) and color is a 3-element RGB tuple defining the color
> of the cylinder (where each value of R, G and B is between 0 and 1
> inclusive). The colors default to (1,1,0).
> 
> 
> Alternatively, draw_cylinder_cgo takes as arguments the start and end
> coordinates of the vector in place of atom1 and atom2.
I could add more instructions here. You can specify the colours by
name and if you have picked the atoms with the mouse you can easily do
something like:
 draw_cylinder dist1, start_color=red, end_color=yellow
and it will default to using atom selections "pk1" and "pk2" and a radius
of 0.1 A.
Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor
Dept. of Biomedical & Molecular Sciences
Botterell Hall Rm 644
Queen's University, 
Kingston, ON K7L 3N6 Canada
Tel: 613-533-6821
<rob...@qu...> http://pldserver1.biochem.queensu.ca/~rlc

Hi Jon,
On Thu, 2012年12月13日 16:09 EST, Jonathan Grimes <jon...@st...>
wrote:
> Hi All,
> 
> I have 2 different states of the same molecule......different
> conformations generated from MD, so the same number of Calpha atoms, with
> a direct 1:1 mapping between Calphas with the same residue numbering.
> 
> I would like to draw a "bond" between equivalent C-alpha atoms, and I
> will then ramp colour along the bond, say blue-white-red.
> 
> Could I get advice how to draw a bond between 2 Calpha atoms (same
> resi) from different states
I have a script for drawing a cylinder (you can specify the radius and the
beginning and ending colors) between two atoms. The script is at:
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/draw_cylinder_cgo.py
First "run" the script via the "File" menu or via the command line:
run draw_cylinder_cgo.py
You will then have two new functions defined "draw_cylinder" and
"draw_cylinder_cgo". The former allows you to pick two atoms to draw the
cylinder between:
 draw_cylinder name, atom1, atom2, radius, start_color, end_color
 where each atom is a standard PyMOL selection (defaults to pk1 and pk2)
 and color is a 3-element RGB tuple defining the color
 of the cylinder (where each value of R, G and B is between 0 and 1
 inclusive). The colors default to (1,1,0).
Alternatively, draw_cylinder_cgo takes as arguments the start and end
coordinates of the vector in place of atom1 and atom2.
Hope that helps.
Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor
Dept. of Biomedical & Molecular Sciences
Botterell Hall Rm 644
Queen's University, 
Kingston, ON K7L 3N6 Canada
Tel: 613-533-6821
<rob...@qu...> http://pldserver1.biochem.queensu.ca/~rlc

 Hi All,
 I have 2 different states of the same molecule......different conformations generated from
 MD, so the same number of Calpha atoms, with a direct 1:1 mapping between Calphas 
 with the same residue numbering.
 I would like to draw a "bond" between equivalent C-alpha atoms, and I will then ramp
 colour along the bond, say blue-white-red.
 Could I get advice how to draw a bond between 2 Calpha atoms (same resi) from different
 states
 Many thanks for the help.
 Jon
Dr. Jonathan M. Grimes, 
NDM Senior Reseach Fellow
University Research Lecturer
Division of Structural Biology
Wellcome Trust Centre for Human Genetics
University of Oxford
Roosevelt Drive,
Oxford OX3 7BN, UK
Email: Jon...@st..., Web: www.strubi.ox.ac.uk 
Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547 

Hi
Sorry for not following up on this, I got side-tracked by a bunch of other stuff.
The problem still persists, unfortunately. 
I'm working on some visualization of volumetric data. My exact script is copied below.
While this runs, and I see all the commands being printed on screen, the resulting png-files contain nothing but a white background, when running in command mode (pymol -c script.pml). This is tested with both v 1.4.1 and 1.5.03.
I've tested Jason's method from below, which works except I have to use:
ray=1
png ~/foo.png, height=768, width=1024
instead of:
png ~/foo.png, height=768, width=1024, ray=1
I'm thankful for any suggestions. 
My final objective is to see if I can use povray (not available on my local machine) to render the volume visualization, but I'm working my way up towards that goal. 
Many thanks
/Per
 
# Load stuff
load density,dx, density
cmd.volume("density","density",1.0)
# Set the maximuym range to be displayed to 5 "sigma"
set volume_data_range, 5
# White background
bg_color white
# Make a color ramp
from pmg_tk.skins.normal.ColorRampModel import ColorRamp
r = ColorRamp(nColors=256)
r.addColor(0,(0,0,0,0),0) # white color for zero-density regions
r.addColor(1,(0.39,0.67,1,0.01),0) #light blue
r.addColor(55,(0,0,1,0.1),0) # darker blue
r.addColor(105,(0.48,0.99,0,0.5),0) # green
r.addColor(155,(1,0.0,0.0,1),0) # red
r.addColor(255,(1,0,0,0.25),0) # red for max density regions
ramp_colors = r.getRamp()
cmd.volume_color("density_volume",ramp_colors)
# Ray trace necessary when running in command mode, make png-pictures
set ray_volume,1
turn x, -90
ray
png volume_x.png,height=768,width=1024
turn y,-90
ray
png volume_y.png,height=768,width=1024
turn x, 90
ray
png volume_z.png,height=768,width=1024
27 nov 2012 kl. 14:58 skrev EPF (Esben Peter Friis):
> Hi Per 
> 
> 
> If you're still having problems, you can try to install and run pymol under the X virtual frame buffer (xvfb).
> 
> 
> Cheers,
> 
> Esben
> 
> 
> Best Regards
> Esben Peter Friis
> Science Manager
> 
> Novozymes A/S
> Krogshoejvej 36
> 
> 2880 Bagsvaerd Denmark
> Phone: +45 44461334
> Mobile: +45 30771334
> E-mail: ep...@no...
> 
> -----------------------------------
> Don't print today - contribute to a better environment tomorrow
> -----------------------------------
> 
> Novozymes A/S (reg. no.:10007127). Registered address: Krogshoejvej 36 DK-2880 Bagsvaerd, Denmark
> This e-mail (including any attachments) is for the intended addressee(s) only and may contain confidential and/or proprietary information protected by law. You are hereby notified that any unauthorized reading, disclosure, copying or distribution of this e-mail or use of information herein is strictly prohibited. If you are not an intended recipient you should delete this e-mail immediately. Thank you.
> 
> -----Original Message-----
> From: Jason Vertrees [mailto:jas...@sc...] 
> Sent: 26. november 2012 17:48
> To: Per Larsson
> Cc: pym...@li...
> Subject: Re: [PyMOL] Pymol in command mode - no output
> 
> Hi Per,
> 
> You'll probably want to use something like this:
> 
> # load the file
> 
> load http://molecules.gnu-darwin.org/html/00150001_00175000/153919/153919.pdb,
> myMolecule
> 
> # ray trace and save the image; you need to do this since you're running # PyMOL headlessly
> 
> png ~/foo.png, height=768, width=1024, ray=1
> 
> 
> As far as missing output that's most likely because you're running remotely and the stdout/stderr are being piped elsewhere. This is common on clusters.
> 
> Cheers,
> 
> -- Jason
> 
> On Mon, Nov 26, 2012 at 10:28 AM, Per Larsson <per...@sb...> wrote:
>> Hi Pymol-users,
>> 
>> I'm running a pml-script file to render some images on a remote server, using pymol 1.4, but I do not get any output at all. And no error message, so it is hard to troubleshoot, unfortunately.
>> 
>> To reduce the complexity of my script, I have reduced it to basically just loading a pdb-file and saving as a png-image (two lines in the pml-script), but even that does not work. Any suggestions?
>> 
>> I envoke the whole thing using
>> $pymol -c script.pml
>> 
>> 
>> Thanks
>> /Per
>> 
>> 
>> 
>> 
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> 
> 
> 
> --
> Jason Vertrees, PhD
> Director of Core Modeling Product Management Schrödinger, Inc.
> 
> (e) Jas...@sc...
> (o) +1 (603) 374-7120
> 
> ------------------------------------------------------------------------------
> Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial.
> Pricing starts from 795ドル for 25 servers or applications!
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> _______________________________________________
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> 
> 

Hi Jon,
> ive been given a pse file.....and i am trying to work out what color
> an object is......
>
> i used the command
>
> get cartoon_color, pT_A
>
> and got back....
>
> get: cartoon_color = default in object pT_A
You're right, that's not very helpful. This will get you the answer,
but it's not very straightforward:
s = cmd.get_session()
print cmd.get_color_tuple(s["names"][1][5][0][2])
To make sure you have right object ensure that,
s["names"][1][5][0][1]
equals your object name.
Cheers,
-- Jason
--
Jason Vertrees, PhD
Director of Core Modeling Product Management
Schrödinger, Inc.
(e) Jas...@sc...
(o) +1 (603) 374-7120

Hey,
I'm a long time user of macports, but recently I have decided to check out
homebrew for a number of reasons. Currently there is no standard way to
install pymol with this technique, but I thought it should be possible. I
set out to install pymol from source without the MacPorts libraries that
had helped me before.
I had significant trouble installing the current stable tarball. After
serious alterations to the setup script and some header files, I finally
got it to compile the cmd library, but any time I tried to load it with
python I had an error saying that it could not find the symbol
`_glutswapbuffers`.
Clearly some of this was a known issue because many of these changes were
addressed in the most recent trunk/head of the svn repository. I had to
make a few minor changes to make sure that it supports non-MacPorts
installations (https://gist.github.com/4267806), but it was rather trivial.
With this, I could install given I had Xquartz installed and a few other
dependencies. I created a homebrew repo that takes advantage of this change
here:
https://github.com/scicalculator/homebrew-pymol
Using the above, you can successfully install pymol using homebrew. The
only problem ... the toolbar fails to function. It does not throw any
errors if you have Pmw installed, but the toolbar widget never shows
itself. I have dome some other testing (https://gist.github.com/4269280) to
see if I can get the toolbar to show up, but no luck.
Does anyone have any hints as to where to look to get passed this part.
Also, if you have any ideas on fixing the `glutswapbuffers` error on the
"stable" branch, I'd love to hear it. Anyway, I hope this helps any users
of homebrew out there.
Derek Thomas

 ive been given a pse file.....and i am trying to work out what color 
 an object is......
 i used the command
 get cartoon_color, pT_A
 and got back....
 get: cartoon_color = default in object pT_A
 which could be more helpful.....
 could i get some clues how best to dig this information out...
 many thanks
 jon
Dr. Jonathan M. Grimes, 
NDM Senior Reseach Fellow
University Research Lecturer
Division of Structural Biology
Wellcome Trust Centre for Human Genetics
University of Oxford
Roosevelt Drive,
Oxford OX3 7BN, UK
Email: Jon...@st..., Web: www.strubi.ox.ac.uk 
Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547 

I don't want to hijack the thread but I was curious if you can point to few pymol
features for generating and rotating molecules and how they would play with
other tools. For example, if I just go download pdb files or take output from DFT,
it may be easier to do analysis with certain alignments. Similarly, I want to
generate hypothetical molecules for various tests and wanted some easy way
to do that. There are many graph, shape, or geometry tools available in various fields, 
maps, CAD etc and apparently they are tools for drawing or editing molecules.
However, I was just looking for something that works from command line and is
reasonably easy to integrate with other things. 
Apparently pymol is all based on python and presumably features, like the plugins
you pointed me to earlier, are easy to mix and match with other tools but not
sure offhand how to approach this. Right now, I'm making my own c++ tool
using Tcl front end so that I can eventually use all the math libraries like lapack
and boost as I want to do larger molecules( and use these for various types of "alignments" that
could generate large matricies ). Should I use python or just use
something that pymol already has? The immediate need is just to generate 
xyz files that look like short polyenes and be able to perturb them using a script.
So for this I end up with Tcl input that looks like a list of atom and direction
commands but there is probably some way to do this much with existing tools.
Thanks.
----------------------------------------
> From: jas...@sc...
> Date: 2012年12月11日 07:38:32 -0600
> To: jon...@st...
> CC: pym...@li...
> Subject: Re: [PyMOL] Help with alignments
>
> Hi Jon,
>
> align prot1 and chain A, prot2 and chain X
>
> 'super' and 'cealign' should work similarly.
>
> Cheers,
>
> -- Jason
>
> On Tue, Dec 11, 2012 at 7:35 AM, Jonathan Grimes
> <jon...@st...> wrote:
> >
> > I am wanting to align proteins based on superposition of
> > particular chains. Is it possible to do the superposition based
> > on the chains, but to move, in this case the entire complex ???
> >
> > Thanks
> > Jon
> >
> > Sent from my iPad
> >
> > ------------------------------------------------------------------------------
> > LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial
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> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > Archives: http://www.mail-archive.com/pym...@li...
>
>
>
> --
> Jason Vertrees, PhD
> Director of Core Modeling Product Management
> Schrödinger, Inc.
>
> (e) Jas...@sc...
> (o) +1 (603) 374-7120
>
> ------------------------------------------------------------------------------
> LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial
> Remotely access PCs and mobile devices and provide instant support
> Improve your efficiency, and focus on delivering more value-add services
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> _______________________________________________
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
 		 	 		 

Hi Jon,
align prot1 and chain A, prot2 and chain X
'super' and 'cealign' should work similarly.
Cheers,
-- Jason
On Tue, Dec 11, 2012 at 7:35 AM, Jonathan Grimes
<jon...@st...> wrote:
>
> I am wanting to align proteins based on superposition of
> particular chains. Is it possible to do the superposition based
> on the chains, but to move, in this case the entire complex ???
>
> Thanks
> Jon
>
> Sent from my iPad
>
> ------------------------------------------------------------------------------
> LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial
> Remotely access PCs and mobile devices and provide instant support
> Improve your efficiency, and focus on delivering more value-add services
> Discover what IT Professionals Know. Rescue delivers
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> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
-- 
Jason Vertrees, PhD
Director of Core Modeling Product Management
Schrödinger, Inc.
(e) Jas...@sc...
(o) +1 (603) 374-7120

 I am wanting to align proteins based on superposition of
 particular chains. Is it possible to do the superposition based 
 on the chains, but to move, in this case the entire complex ???
 Thanks
 Jon
Sent from my iPad

Hena,
> I created two objects as follows:
>
> pseudoatom A1, pos=[10.0, 10.0, 100.0]
> pseudoatom A2, pos=[10.0, 10.0, -200.0]
>
> I want to create a bond between these two atoms. Could you please help me? I
> need to display a 2 fold axis passing through these points.
You can create a distance measure between them as shown here,
http://www.pymolwiki.org/index.php/Pseudoatom. Or you can do this:
pseudoatom foo1, pos=[0,0,0], name=CA
pseudoatom foo2, pos=[1,1,1], name=CB
create foo, foo1 or foo2
bond foo////CA, foo////CB
which creates a single object from the two pseudoatoms and bonds the
two pseudoatoms.
Cheers,
-- Jason
--
Jason Vertrees, PhD
Director of Core Modeling Product Management
Schrödinger, Inc.
(e) Jas...@sc...
(o) +1 (603) 374-7120

Hi,
I created two objects as follows:
pseudoatom A1, pos=[10.0, 10.0, 100.0]
pseudoatom A2, pos=[10.0, 10.0, -200.0]
I want to create a bond between these two atoms. Could you please help me?
I need to display a 2 fold axis passing through these points.
I tried to use make and fuse command. Might be I am doing some thing wrong.
Please tell me the exact command, I should use.
My regards...
Hena

 is there a way of getting the alignto command to print out RMS deviations over
 the aligned regions of the structures.
 thanks
 jon
Dr. Jonathan M. Grimes, 
NDM Senior Reseach Fellow
University Research Lecturer
Division of Structural Biology
Wellcome Trust Centre for Human Genetics
University of Oxford
Roosevelt Drive,
Oxford OX3 7BN, UK
Email: Jon...@st..., Web: www.strubi.ox.ac.uk 
Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547 

Hi Vitaly,
Try
for i in cmd.get_object_list(): cmd.get_model(i).get_coord_list() or
cmd.delete(i)
Ciao!
Tsjerk
On Tue, Dec 11, 2012 at 9:31 AM, V.V. <vv...@gm...> wrote:
> Hello,
> Is there a quick way to delete the objects that do not contain any atoms?
>
> Thank you in advance,
> Vitaly
>
>
> ------------------------------------------------------------------------------
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> Remotely access PCs and mobile devices and provide instant support
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> _______________________________________________
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>
-- 
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4
Canada

Hello,
Is there a quick way to delete the objects that do not contain any atoms?
Thank you in advance,
Vitaly

Hi PyMOLers
We recently bought Asus V278H monitors, which displays nice stereo under Linux (Ubuntu 12.04). The monitors were bundled with Nvidia 3D vision v2 glasses. We have Quadro FX5800 cards, but we do NOT use the 3-pin stereo port, but rather the built-in emitter in the monitors. I have pasted my notes from the installation below. Is works with PyMOL as well as other OpenGL applications, such as VMD, Accelrys Discovery studio, CCDC GOLD/Hermes, Yasara, etc.
Cheers,
Esben
Asus VG278H flat panel 3D screens and Ubuntu 12.04
These screens have built-in emitters that actually work under Linux, with Nvidia drivers version 310 or newer. (These drivers are packaged in Ubuntu 12.04, so they're easy to install)
Install by closing X and install:
 sudo service lightdm stop
use Ctrl-Alt-F1 to swith to a text console and login (possibly, but not strictly necessary) as root
 wajig install nvidia-experimental-310
/etc/lightdm/lightdm.conf
This file is very important for geting the right video mode for the login screen (via the script in /etc/X11/set_1920x1080.sh, otherwise the X-server doesn't start at all). It also makes sure that the username has to be typed instead of selected from a list (very important when the system has many users)
[SeatDefaults]
user-session=ubuntu
greeter-session=unity-greeter
greeter-show-manual-login=true
greeter-hide-users=true
display-setup-script=/etc/X11/set_1920x1080.sh
session-setup-script=/etc/X11/set_1920x1080.sh
/etc/X11/set_1920x1080.sh
This script calls the xrandr tool to set the videomode
#!/bin/bash
xrandr --output DVI-I-3 --mode 1920x1080 --rate 120
Note!!
It seems that when everything is installed, there are still some tweaks to do (not completely sure though)
 * Reboot
 * For stereo to work the first time, I had to stop lightdm (see above), switch to a text console and login as normal user, then do startx to start the X-window system. Now check if stereo works. If so, then switch back to the text console and kill the X-server (Ctrl-C). The restart lightdm and login from the graphical login screen. Then it should work.
/etc/X11/xorg.conf
I dont know how important the xorg.conf file actually is, but here's my copy
# nvidia-xconfig: X configuration file generated by nvidia-xconfig
# nvidia-xconfig: version 310.14 (bui...@sw...) Tue Oct 9 13:04:01 PDT 2012
Section "ServerLayout"
 Identifier "Layout0"
 Screen "Screen0"
 InputDevice "Keyboard0" "CoreKeyboard"
 InputDevice "Mouse0" "CorePointer"
EndSection
Section "Files"
EndSection
Section "InputDevice"
 # generated from default
 Identifier "Mouse0"
 Driver "mouse"
 Option "Protocol" "auto"
 Option "Device" "/dev/psaux"
 Option "Emulate3Buttons" "no"
 Option "ZAxisMapping" "4 5"
EndSection
Section "InputDevice"
 # generated from default
 Identifier "Keyboard0"
 Driver "kbd"
EndSection
Section "Monitor"
 Identifier "Monitor0"
 VendorName "Unknown"
 ModelName "Unknown"
 HorizSync 28.0 - 400.0
 VertRefresh 43.0 - 120.0
 Option "DPMS"
EndSection
Section "Device"
 Identifier "Device0"
 Driver "nvidia"
 VendorName "NVIDIA Corporation"
EndSection
Section "Screen"
 Identifier "Screen0"
 Device "Device0"
 Monitor "Monitor0"
 DefaultDepth 24
 Option "NoPowerConnectorCheck" "True"
 Option "UseEdid" "True"
 Option "ModeDebug" "True"
 Option "Stereo" "10"
 Option "3DVisionDisplayType" "1"
 SubSection "Display"
 Depth 24
 EndSubSection
EndSection
Section "Extensions"
 Option "Composite" "Disable"
EndSection
Best Regards
Esben Peter Friis
Science Manager
Novozymes A/S
Krogshoejvej 36
2880 Bagsvaerd Denmark
Phone: +45 44461334
Mobile: +45 30771334
E-mail: ep...@no...
-----------------------------------
Don't print today - contribute to a better environment tomorrow
-----------------------------------
Novozymes A/S (reg. no.:10007127). Registered address: Krogshoejvej 36 DK-2880 Bagsvaerd, Denmark
This e-mail (including any attachments) is for the intended addressee(s) only and may contain confidential and/or proprietary information protected by law. You are hereby notified that any unauthorized reading, disclosure, copying or distribution of this e-mail or use of information herein is strictly prohibited. If you are not an intended recipient you should delete this e-mail immediately. Thank you.
From: Max Ferretti [mailto:MFe...@sc...]
Sent: 10. december 2012 17:22
To: pym...@li...
Subject: [PyMOL] Viewing PyMol in 3D
Hey everyone,
Does anyone have experience setting up pymol to be viewed in 3D with glasses? I'm hoping to build a system for this purpose.
>From what I have read, I will need a recent NVidia Quadro card and a 3D-capable LCD monitor with a resolution of at least 120Hz. I'm not sure if I need to be more specific than that (if there are particular cards/monitors that are known to work/not work). I'm also not quite sure if this is possible on Windows 7. I've seen reports of people doing this with Windows XP and Vista, but I would prefer to avoid those operating systems.
Any suggestions or advice would be greatly appreciated.
-Max F

Thanks Sabuj,
useful info indeed.
-----Original Message-----
From: Sabuj Pattanayek [mailto:sa...@gm...] 
Sent: Monday, December 10, 2012 4:18 PM
To: Schubert, Carsten [JRDUS]
Cc: Max Ferretti; pym...@li...
Subject: Re: [PyMOL] Viewing PyMol in 3D
You don't need a quadro with a 3 pin port to do stereo in linux
anymore, but you do need a "new" model quadro, e.g. a quadro 600. The
tradeoff is that you'll pay more for the 120hz monitors with the
built-in 3d vision v2 emitters, see here :
http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-November/008177.html
I haven't' tested a standalone 3d vision v2 emitter with linux, it may
behave the same way as the lcd's with the built-in v2 emitter.
> NVIDIA quadro card and Nvidia 3D kit. The only caveat is that under Linux
> you need to have a card which supports the external 3 pin stereo connector,
> you don't need that under any of the windows flavors. Check the Nivida

You don't need a quadro with a 3 pin port to do stereo in linux
anymore, but you do need a "new" model quadro, e.g. a quadro 600. The
tradeoff is that you'll pay more for the 120hz monitors with the
built-in 3d vision v2 emitters, see here :
http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-November/008177.html
I haven't' tested a standalone 3d vision v2 emitter with linux, it may
behave the same way as the lcd's with the built-in v2 emitter.
> NVIDIA quadro card and Nvidia 3D kit. The only caveat is that under Linux
> you need to have a card which supports the external 3 pin stereo connector,
> you don’t need that under any of the windows flavors. Check the Nivida

Alex, there is a little rectangle under the S of "State" in the lower left of the sidebar or to the left of the |< button. You can use that as a slider for the sidebar
From: Alex Truong [mailto:at...@bu...]
Sent: Monday, December 10, 2012 3:03 PM
To: pym...@li...
Subject: [PyMOL] Shrinking the sidebar
Hi All,
I was just wondering if it was possible to shrink the sidebar width so I have more viewing space? I regularly work with multiple windows open, usually splitscreen (vertically split). Since I do most of my work on a laptop with a 14-inch screen, that doesn't afford me much space to investigate my models with. I've tried dragging; it hasn't worked. Is there a a way to do it, or would the actual GUI source code have to be edited?
Thanks,
Alex

Sorry, I forgot the [PyMOL] subject header.
On Mon, Dec 10, 2012 at 3:02 PM, Alex Truong <at...@bu...> wrote:
> Hi All,
>
> I was just wondering if it was possible to shrink the sidebar width so I
> have more viewing space? I regularly work with multiple windows open,
> usually splitscreen (vertically split). Since I do most of my work on a
> laptop with a 14-inch screen, that doesn't afford me much space to
> investigate my models with. I've tried dragging; it hasn't worked. Is there
> a a way to do it, or would the actual GUI source code have to be edited?
>
> Thanks,
> Alex
>

On Mon, Dec 10, 2012 at 12:02 PM, Alex Truong <at...@bu...> wrote:
> I was just wondering if it was possible to shrink the sidebar width so I
> have more viewing space? I regularly work with multiple windows open,
> usually splitscreen (vertically split). Since I do most of my work on a
> laptop with a 14-inch screen, that doesn't afford me much space to
> investigate my models with. I've tried dragging; it hasn't worked. Is there
> a a way to do it, or would the actual GUI source code have to be edited?
Is this what you wanted?
set internal_gui_width, 100
Or to really get rid of it:
set internal_gui, 0
-Nat

Hi All,
I was just wondering if it was possible to shrink the sidebar width so I
have more viewing space? I regularly work with multiple windows open,
usually splitscreen (vertically split). Since I do most of my work on a
laptop with a 14-inch screen, that doesn't afford me much space to
investigate my models with. I've tried dragging; it hasn't worked. Is there
a a way to do it, or would the actual GUI source code have to be edited?
Thanks,
Alex

Hi Max,
you are already pretty much spot on. Pymol stereo works under XP, Vista, W7 and as far as I know any Linux flavor, as long as you purchase a compatible NVIDIA quadro card and Nvidia 3D kit. The only caveat is that under Linux you need to have a card which supports the external 3 pin stereo connector, you don't need that under any of the windows flavors. Check the Nivida website for compatible cards, machines and monitors.
I'm sure you can also find some structural biology groups at Scripps who are already setup with this equipment.
HTH
 Carsten
From: Max Ferretti [mailto:MFe...@sc...]
Sent: Monday, December 10, 2012 11:22 AM
To: pym...@li...
Subject: [PyMOL] Viewing PyMol in 3D
Hey everyone,
Does anyone have experience setting up pymol to be viewed in 3D with glasses? I'm hoping to build a system for this purpose.
>From what I have read, I will need a recent NVidia Quadro card and a 3D-capable LCD monitor with a resolution of at least 120Hz. I'm not sure if I need to be more specific than that (if there are particular cards/monitors that are known to work/not work). I'm also not quite sure if this is possible on Windows 7. I've seen reports of people doing this with Windows XP and Vista, but I would prefer to avoid those operating systems.
Any suggestions or advice would be greatly appreciated.
-Max F

Hey everyone,
Does anyone have experience setting up pymol to be viewed in 3D with glasses? I'm hoping to build a system for this purpose.
>From what I have read, I will need a recent NVidia Quadro card and a 3D-capable LCD monitor with a resolution of at least 120Hz. I'm not sure if I need to be more specific than that (if there are particular cards/monitors that are known to work/not work). I'm also not quite sure if this is possible on Windows 7. I've seen reports of people doing this with Windows XP and Vista, but I would prefer to avoid those operating systems.
Any suggestions or advice would be greatly appreciated.
-Max F

Hi Stephan Lloyd Watkins,
> I am no longer able to use the rendering plugin , which is a vlauble asset as I am at this moment in the midst of making some publication quality figures.
Which rendering plugin are you referring to? What type of computer are
you using?
> Additional, the standard ray trace option will only work if I use a white background, and zoom out further than would make a good image, ie a 300 amino protein about 1 inch square on an 8x8 inch window (visual field).
How are you ray tracing? Using the 'ray' command? Clicking the 'ray'
button? What happens if you do not use a white background? These bugs
sound like they're related to the plugin, not PyMOL itself. Can you
share your PyMOL session file with me?
> As it is both the rendering types, I assume it is some change to memory utilized by the shaders, as it crashes everytime. I have a similar problem now with gimp as well, however the memory cap is easy to see and maxes out around 3-4 G before crashing, however there is a 16 G memory, along with 4G on the GPU so I do not know where the errors come from. I do not get the errors on VMD, however prefer Pymol for the ease of use and also the images are nice.
If you have Intel-based hardware you might try the following settings
upon startup:
set use_shaders, 0
set sphere_mode, 0
and then try your rendering plugin.
Cheers,
-- Jason
--
Jason Vertrees, PhD
Director of Core Modeling Product Management
Schrödinger, Inc.
(e) Jas...@sc...
(o) +1 (603) 374-7120