pymol-users Mailing List for PyMOL Molecular Graphics System

Hi Anasuya,
Happy New Year!
sphere_mode only controls the appearance. You probably want to try
sphere_scale.
Enjoy,
Tsjerk
On Mon, Dec 31, 2012 at 12:14 PM, Anasuya Dighe
<an...@mb...>wrote:
> Hi,
>
> I am representing C-alpha atoms of binding site as spheres.
> I am using the set sphere_mode command to adjust the radius of the
> spheres. I
> use the sphere_mode as 4.
> However, when I do a ray tracing, no matter how small the spheres I set,
> they
> appear very large once the ray tracing is carried out.
> This auto-enlargement after ray-tracing is not what I wish to obtain.
>
> I am looking forward to obtain small spheres after I do a ray tracing.
>
> Please help.
> - Anasuya
>
>
>
>
>
>
> --
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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

Hi,
I am representing C-alpha atoms of binding site as spheres.
I am using the set sphere_mode command to adjust the radius of the spheres. I
use the sphere_mode as 4.
However, when I do a ray tracing, no matter how small the spheres I set, they
appear very large once the ray tracing is carried out.
This auto-enlargement after ray-tracing is not what I wish to obtain.
I am looking forward to obtain small spheres after I do a ray tracing.
Please help.
- Anasuya
-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.

What does Chimera do? I finally wrote my own c++ tool that let's a TcL script
specify a molecule's layout in terms of relevance like bond length and angle. 
I decided it was worth the effort since I didn't want to look around much for existing
stuff and would eventually add my own stuff for analysis. The real decision was
to learn python or just use TcL. I guess if I was looking for a tool to generate 
from a script I'd probably prefer python. Thanks.
----------------------------------------
> Date: 2012年12月28日 05:42:27 -0800
> From: jms...@gm...
> To: pym...@li...
> Subject: Re: [PyMOL] Building of the Carbon lattice
>
> Hi Tsjerk!
>
> This is the example of such lattice which I've built using Chimera!
> http://imageshack.us/photo/my-images/543/lattice.png/
>
> this is simple model of the Carbon-contained lattice without hydrogens.
> So I'd like to build such lattices from different atoms as nodes
> defining only atom type as well as number of nodes.
>
> Also I'd like to simulate this model using PBC so it seems that big
> dimensions of such lattice doesn't matter, doesn’t it ? ( It will be
> simpler to build smaller symmetric model )
>
> James
>
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Hi Tsjerk!
This is the example of such lattice which I've built using Chimera!
http://imageshack.us/photo/my-images/543/lattice.png/
this is simple model of the Carbon-contained lattice without hydrogens.
So I'd like to build such lattices from different atoms as nodes
defining only atom type as well as number of nodes.
Also I'd like to simulate this model using PBC so it seems that big
dimensions of such lattice doesn't matter, doesn’t it ? ( It will be
simpler to build smaller symmetric model )
James

Dear PyMol users!
I'd like to build simple 2D lattice model consisted of the Carbon
atoms connected by the single bonds. Could you provide me with some
script which can build such lattices of the desired dimensions ?
Thanks for help
James

Hi Krisztina,
> I wonder if there is any way to list atoms an atom is bonded to?
Use the "neighbor" selection operator:
PyMOL> select newsele, neighbor (othersele)
See also:
http://pymolwiki.org/index.php/Selection_Algebra
> I would
> like to list H bonded pairs but the available scritps (list_hbonds.py,
> or polarpairs.py) only check for distance and angle between heteroatoms,
> but not if any of them is actually connected to a hydrogen. As a result
> two carbonyl atoms are listed too.
Have you also tried the "distance" command? It is very similar to
list_hbonds/polarpairs:
PyMOL> distance hbonds, all, all, mode=2
There is no direct way to list these pairs, but you can use
get_raw_distances script from the PyMOLWiki:
http://pymolwiki.org/index.php/Get_raw_distances
Hope that helps.
Cheers,
 Thomas
-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

Hi,
I wonder if there is any way to list atoms an atom is bonded to? I would like to list H bonded pairs but the available scritps (list_hbonds.py, or polarpairs.py) only check for distance and angle between heteroatoms, but not if any of them is actually connected to a hydrogen. As a result two carbonyl atoms are listed too.
Thanks in advance,
Krisztina 

Hi Thomas, thanks for the feedback.
I would like to point out that I observe this with version PyMOL 1.3 
(also Hybrid), where, correct me if I'm wrong, there is no undo feature 
available (at least I have never used or seen it here). To me this would 
mean, the problem has to be with something else (possibly in addition to 
undo).
To perfectly reproduce my situation, you can run the script that I 
posted on pastebin (http://pastebin.com/mC6Rs6wk). Let me know if you 
need some guidance with all the variables, I'm sorry for the terrible 
code. I can also send you the PDB file I used when I got into this 
problem, then you dont need to adjust any variables.
Best regards
Martin
On 21.12.12 17:31, Thomas Holder wrote:
> Hi Gianluigi and Martin,
>
> thanks for reporting, this is a serious issue and we are looking into it.
>
> As far as we can reproduce, it's related to the undo feature. Adding this to your scripts should help:
>
> cmd.set("suspend_undo", 1)
>
> Cheers,
> Thomas
>
> On Dec 21, 2012, at 9:53 AM, Gianluigi Caltabiano <chi...@ya...> wrote:
>
>> I have the same problem since pymol 1.5, mainly with the hybrid (I can reach 10GB of ram memory with relatively small sessions). I'm on MAC OS 10.7.5 and pymol version 1.5.0.3.
>> I had to renounce working with Hybrid unless I really need some plug-in.
>>
>> Gianluigi
>>
>>
>> Da: Jason Vertrees <jas...@sc...>
>> A: Martin Hediger <ma...@bl...>
>> Cc: "pym...@li..." <pym...@li...>
>> Inviato: Giovedì 20 Dicembre 2012 17:05
>> Oggetto: Re: [PyMOL] Memory not released after load and delete of structure
>>
>> Martin,
>>
>> That sounds like a memory leak in v1.3. Can you try a newer version of
>> PyMOL and let us know if it still happens? We've fixed lots of bugs
>> since v1.3.
>>
>> Also, is your script simply iterating over structures and deleting
>> them when done? You sure you're not missing a cleanup step somewhere?
>> (Any chance we can see the script or a stub of it?)
>>
>> Cheers,
>>
>> -- Jason
>>
>> On Fri, Dec 21, 2012 at 3:17 AM, Martin Hediger <ma...@bl...> wrote:
>>> Hi Jason,
>>> I'm using PyMOL 1.3.
>>>
>>> Best regards
>>> Martin
>>>
>>>
>>>
>>> On 20.12.12 15:53, Jason Vertrees wrote:
>>>> Hi Martin,
>>>>
>>>> Which version of PyMOL are you using?
>>>>
>>>> Cheers,
>>>>
>>>> -- Jason
>>>>
>>>> On Fri, Dec 21, 2012 at 1:37 AM, Martin Hediger <ma...@bl...> wrote:
>>>>> Dear PyMOL users
>>>>> In a directory are PDB files of combined size equal to around 3MB. When
>>>>> I load all files into PyMOL, I observe that the required RAM of PyMOL
>>>>> (MacOS X 10.6) increases by roughly this amount.
>>>>> When I delete all objects, the RAM requirement remains the same and when
>>>>> I then reload all structures, the RAM requirement increases even further.
>>>>> I'm currently using PyMOL to batch process a number of files where a
>>>>> structure is loaded, modified and then deleted again from the objects
>>>>> list. This then results in RAM requirements of over 1GB and together
>>>>> with other applications, I run out of memory.
>>>>> Is there a way I can prevent PyMOL from behaving this way?
>>>>>
>>>>> Best regards and thanks for any help
>>>>> Martin
>> -- 
>> Jason Vertrees, PhD
>> Director of Core Modeling Product Management
>> Schrödinger, Inc.
>>
>> (e) Jas...@sc...
>> (o) +1 (603) 374-7120

Hi Gianluigi and Martin,
thanks for reporting, this is a serious issue and we are looking into it.
As far as we can reproduce, it's related to the undo feature. Adding this to your scripts should help:
cmd.set("suspend_undo", 1)
Cheers,
 Thomas
On Dec 21, 2012, at 9:53 AM, Gianluigi Caltabiano <chi...@ya...> wrote:
> I have the same problem since pymol 1.5, mainly with the hybrid (I can reach 10GB of ram memory with relatively small sessions). I'm on MAC OS 10.7.5 and pymol version 1.5.0.3.
> I had to renounce working with Hybrid unless I really need some plug-in.
> 
> Gianluigi
> 
> 
> Da: Jason Vertrees <jas...@sc...>
> A: Martin Hediger <ma...@bl...> 
> Cc: "pym...@li..." <pym...@li...> 
> Inviato: Giovedì 20 Dicembre 2012 17:05
> Oggetto: Re: [PyMOL] Memory not released after load and delete of structure
> 
> Martin,
> 
> That sounds like a memory leak in v1.3. Can you try a newer version of
> PyMOL and let us know if it still happens? We've fixed lots of bugs
> since v1.3.
> 
> Also, is your script simply iterating over structures and deleting
> them when done? You sure you're not missing a cleanup step somewhere?
> (Any chance we can see the script or a stub of it?)
> 
> Cheers,
> 
> -- Jason
> 
> On Fri, Dec 21, 2012 at 3:17 AM, Martin Hediger <ma...@bl...> wrote:
> > Hi Jason,
> > I'm using PyMOL 1.3.
> >
> > Best regards
> > Martin
> >
> >
> >
> > On 20.12.12 15:53, Jason Vertrees wrote:
> >>
> >> Hi Martin,
> >>
> >> Which version of PyMOL are you using?
> >>
> >> Cheers,
> >>
> >> -- Jason
> >>
> >> On Fri, Dec 21, 2012 at 1:37 AM, Martin Hediger <ma...@bl...> wrote:
> >>>
> >>> Dear PyMOL users
> >>> In a directory are PDB files of combined size equal to around 3MB. When
> >>> I load all files into PyMOL, I observe that the required RAM of PyMOL
> >>> (MacOS X 10.6) increases by roughly this amount.
> >>> When I delete all objects, the RAM requirement remains the same and when
> >>> I then reload all structures, the RAM requirement increases even further.
> >>> I'm currently using PyMOL to batch process a number of files where a
> >>> structure is loaded, modified and then deleted again from the objects
> >>> list. This then results in RAM requirements of over 1GB and together
> >>> with other applications, I run out of memory.
> >>> Is there a way I can prevent PyMOL from behaving this way?
> >>>
> >>> Best regards and thanks for any help
> >>> Martin
> 
> -- 
> Jason Vertrees, PhD
> Director of Core Modeling Product Management
> Schrödinger, Inc.
> 
> (e) Jas...@sc...
> (o) +1 (603) 374-7120
-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

Today I managed to get Coot (and Pymol etc) running under Linux in stereo.
Here is the setup for those that are interested:
For the stereophiles with a linux box,
System: Dell precision 3600 with nvidia quadro 2000 (no 3-pin connector)
Linux: Latest version of openSuse but we had to download and install 
latest nvidia driver ourselves
Screen: ASUS VG278H (with build-in IR emitter!! for driving nvidia 
stereo glasses)
First set the resolution to 1920x1080@120Hz and then edit the xorg.conf 
file in /etc/X11/ as follows:
1) in Section "Screen" change Option "Stereo" "0" to "11" (7, 8, 9, 10, 
or 12 did not work at all!). "11" activates "nvidia vision pro"....
2) did NOT add the line with "3DVisionDisplayType" "1" because the ASUS 
monitor is nvidia certified
3) added the following too (but did not test if this is really needed)
Section "Extensions"
 Option "Composite" "Disable"
EndSection
4) save the file, log out, log in again.
Hoppla, the 3D light is switches on (also happened with "Stereo" "10" 
but stereo was not active at all) and Coot in stereo looks just great!
Pymol also works.
Jeroen.
p.s. season's greetings to all of you out there!
-- 
Dr. Jeroen R. Mesters
Gruppenleiter Strukturelle Neurobiologie und Kristallogenese
Institut für Biochemie
Universität zu Lübeck
Zentrum für Medizinische Struktur- und Zellbiologie
Ratzeburger Allee 160, D-23538 Lübeck
Tel: +49-451-5004065
Fax: +49-451-5004068
Http://www.biochem.uni-luebeck.de
Http://www.iobcr.org
Http://www.selfish-brain.org
Http://www.opticryst.org
--
Any intelligent fool can make things bigger and more complex. It takes a 
lot of genius and a lot of courage to move in the opposite direction 
(Albert Einstein, 1879-1955)
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Hi grid bird,
the label command is parsed in "literal" mode, which means the semicolon
is not recognized as command separator. Try this instead:
/usr/bin/pymol -d 'fetch 1D5R, async=0; show_as cartoon; spectrum b;
select t0, (resi 30); color red, selection=t0; show spheres,
selection=t0; label t0, "test message"' -d 'save t0.pse'
Cheers,
 Thomas
grid bird wrote, On 12/20/12 17:49:
> Hi all,
> 
> I am trying to use PyMol version 1.2r1 to do one test but I always
> failed to label my selection.
> the command line I used is the following:
> 
> /usr/bin/pymol 1D5R.pdb 'show_as cartoon; spectrum b; sele t0, (resi
> 30); color red, selection=t0; show spheres, selection=t0; label t0,
> "test message"; save t0.pse;'
> 
> I always got the error message as the following. Actually , I just want
> to label my selection t0 with one string message. Any ideas ? thank you.
> 
> Spectrum: range ( 9.77000 to 117.74000).
> Selector: selection "t0" defined with 7 atoms.
> Executive: Colored 7 atoms.
> File "<string>", line 1
> label="test message"; save t0.pse;
> ^
> SyntaxError: invalid syntax
> Label: labelled 0 atoms.
-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

I have the same problem since pymol 1.5, mainly with the hybrid (I can reach 10GB of ram memory with relatively small sessions). I'm on MAC OS 10.7.5 and pymol version 1.5.0.3.
I had to renounce working with Hybrid unless I really need some plug-in. 
Gianluigi
________________________________
 Da: Jason Vertrees <jas...@sc...>
A: Martin Hediger <ma...@bl...> 
Cc: "pym...@li..." <pym...@li...> 
Inviato: Giovedì 20 Dicembre 2012 17:05
Oggetto: Re: [PyMOL] Memory not released after load and delete of structure
 
Martin,
That sounds like a memory leak in v1.3. Can you try a newer version of
PyMOL and let us know if it still happens? We've fixed lots of bugs
since v1.3.
Also, is your script simply iterating over structures and deleting
them when done? You sure you're not missing a cleanup step somewhere?
(Any chance we can see the script or a stub of it?)
Cheers,
-- Jason
On Fri, Dec 21, 2012 at 3:17 AM, Martin Hediger <ma...@bl...> wrote:
> Hi Jason,
> I'm using PyMOL 1.3.
>
> Best regards
> Martin
>
>
>
>
>
> On 20.12.12 15:53, Jason Vertrees wrote:
>>
>> Hi Martin,
>>
>> Which version of PyMOL are you using?
>>
>> Cheers,
>>
>> -- Jason
>>
>> On Fri, Dec 21, 2012 at 1:37 AM, Martin Hediger <ma...@bl...> wrote:
>>>
>>> Dear PyMOL users
>>> In a directory are PDB files of combined size equal to around 3MB. When
>>> I load all files into PyMOL, I observe that the required RAM of PyMOL
>>> (MacOS X 10.6) increases by roughly this amount.
>>> When I delete all objects, the RAM requirement remains the same and when
>>> I then reload all structures, the RAM requirement increases even further.
>>> I'm currently using PyMOL to batch process a number of files where a
>>> structure is loaded, modified and then deleted again from the objects
>>> list. This then results in RAM requirements of over 1GB and together
>>> with other applications, I run out of memory.
>>> Is there a way I can prevent PyMOL from behaving this way?
>>>
>>> Best regards and thanks for any help
>>> Martin
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> 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
------------------------------------------------------------------------------
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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Archives: http://www.mail-archive.com/pym...@li... 

Hi all,
I am trying to use PyMol version 1.2r1 to do one test but I always failed
to label my selection.
the command line I used is the following:
 /usr/bin/pymol 1D5R.pdb 'show_as cartoon; spectrum b; sele t0, (resi
30); color red, selection=t0; show spheres, selection=t0; label t0, "test
message"; save t0.pse;'
I always got the error message as the following. Actually , I just want to
label my selection t0 with one string message. Any ideas ? thank you.
Spectrum: range ( 9.77000 to 117.74000).
 Selector: selection "t0" defined with 7 atoms.
 Executive: Colored 7 atoms.
 File "<string>", line 1
 label="test message"; save t0.pse;
 ^
SyntaxError: invalid syntax
 Label: labelled 0 atoms.

I'll give it a try with the newer versions.
I just checked, and I believe I'm doing some cleaning up.
Sure, I posted the scripte on this pastebin:
http://pastebin.com/mC6Rs6wk
Sorry for the layout (all pretty in development). In production, the 
script is invoked from the "frag" function.
Martin
On 20.12.12 17:05, Jason Vertrees wrote:
> Martin,
>
> That sounds like a memory leak in v1.3. Can you try a newer version of
> PyMOL and let us know if it still happens? We've fixed lots of bugs
> since v1.3.
>
> Also, is your script simply iterating over structures and deleting
> them when done? You sure you're not missing a cleanup step somewhere?
> (Any chance we can see the script or a stub of it?)
>
> Cheers,
>
> -- Jason
>
> On Fri, Dec 21, 2012 at 3:17 AM, Martin Hediger <ma...@bl...> wrote:
>> Hi Jason,
>> I'm using PyMOL 1.3.
>>
>> Best regards
>> Martin
>>
>>
>>
>>
>>
>> On 20.12.12 15:53, Jason Vertrees wrote:
>>> Hi Martin,
>>>
>>> Which version of PyMOL are you using?
>>>
>>> Cheers,
>>>
>>> -- Jason
>>>
>>> On Fri, Dec 21, 2012 at 1:37 AM, Martin Hediger <ma...@bl...> wrote:
>>>> Dear PyMOL users
>>>> In a directory are PDB files of combined size equal to around 3MB. When
>>>> I load all files into PyMOL, I observe that the required RAM of PyMOL
>>>> (MacOS X 10.6) increases by roughly this amount.
>>>> When I delete all objects, the RAM requirement remains the same and when
>>>> I then reload all structures, the RAM requirement increases even further.
>>>> I'm currently using PyMOL to batch process a number of files where a
>>>> structure is loaded, modified and then deleted again from the objects
>>>> list. This then results in RAM requirements of over 1GB and together
>>>> with other applications, I run out of memory.
>>>> Is there a way I can prevent PyMOL from behaving this way?
>>>>
>>>> Best regards and thanks for any help
>>>> Martin
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> 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
>>>> http://p.sf.net/sfu/logmein_12329d2d
>>>> _______________________________________________
>>>> PyMOL-users mailing list (PyM...@li...)
>>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>>> Archives: http://www.mail-archive.com/pym...@li...
>>>
>>>
>
>

Martin,
That sounds like a memory leak in v1.3. Can you try a newer version of
PyMOL and let us know if it still happens? We've fixed lots of bugs
since v1.3.
Also, is your script simply iterating over structures and deleting
them when done? You sure you're not missing a cleanup step somewhere?
(Any chance we can see the script or a stub of it?)
Cheers,
-- Jason
On Fri, Dec 21, 2012 at 3:17 AM, Martin Hediger <ma...@bl...> wrote:
> Hi Jason,
> I'm using PyMOL 1.3.
>
> Best regards
> Martin
>
>
>
>
>
> On 20.12.12 15:53, Jason Vertrees wrote:
>>
>> Hi Martin,
>>
>> Which version of PyMOL are you using?
>>
>> Cheers,
>>
>> -- Jason
>>
>> On Fri, Dec 21, 2012 at 1:37 AM, Martin Hediger <ma...@bl...> wrote:
>>>
>>> Dear PyMOL users
>>> In a directory are PDB files of combined size equal to around 3MB. When
>>> I load all files into PyMOL, I observe that the required RAM of PyMOL
>>> (MacOS X 10.6) increases by roughly this amount.
>>> When I delete all objects, the RAM requirement remains the same and when
>>> I then reload all structures, the RAM requirement increases even further.
>>> I'm currently using PyMOL to batch process a number of files where a
>>> structure is loaded, modified and then deleted again from the objects
>>> list. This then results in RAM requirements of over 1GB and together
>>> with other applications, I run out of memory.
>>> Is there a way I can prevent PyMOL from behaving this way?
>>>
>>> Best regards and thanks for any help
>>> Martin
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> 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
>>> http://p.sf.net/sfu/logmein_12329d2d
>>> _______________________________________________
>>> 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

Hi Jason,
I'm using PyMOL 1.3.
Best regards
Martin
On 20.12.12 15:53, Jason Vertrees wrote:
> Hi Martin,
>
> Which version of PyMOL are you using?
>
> Cheers,
>
> -- Jason
>
> On Fri, Dec 21, 2012 at 1:37 AM, Martin Hediger <ma...@bl...> wrote:
>> Dear PyMOL users
>> In a directory are PDB files of combined size equal to around 3MB. When
>> I load all files into PyMOL, I observe that the required RAM of PyMOL
>> (MacOS X 10.6) increases by roughly this amount.
>> When I delete all objects, the RAM requirement remains the same and when
>> I then reload all structures, the RAM requirement increases even further.
>> I'm currently using PyMOL to batch process a number of files where a
>> structure is loaded, modified and then deleted again from the objects
>> list. This then results in RAM requirements of over 1GB and together
>> with other applications, I run out of memory.
>> Is there a way I can prevent PyMOL from behaving this way?
>>
>> Best regards and thanks for any help
>> Martin
>>
>> ------------------------------------------------------------------------------
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>
>

Hi Martin,
Which version of PyMOL are you using?
Cheers,
-- Jason
On Fri, Dec 21, 2012 at 1:37 AM, Martin Hediger <ma...@bl...> wrote:
> Dear PyMOL users
> In a directory are PDB files of combined size equal to around 3MB. When
> I load all files into PyMOL, I observe that the required RAM of PyMOL
> (MacOS X 10.6) increases by roughly this amount.
> When I delete all objects, the RAM requirement remains the same and when
> I then reload all structures, the RAM requirement increases even further.
> I'm currently using PyMOL to batch process a number of files where a
> structure is loaded, modified and then deleted again from the objects
> list. This then results in RAM requirements of over 1GB and together
> with other applications, I run out of memory.
> Is there a way I can prevent PyMOL from behaving this way?
>
> Best regards and thanks for any help
> Martin
>
> ------------------------------------------------------------------------------
> 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...
-- 
Jason Vertrees, PhD
Director of Core Modeling Product Management
Schrödinger, Inc.
(e) Jas...@sc...
(o) +1 (603) 374-7120

Dear PyMOL users
In a directory are PDB files of combined size equal to around 3MB. When 
I load all files into PyMOL, I observe that the required RAM of PyMOL 
(MacOS X 10.6) increases by roughly this amount.
When I delete all objects, the RAM requirement remains the same and when 
I then reload all structures, the RAM requirement increases even further.
I'm currently using PyMOL to batch process a number of files where a 
structure is loaded, modified and then deleted again from the objects 
list. This then results in RAM requirements of over 1GB and together 
with other applications, I run out of memory.
Is there a way I can prevent PyMOL from behaving this way?
Best regards and thanks for any help
Martin

Hi Stephan,
I use Ubuntu 12 and haven't had any problems with PyMOL. I do have
problems with my mouse in all apps, but that's not PyMOL's fault.
Do you know anyone else with these problems? Have you asked around the
Ubuntu community?
Cheers,
-- Jason
On Sun, Dec 16, 2012 at 10:37 AM, lloyd riggs <llo...@gm...> wrote:
>
> Dear All,
>
> I have a wierd bug with pymol after a recent update to Ubuntu 12.10. If I use any auxiliary (not in pymol) software such as notepads, gedit, etc..Pymol then does some sort of switch if it is open at the same time for selections. It changes from residue, to atom, to whole molecule in the selection, depending on how much or how many times you go and type something in gedit. It then does not allow you to rotate the molecule, or change the menu selections anymore. I then have to re-start the computer, or re-install pymol to re-set the normal operations. This is extremely problematic, as pymol is a good program to quickly look at specific residues, etc...when doing massive text based tabulations of specific residues, and a necessary orientation and check visually is needed on the side to keep track of things. Needless to say the uses for anything else, such as making images, etc..
>
> Has anyone experienced this, or more importantly, does anyone have a patch or bug fix.
>
> Sincerely,
>
> Stephan Watkins
>
> ------------------------------------------------------------------------------
> 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
> http://p.sf.net/sfu/logmein_12329d2d
> _______________________________________________
> 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

Dear All,
I have a wierd bug with pymol after a recent update to Ubuntu 12.10. If I use any auxiliary (not in pymol) software such as notepads, gedit, etc..Pymol then does some sort of switch if it is open at the same time for selections. It changes from residue, to atom, to whole molecule in the selection, depending on how much or how many times you go and type something in gedit. It then does not allow you to rotate the molecule, or change the menu selections anymore. I then have to re-start the computer, or re-install pymol to re-set the normal operations. This is extremely problematic, as pymol is a good program to quickly look at specific residues, etc...when doing massive text based tabulations of specific residues, and a necessary orientation and check visually is needed on the side to keep track of things. Needless to say the uses for anything else, such as making images, etc..
Has anyone experienced this, or more importantly, does anyone have a patch or bug fix.
Sincerely,
Stephan Watkins

> It takes a bit of understanding. Am I correct that if the monitor does
> not have a built in emitter, the glasses need to be triggered from
> either a remote transmitter plugged into the 3 pin mini din port of a
> suitable quadro card for quad buffered, or to a USB port in the case of
> consumer GTX (not quad buffered and not supported by molecular modeling
> software, for software enabled games etc.).
In Windows I don't know if the GTX cards allow qbs in a window. I
haven't tested such a configuration at all. But with a quadro and
external emitter in Windows you only need the USB connection to the
emitter. In linux you need both the 3 pin and usb connections for
external emitters.
> If the monitor does have a built in emitter, the glasses are triggered
> from the monitor directly with no link to the video board except the
> video signal, so any quad-buffered board will work. Are the glasses
> triggered effectively directly by the sync-signals within the monitor?
> If so why won't Linux work?
Let's be specific. The glasses are triggered from a sync signal that
comes out of the emitter housed at the top of the monitor. The signal
is sent over the dual link DVI-D cable from the quadro, there's no usb
or 3 pin mini din cable involved anywhere. The catch is the linux &
windows nvidia drivers have built in code specifically to detect
monitors that have the built-in 3d vision v2 emitters such as the Asus
VG278H. Again, this works fine in Linux and Windows with recent
quadro's, but I don't know if GTX cards can do the qbs in a window in
Windows (definitely not in Linux).
> Asus VG236HE, Acer GD235Hzbid, or BenQ XL2420T are difficult to find
> here and very expensive compared to normal list price.
I don't know what price range you're looking for but the ones with the
built-in emitters like the VG278H are more expensive. It's currently
~500ドル USD, so your total with a quadro 600 would be ~650,ドル or you
could get a refurbished quadro 3700 or quadro 370 for much less than
the 130ドル I'm seeing for the 600. There's a list of 3d vision capable
monitors below.
> I assume the Acer GR235HAbmii won't work with PyMol, Chimera, VMD etc as
> it is a passive system. Am I correct?
I don't think that's passive since it says it supports one of the 3d
methods that bluray devices use (HDMI 1.4) use, but it's not 3d vision
or qbs, see Q12 here :
http://www.mitsubishi-tv.com/feature/3DTV/3D_FAQ
i.e. frame packing != frame sequential != qbs
> Can you advise whether the smaller 23" S23A750D might work with a
> suitable Quadro e.g. 300, 410, 600. This model includes 3D glasses but I
> can't work out whether it has a compatible 3d vision v2 built-in emitter
> or not.
Looking more at these samsung monitors, I don't think any of these are
3d vision, incl the one I posted on the chimera mailing list. I found
this list here of the 3d vision v2 compatible monitors with the
lightboost tech :
http://hardforum.com/showthread.php?t=1680564
and this is a list from nvidia which includes monitors with built-in
emitters and without :
http://www.nvidia.com/object/3d-vision-system-requirements.html
I also think I found the code that your previous stackoverflow link
was referencing :
http://stackoverflow.com/questions/6827737/how-do-i-output-3d-images-to-my-3d-tv/6828590#6828590
..and they're basically saying the same thing regarding quadro's and
quad buffers, except this bit is interesting :
"With any luck, Direct3D 12 will require QBS, and thus NVIDIA (and
AMD) will expose it in OpenGL" (for consumer cards).

Hi Jon,
You also have to update the three numbers before. So to go from white to
blue is
cmd.load_cgo([i for j in x for u,v,f in zip(j,j[1:],range(n)) for i in
[9.0]+u+v+[1.3, 1-(1.*f)/n,1-(1.*f)/n,1, 1-(1.+f)/n,1-(1.+f)/n,1
 ]],"trace")
If you want to go from blue to white to red, it's probably easiest to split
it in two:
a=n/2
b=n-n/2
cmd.load_cgo([i for j in x for u,v,f in zip(j,j[1:],range(n))[:a] for i in
[9.0]+u+v+[1.3, (1.*f)/a,(1.*f)/a,1, (1.+f)/a,(1.+f)/a,1 ]],"trace_a")
cmd.load_cgo([i for j in x for u,v,f in zip(j,j[1:],range(n))[a:] for i in
[9.0]+u+v+[1.3, 1,1-(1.*f-a)/b,1-(1.*f-a)/b,
1,1-(1.+f-a)/b,1-(1.+f-a)/b ]],"trace_b")
For the capping, you can use spheres:
cmd.load_cgo([i for j in x for u,f in zip(j,range(n))[:a] for i in [6.0,
(1.*f)/a,(1.*f)/a,1, 7.0]+u+[1.3]],"spheres_a")
cmd.load_cgo([i for j in x for u,f in zip(j,range(n))[a:] for i in [6.0,
1,1-(1.*f-a)/b,1-(1.*f-a)/b, 7.0]+u+[1.3]],"spheres_b")
For more complex color schemes, you would definitely want a rgb function.
Hope it helps,
Tsjerk
On Fri, Dec 14, 2012 at 12:25 PM, Jonathan Grimes
<jon...@st...>wrote:
>
> thanks tsjerk
>
> ive been playing with the values at the end......and i can,t change it
> to go from
> white to blue....or even red to blue....
>
> i tried....white to blue....so 1,1,1 to 0,0, 1
>
> cmd.load_cgo([i for j in x for u,v,f in zip(j,j[1:],range(n)) for i in
> [9.0]+u+v+[1.3,1,1-(1.*f)/n,1-(1.*f)/n, 1-(1.+f)/n,1-(1.+f)/n,1 ]],"trace")
>
> so 1,1-(1.*f)/n,1-(1.*f)/n, corresponds to 1,1,1....where f/n is the
> fraction along the cylinder.....
>
> and then i changed the last 3 numbers to 1-(1.+f)/n,1-(1.+f)/n,1....which
> i thought would go to 0 , 0 ,1
>
> but i get a bond but the color doesnt go smoothly from white to blue ??
>
> is there also a nice way to cap the cylinder so it had a rounded end ??
>
> 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
>
>
>
> On 14 Dec 2012, at 09:13, Tsjerk Wassenaar wrote:
>
> Hey :)
>
> Can't resist the challenge...
> For any given ensemble, you can draw a trace through the C-alphas using
> the following lines, illustrated here for the NMR ensemble '1NMR':
>
> # Get the structure
> fetch 1nmr
>
> # Get the number of states
> n = cmd.count_states('1nmr')
>
> # Collect the C-alpha coordinates
> # This calls get_model for every state and extracts the coordinates for
> every model-state
> # The resulting list is transposed, such that each list entry contains the
> coordinates for one C-alpha over all states
> x=zip(*[cmd.get_model('1nmr and n. ca',state=i+1).get_coord_list() for i
> in range(n)] )
>
> # Now draw the traces by building a CGO model
> cmd.load_cgo([i for j in x for u,v,f in zip(j,j[1:],range(r)) for i in
> [9.0]+u+v+[0.1,1,1-(1.*f)/r,1-(1.*f)/r,1,1-(1.+f)/r,1-(1.+f)/r]],"trace")
>
> The 9.0 is the CGO code for a cylinder (pymol.cgo.CYLINDER). The 0.1 is
> the radius, and the following six values are the start and end RGB values,
> which are related to the state number, such that they end up from white to
> red. For more complex colors it would be nice to have a rgb() function that
> would return a color according to some scheme, given a fraction, which
> would make that last command
>
> cmd.load_cgo([i for j in x for u,v,f in zip(j,j[1:],range(r)) for i in
> [9.0]+u+v+[0.1]+rgb((1.*f)/r,scheme=...)+rgb((1.+f)/r,scheme=...)],"trace")
>
> Hope it helps,
>
> Tsjerk
>
>
> On Thu, Dec 13, 2012 at 10:54 PM, Robert Campbell <
> rob...@qu...> wrote:
>
>> 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
>>
>>
>> ------------------------------------------------------------------------------
>> 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
>> http://p.sf.net/sfu/logmein_12329d2d
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Biocomputing Group
> Department of Biological Sciences
> 2500 University Drive NW
> Calgary, AB T2N 1N4
> Canada
>
> ------------------------------------------------------------------------------
> 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
>
> http://p.sf.net/sfu/logmein_12329d2d_______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>
>
>
-- 
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4
Canada

Hey :)
Can't resist the challenge...
For any given ensemble, you can draw a trace through the C-alphas using the
following lines, illustrated here for the NMR ensemble '1NMR':
# Get the structure
fetch 1nmr
# Get the number of states
n = cmd.count_states('1nmr')
# Collect the C-alpha coordinates
# This calls get_model for every state and extracts the coordinates for
every model-state
# The resulting list is transposed, such that each list entry contains the
coordinates for one C-alpha over all states
x=zip(*[cmd.get_model('1nmr and n. ca',state=i+1).get_coord_list() for i in
range(n)] )
# Now draw the traces by building a CGO model
cmd.load_cgo([i for j in x for u,v,f in zip(j,j[1:],range(r)) for i in
[9.0]+u+v+[0.1,1,1-(1.*f)/r,1-(1.*f)/r,1,1-(1.+f)/r,1-(1.+f)/r]],"trace")
The 9.0 is the CGO code for a cylinder (pymol.cgo.CYLINDER). The 0.1 is the
radius, and the following six values are the start and end RGB values,
which are related to the state number, such that they end up from white to
red. For more complex colors it would be nice to have a rgb() function that
would return a color according to some scheme, given a fraction, which
would make that last command
cmd.load_cgo([i for j in x for u,v,f in zip(j,j[1:],range(r)) for i in
[9.0]+u+v+[0.1]+rgb((1.*f)/r,scheme=...)+rgb((1.+f)/r,scheme=...)],"trace")
Hope it helps,
Tsjerk
On Thu, Dec 13, 2012 at 10:54 PM, Robert Campbell <
rob...@qu...> wrote:
> 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
>
>
> ------------------------------------------------------------------------------
> 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
> http://p.sf.net/sfu/logmein_12329d2d
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>
-- 
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4
Canada

Even if this were true, the driver in linux won't allow 3d vision
(i.e. won't communicate with the emitter) unless it detects a quadro,
i.e. you'd need a driver hack.
On Thu, Dec 13, 2012 at 10:25 PM, Jeff Johns เจฟ จอห์น <jj...@kk...> wrote:
> From
> http://stackoverflow.com/questions/8918945/how-to-do-stereoscopic-3d-with-opengl-on-gtx-560-and-later
>
> "The NVision3D API does allow you to blit images for specific eyes (this
> is meant for movie players and image viewers). But it also allows you to
> emulate quadbuffer stereo: Instead of GL_BACK_LEFT and GL_BACK_RIGHT
> buffers create two Framebuffer Objects, which you bind and use as if
> they were quadbuffer stereo. Then after rendering you blit the resulting
> images (as textures) to the NVision3D API."
>
> "With only as little as 50 lines of management code you can build a
> program that seamlessly works on both NVision3D as well as quadbuffer
> stereo. What NVidia does is pointless and they should just stop it now
> and properly support quadbuffer stereo pixelformats on consumer GPUs as
> well."
>
> Is this true and could code be added to PyMol to allow GTX cards to
> provide 3D for PyMol? Windows and Linux?
>
>
>> On December 11, 2012 5:20:18 PM ICT, "EPF (Esben Peter Friis)"
> <EP...@no...> wrote:
>>
>>
>> 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
>
> Dr Jeff Johns
> Melatonin Research Group
> Faculty of Pharmaceutical Sciences
> Khon Kaen University
> Khon Kaen 40002
> Thailand
> Phone: +66 (0)43 202 378
> Email: jj...@kk...
> Alternative email: jef...@ho...
>
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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...

From
http://stackoverflow.com/questions/8918945/how-to-do-stereoscopic-3d-with-opengl-on-gtx-560-and-later
"The NVision3D API does allow you to blit images for specific eyes (this
is meant for movie players and image viewers). But it also allows you to
emulate quadbuffer stereo: Instead of GL_BACK_LEFT and GL_BACK_RIGHT
buffers create two Framebuffer Objects, which you bind and use as if
they were quadbuffer stereo. Then after rendering you blit the resulting
images (as textures) to the NVision3D API."
"With only as little as 50 lines of management code you can build a
program that seamlessly works on both NVision3D as well as quadbuffer
stereo. What NVidia does is pointless and they should just stop it now
and properly support quadbuffer stereo pixelformats on consumer GPUs as
well."
Is this true and could code be added to PyMol to allow GTX cards to
provide 3D for PyMol? Windows and Linux?
> On December 11, 2012 5:20:18 PM ICT, "EPF (Esben Peter Friis)"
<EP...@no...> wrote:
> 
> 
> 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
Dr Jeff Johns
Melatonin Research Group
Faculty of Pharmaceutical Sciences
Khon Kaen University
Khon Kaen 40002
Thailand
Phone: +66 (0)43 202 378
Email: jj...@kk...
Alternative email: jef...@ho...