Re: [PyMOL] bond connection file

[Thomas Holder]

Hi Vishwas,

atom connectivity is the same for all states unless you have a 
"discrete" object. Try this:

PyMOL> set connect_mode, 1
PyMOL> load file.pdb, discrete=1

Cheers,
   Thomas

Vishwas Vasisht wrote, On 10/05/12 08:59:
> Hi Thomas,
> 
>  Thanks, it works for single frame. But when I use multiple frame 
> (using 
> MODEL and ENDMDL), the connections which i specified in the first frame 
> is retained for rest of the frames. Am I doing some mistake in the way I 
> wrote
> my PDB file?
> 
> Regards
> Vishwas
> 
> 2012/10/4 Thomas Holder  >
> 
> Hi Vishwas,
> 
> you can use PDB format with CONECT records. You need to set
> connect_mode=1 before loading the PDB file into PyMOL.
> 
> http://pymolwiki.org/index.php/Connect_mode
> 
> http://www.wwpdb.org/documentation/format33/sect10.html#CONECT
> 
> Hope that helps.
> 
> Cheers,
>   Thomas
> 
> Vishwas Vasisht wrote, On 10/04/12 16:52:
> 
> Hi,
> 
> I want to feed in a coordinates of atoms along with bond
> connection information. Since the bonding is based on some
> calculation I do, I need to include this information by hand.
> I tried to output the trajectory from my analysis in .mol format
> (following some example .mol file), but particles are
> overlapping on each other.
> Can somebody suggest me a better way to feed in coordinates and
> bonding information
> to pymol.
> 
> Regards
> Vishwas

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

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Re: [PyMOL] bond connection file

[Jordan Willis]

Does every MODEL ENDMDL have a unique Connection list?

Can you show me your PDB file?

Jordan





On Oct 5, 2012, at 1:59 AM, Vishwas Vasisht  wrote:

> Hi Thomas,
> 
>  Thanks, it works for single frame. But when I use multiple frame (using 
> MODEL and ENDMDL), the connections which i specified in the first frame 
> is retained for rest of the frames. Am I doing some mistake in the way I wrote
> my PDB file?
> 
> Regards
> Vishwas
> 
> 2012/10/4 Thomas Holder 
> Hi Vishwas,
> 
> you can use PDB format with CONECT records. You need to set connect_mode=1 
> before loading the PDB file into PyMOL.
> 
> http://pymolwiki.org/index.php/Connect_mode
> 
> http://www.wwpdb.org/documentation/format33/sect10.html#CONECT
> 
> Hope that helps.
> 
> Cheers,
>   Thomas
> 
> Vishwas Vasisht wrote, On 10/04/12 16:52:
> 
> Hi,
> 
> I want to feed in a coordinates of atoms along with bond connection 
> information. Since the bonding is based on some calculation I do, I need to 
> include this information by hand. 
> I tried to output the trajectory from my analysis in .mol format (following 
> some example .mol file), but particles are overlapping on each other. 
> Can somebody suggest me a better way to feed in coordinates and bonding 
> information
> to pymol.
> 
> Regards
> Vishwas
> 
> -- 
> Thomas Holder
> MPI for Developmental Biology
> Spemannstr. 35
> D-72076 Tübingen
> 
> 
> 
> -- 
> Whoever fights monsters should see to it that in the
> process he does not become a monster.  And when
> you look into an abyss, the abyss also looks into you.
>  -- Friedrich Nietzsche
> --
> Don't let slow site performance ruin your business. Deploy New Relic APM
> Deploy New Relic app performance management and know exactly
> what is happening inside your Ruby, Python, PHP, Java, and .NET app
> Try New Relic at no cost today and get our sweet Data Nerd shirt too!
> http://p.sf.net/sfu/newrelic-dev2dev___
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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Re: [PyMOL] I just built pymol, comes up but hangs on any attempt to view a "test" pdb.

[Jason Vertrees]

Mike,

Many distros have PyMOL already in their package management system.
Have you tried that first?

I suggest downloading the latest code, v1.5.0.4, from the open-source
project page, if you want to build by hand.

To build, you need Python 2.7 or later and the process is very simple:

sudo python setup.py install
sudo python setup2.py install

Then, follow the directions for copying "pymol" to /usr/local/bin or
wherever you want.

If your machine does have shader issues and they don't automatically
disable, please let us know. You do not need a license to run the
open-source version. If the splash screen says that, I need to change
that.

I routinely build on Ubuntu without problems. Just make sure the
python you build with is the same that you run with.

Cheers,

-- Jason


On Thu, Oct 4, 2012 at 9:18 PM, Mike Marchywka  wrote:
>
>
>
> 
>> CC: pymol-users@lists.sourceforge.net
>> From: li...@cowsandmilk.net
>> Subject: Re: [PyMOL] I just built pymol, comes up but hangs on any attempt 
>> to view a "test" pdb.
>> Date: Thu, 4 Oct 2012 22:03:59 -0400
>> To: marchy...@hotmail.com
>>
>> You don't need a license for the open source version.
>>
>> If you provided details on what OS/distribution you are building on, people 
>> may try to replicate and understand why the python version hung. In my 
>> experience, using setup.py generally worked out of the box.
>
> Well, I thought there may be a dev list or something for the most of this 
> stuff but in any case I'm on Ubuntu
> but that probably was not a big factor for some of the issues I ran into  I 
> just wanted to display
> 2 molecules side by side and could not get jmol or gdis to work right away 
> and someone suggested
> this. ( fwiw, I have my own molecule viewer that IIRC I wrote to learn glut 
> on cygwin but
> I imagine that would be an even bigger chore to port LOL).
>
> If I can reconstruct, I apparently started with pymol-v1.5.0.1.tar and I 
> think at some point I ran
> autoreconf -l thinking I could go the "configure" route but then did python 
> setup.py  build and
> install in separeate steps., This seemed to work but attempts to display the 
> test pdb
> files never displayed anything, I could not get any more menu's and one core 
> was running
> at 100 percent until I killed it.
>
> Going the confugre route,  I think the first problem was with a bunch of 
> undefined CGO things.
> but you can see the changes below. The EXT thing was spurious probably as 
> there was a missing -lGLEW
> and I had to relink. This is obviously a raw dump of things that I tried 
> along with stuff that ultimately
> worked but fwiw.
>
>
> marchywka@marchywka-Latitude-E6510:~/d/pymol/pymol$ find -mtime -2 -name "*.h"
> ./layer0/os_gl.h
> ./contrib/uiuc/plugins/include/molfile_plugin.h
> ./generated/include/ShaderText.h
> ./config.h
> marchywka@marchywka-Latitude-E6510:~/d/pymol/pymol$ find -mtime -2 -name "*.c"
> ./layer0/ShaderText.c
> ./layer0/ShaderMgr.c
> ./layer3/Executive.c
> ./generated/src/ShaderText.c
> ./layer2/ObjectVolume.c
> ./layer1/CGO.c
> ./layer1/Scene.c
> marchywka@marchywka-Latitude-E6510:~/d/pymol/pymol$
>
>
>
> marchywka@marchywka-Latitude-E6510:~/d/pymol/pymol$ grep -n -A 2 mjm `find 
> -mtime -2 -name "*.c" `
> ./layer0/ShaderMgr.c:97:  FeedbackAdd(G, " mjm forcing glew ok  Shaders 
> available.\n");
> ./layer0/ShaderMgr.c:98:// this should work but turn off for now mjm
> ./layer0/ShaderMgr.c-99-//if (GLEW_VERSION_2_0)
> ./layer0/ShaderMgr.c-100-if (1)
> --
> ./layer3/Executive.c:76:// mjm
> ./layer3/Executive.c-77-#include"modules/cealign/src/ce_types.h"
> ./layer3/Executive.c-78-/* Externals for CEAlign  */
> --
> ./layer1/Scene.c:2910://mjm
> ./layer1/Scene.c-2911-  1.0F, 1.0F, 0.1F, 1.f
> ./layer1/Scene.c-2912-  };
> --
> ./layer1/Scene.c:1:   //mjm
> ./layer1/Scene.c-10001-//glBlitFramebufferEXT (0, 0, I->offscreen_width / 2, 
> I->offscreen_height,
> ./layer1/Scene.c-10002-   glBlitFramebuffer (0, 0, I->offscreen_width / 2, 
> I->offscreen_height,
> --
> ./layer1/Scene.c:10007://mjm
> ./layer1/Scene.c-10008-   glBlitFramebuffer (I->offscreen_width / 2, 0, 
> I->offscreen_width, I->offscreen_height,
> ./layer1/Scene.c-10009-   //glBlitFramebufferEXT (I->offscreen_width / 2, 0, 
> I->offscreen_width, I->offscreen_height,
> --
> ./layer1/Scene.c:10016:  //mjm
> ./layer1/Scene.c-10017- //glBlitFramebufferEXT (0, 0, I->offscreen_width, 
> I->offscreen_height,
> ./layer1/Scene.c-10018-   glBlitFramebuffer (0, 0, I->offscreen_width, 
> I->offscreen_height,
> --
> ./layer1/Scene.c:10024: //mjm
> ./layer1/Scene.c-10025-//  glBlitFramebufferEXT (0, 0, I->offscreen_width, 
> I->offscreen_height,
> ./layer1/Scene.c-10026-   glBlitFramebuffer (0, 0, I->offscreen_width, 
> I->offscreen_height,
> marchywka@marchywka-Latitude-E6510:~/d/pymol/pymol$
>
>
> marchywka@marchywka-Latitude-E6510:~/d/pymol/pymol$ grep -n -A 2 mjm `find 
> -mtime -2 -name "*.h" `
> ./layer0/os_gl.h:6:// mjm
> ./laye

Re: [PyMOL] I just built pymol, comes up but hangs on any attempt to view a "test" pdb.

[Mike Marchywka]

> From: jason.vertr...@schrodinger.com
> Date: Fri, 5 Oct 2012 09:08:44 -0500
> Subject: Re: [PyMOL] I just built pymol, comes up but hangs on any attempt to 
> view a "test" pdb.
> To: marchy...@hotmail.com
> CC: li...@cowsandmilk.net; pymol-users@lists.sourceforge.net
>
> Mike,
>
> Many distros have PyMOL already in their package management system.
> Have you tried that first?
>
no, I think I tried to download from sourceforge first.


> I suggest downloading the latest code, v1.5.0.4, from the open-source
> project page, if you want to build by hand.
>
see comments in my last post, I think that is what I did. Although
autoreconf may not have helped anything. 

> To build, you need Python 2.7 or later and the process is very simple:
>
> sudo python setup.py install
> sudo python setup2.py install
>
that was what created the first version I ran, it seemed fine until
I tried to display a test pdb then it hung in 100 cpu on one core. 


> Then, follow the directions for copying "pymol" to /usr/local/bin or
> wherever you want.
>
> If your machine does have shader issues and they don't automatically
> disable, please let us know. You do not need a license to run the
> open-source version. If the splash screen says that, I need to change
> that.

I don't really recall what the first version said, I think it was hypothetical
as in "may need license" etc. The version from "./configure" had a whole
bunch of problems- simple syntax errors like missing comma to no
link to the ccealignmodule but once I kluged around the CGO problems
I think I was on my own :)

Anyway it seems fine now, although attempting to use "fit" on my 
2 molecules gave a non-intuitive result I think the one was so mangled that
it had problems aligning them. 



>
> I routinely build on Ubuntu without problems. Just make sure the
> python you build with is the same that you run with.
>
> Cheers,
>
> -- Jason
>
>
> On Thu, Oct 4, 2012 at 9:18 PM, Mike Marchywka  wrote:
> >
> >
> >
> > 
> >> CC: pymol-users@lists.sourceforge.net
> >> From: li...@cowsandmilk.net
> >> Subject: Re: [PyMOL] I just built pymol, comes up but hangs on any attempt 
> >> to view a "test" pdb.
> >> Date: Thu, 4 Oct 2012 22:03:59 -0400
> >> To: marchy...@hotmail.com
> >>
> >> You don't need a license for the open source version.
> >>
> >> If you provided details on what OS/distribution you are building on, 
> >> people may try to replicate and understand why the python version hung. In 
> >> my experience, using setup.py generally worked out of the box.
> >
> > Well, I thought there may be a dev list or something for the most of this 
> > stuff but in any case I'm on Ubuntu
> > but that probably was not a big factor for some of the issues I ran into I 
> > just wanted to display
> > 2 molecules side by side and could not get jmol or gdis to work right away 
> > and someone suggested
> > this. ( fwiw, I have my own molecule viewer that IIRC I wrote to learn glut 
> > on cygwin but
> > I imagine that would be an even bigger chore to port LOL).
> >
> > If I can reconstruct, I apparently started with pymol-v1.5.0.1.tar and I 
> > think at some point I ran
> > autoreconf -l thinking I could go the "configure" route but then did python 
> > setup.py build and
> > install in separeate steps., This seemed to work but attempts to display 
> > the test pdb
> > files never displayed anything, I could not get any more menu's and one 
> > core was running
> > at 100 percent until I killed it.
> >
> > Going the confugre route, I think the first problem was with a bunch of 
> > undefined CGO things.
> > but you can see the changes below. The EXT thing was spurious probably as 
> > there was a missing -lGLEW
> > and I had to relink. This is obviously a raw dump of things that I tried 
> > along with stuff that ultimately
> > worked but fwiw.
> >
> >
> > marchywka@marchywka-Latitude-E6510:~/d/pymol/pymol$ find -mtime -2 -name 
> > "*.h"
> > ./layer0/os_gl.h
> > ./contrib/uiuc/plugins/include/molfile_plugin.h
> > ./generated/include/ShaderText.h
> > ./config.h
> > marchywka@marchywka-Latitude-E6510:~/d/pymol/pymol$ find -mtime -2 -name 
> > "*.c"
> > ./layer0/ShaderText.c
> > ./layer0/ShaderMgr.c
> > ./layer3/Executive.c
> > ./generated/src/ShaderText.c
> > ./layer2/ObjectVolume.c
> > ./layer1/CGO.c
> > ./layer1/Scene.c
> > marchywka@marchywka-Latitude-E6510:~/d/pymol/pymol$
> >
> >
> >
> > marchywka@marchywka-Latitude-E6510:~/d/pymol/pymol$ grep -n -A 2 mjm `find 
> > -mtime -2 -name "*.c" `
> > ./layer0/ShaderMgr.c:97: FeedbackAdd(G, " mjm forcing glew ok Shaders 
> > available.\n");
> > ./layer0/ShaderMgr.c:98:// this should work but turn off for now mjm
> > ./layer0/ShaderMgr.c-99-// if (GLEW_VERSION_2_0)
> > ./layer0/ShaderMgr.c-100- if (1)
> > --
> > ./layer3/Executive.c:76:// mjm
> > ./layer3/Executive.c-77-#include"modules/cealign/src/ce_types.h"
> > ./layer3/Executive.c-78-/* Externals for CEAlign

Re: [PyMOL] I just built pymol, comes up but hangs on any attempt to view a "test" pdb.

[Jason Vertrees]

Hi Mike,

>> I suggest downloading the latest code, v1.5.0.4, from the open-source
>> project page, if you want to build by hand.
>>
> see comments in my last post, I think that is what I did. Although
> autoreconf may not have helped anything.

I see the confusion now. We'll update SourceForge on our next release
so that it says the latest is v1.5.0.5, not v1.5.0.1. To get the
latest code, please do this:

svn co 
https://pymol.svn.sourceforge.net/svnroot/pymol/root/pymol/trunk/pymol
pymol


>> To build, you need Python 2.7 or later and the process is very simple:
>>
>> sudo python setup.py install
>> sudo python setup2.py install
>>
> that was what created the first version I ran, it seemed fine until
> I tried to display a test pdb then it hung in 100 cpu on one core.

What kind of computer is this? What video card do you have?


> I don't really recall what the first version said, I think it was hypothetical
> as in "may need license" etc. The version from "./configure" had a whole
> bunch of problems- simple syntax errors like missing comma to no
> link to the ccealignmodule but once I kluged around the CGO problems
> I think I was on my own :)

The "make; make install" setup was deprecated a long time ago which is
why this didn't work. We use Python distutils to build, as you've
found out.


> Anyway it seems fine now, although attempting to use "fit" on my
> 2 molecules gave a non-intuitive result I think the one was so mangled that
> it had problems aligning them.

Glad it's working. Fit is a mathematically optimal superposition of
vector sets. Are your atom pairings correct? If you want to specify
them manually, check out Wizard > Pair Fitting. If you send me the
molecules I'm happy to take a look for you, too.


Cheers,

-- Jason



>>
>>
>> On Thu, Oct 4, 2012 at 9:18 PM, Mike Marchywka  wrote:
>> >
>> >
>> >
>> > 
>> >> CC: pymol-users@lists.sourceforge.net
>> >> From: li...@cowsandmilk.net
>> >> Subject: Re: [PyMOL] I just built pymol, comes up but hangs on any 
>> >> attempt to view a "test" pdb.
>> >> Date: Thu, 4 Oct 2012 22:03:59 -0400
>> >> To: marchy...@hotmail.com
>> >>
>> >> You don't need a license for the open source version.
>> >>
>> >> If you provided details on what OS/distribution you are building on, 
>> >> people may try to replicate and understand why the python version hung. 
>> >> In my experience, using setup.py generally worked out of the box.
>> >
>> > Well, I thought there may be a dev list or something for the most of this 
>> > stuff but in any case I'm on Ubuntu
>> > but that probably was not a big factor for some of the issues I ran into I 
>> > just wanted to display
>> > 2 molecules side by side and could not get jmol or gdis to work right away 
>> > and someone suggested
>> > this. ( fwiw, I have my own molecule viewer that IIRC I wrote to learn 
>> > glut on cygwin but
>> > I imagine that would be an even bigger chore to port LOL).
>> >
>> > If I can reconstruct, I apparently started with pymol-v1.5.0.1.tar and I 
>> > think at some point I ran
>> > autoreconf -l thinking I could go the "configure" route but then did 
>> > python setup.py build and
>> > install in separeate steps., This seemed to work but attempts to display 
>> > the test pdb
>> > files never displayed anything, I could not get any more menu's and one 
>> > core was running
>> > at 100 percent until I killed it.
>> >
>> > Going the confugre route, I think the first problem was with a bunch of 
>> > undefined CGO things.
>> > but you can see the changes below. The EXT thing was spurious probably as 
>> > there was a missing -lGLEW
>> > and I had to relink. This is obviously a raw dump of things that I tried 
>> > along with stuff that ultimately
>> > worked but fwiw.
>> >
>> >
>> > marchywka@marchywka-Latitude-E6510:~/d/pymol/pymol$ find -mtime -2 -name 
>> > "*.h"
>> > ./layer0/os_gl.h
>> > ./contrib/uiuc/plugins/include/molfile_plugin.h
>> > ./generated/include/ShaderText.h
>> > ./config.h
>> > marchywka@marchywka-Latitude-E6510:~/d/pymol/pymol$ find -mtime -2 -name 
>> > "*.c"
>> > ./layer0/ShaderText.c
>> > ./layer0/ShaderMgr.c
>> > ./layer3/Executive.c
>> > ./generated/src/ShaderText.c
>> > ./layer2/ObjectVolume.c
>> > ./layer1/CGO.c
>> > ./layer1/Scene.c
>> > marchywka@marchywka-Latitude-E6510:~/d/pymol/pymol$
>> >
>> >
>> >
>> > marchywka@marchywka-Latitude-E6510:~/d/pymol/pymol$ grep -n -A 2 mjm `find 
>> > -mtime -2 -name "*.c" `
>> > ./layer0/ShaderMgr.c:97: FeedbackAdd(G, " mjm forcing glew ok Shaders 
>> > available.\n");
>> > ./layer0/ShaderMgr.c:98:// this should work but turn off for now mjm
>> > ./layer0/ShaderMgr.c-99-// if (GLEW_VERSION_2_0)
>> > ./layer0/ShaderMgr.c-100- if (1)
>> > --
>> > ./layer3/Executive.c:76:// mjm
>> > ./layer3/Executive.c-77-#include"modules/cealign/src/ce_types.h"
>> > ./layer3/Executive.c-78-/* Externals for CEAlign */
>> > --
>> > ./layer1/Scene.c:2910://mjm
>> > ./layer1/Scene.c-2911- 1.0F, 1.0F, 0.1F, 1.f

Re: [PyMOL] I just built pymol, comes up but hangs on any attempt to view a "test" pdb.

[Mike Marchywka]

> From: jason.vertr...@schrodinger.com
> Date: Fri, 5 Oct 2012 09:36:29 -0500
> Subject: Re: [PyMOL] I just built pymol, comes up but hangs on any attempt to 
> view a "test" pdb.
> To: marchy...@hotmail.com
> CC: li...@cowsandmilk.net; pymol-users@lists.sourceforge.net
>
> Hi Mike,
>
> >> I suggest downloading the latest code, v1.5.0.4, from the open-source
> >> project page, if you want to build by hand.
> >>
> > see comments in my last post, I think that is what I did. Although
> > autoreconf may not have helped anything.
>
> I see the confusion now. We'll update SourceForge on our next release
> so that it says the latest is v1.5.0.5, not v1.5.0.1. To get the
> latest code, please do this:
>
> svn co https://pymol.svn.sourceforge.net/svnroot/pymol/root/pymol/trunk/pymol
> pymol
>
>
> >> To build, you need Python 2.7 or later and the process is very simple:
> >>
> >> sudo python setup.py install
> >> sudo python setup2.py install
> >>
> > that was what created the first version I ran, it seemed fine until
> > I tried to display a test pdb then it hung in 100 cpu on one core.
>
> What kind of computer is this? What video card do you have?
>
Dell Laitittude, but this is probably due to other issues.


>
> > I don't really recall what the first version said, I think it was 
> > hypothetical
> > as in "may need license" etc. The version from "./configure" had a whole
> > bunch of problems- simple syntax errors like missing comma to no
> > link to the ccealignmodule but once I kluged around the CGO problems
> > I think I was on my own :)
>
> The "make; make install" setup was deprecated a long time ago which is
> why this didn't work. We use Python distutils to build, as you've
> found out.
>
I never use python and I probably never would have gotten .1 to work if
I had to deal with that :)  I'm not sure of the rationale here but while
you were phasing out a number of things I thought that "make" was
just lagging, intended for developers. 


>
> > Anyway it seems fine now, although attempting to use "fit" on my
> > 2 molecules gave a non-intuitive result I think the one was so mangled that
> > it had problems aligning them.
>
> Glad it's working. Fit is a mathematically optimal superposition of
> vector sets. Are your atom pairings correct? If you want to specify
> them manually, check out Wizard > Pair Fitting. If you send me the
> molecules I'm happy to take a look for you, too.
>
Thanks, I have no idea. Naive overlap was a bit confusing but I'm
dealing with simple things right now. I have 2 beta-carotene xtz files
created from scripts, one from the mmcif files on pdb.org and another
derived from jdftx after 300 position iterations using very
simple C and H models. In any case, I think part of the problem
is just using .53 for atomic/angstrom conversions but it looks like
"fit" results were bizarre: the 2 ends of the molecule were in about the same 
place
but the chains extended in opposite directions from there ( it wasn't 
immediately
obvious if I created some wierd linking errors based on this behaviour LOL).






>
> Cheers,
>
> -- Jason
>
>
>
> >>
> >>
> >> On Thu, Oct 4, 2012 at 9:18 PM, Mike Marchywka  
> >> wrote:
> >> >
> >> >
> >> >
> >> > 
> >> >> CC: pymol-users@lists.sourceforge.net
> >> >> From: li...@cowsandmilk.net
> >> >> Subject: Re: [PyMOL] I just built pymol, comes up but hangs on any 
> >> >> attempt to view a "test" pdb.
> >> >> Date: Thu, 4 Oct 2012 22:03:59 -0400
> >> >> To: marchy...@hotmail.com
> >> >>
> >> >> You don't need a license for the open source version.
> >> >>
> >> >> If you provided details on what OS/distribution you are building on, 
> >> >> people may try to replicate and understand why the python version hung. 
> >> >> In my experience, using setup.py generally worked out of the box.
> >> >
> >> > Well, I thought there may be a dev list or something for the most of 
> >> > this stuff but in any case I'm on Ubuntu
> >> > but that probably was not a big factor for some of the issues I ran into 
> >> > I just wanted to display
> >> > 2 molecules side by side and could not get jmol or gdis to work right 
> >> > away and someone suggested
> >> > this. ( fwiw, I have my own molecule viewer that IIRC I wrote to learn 
> >> > glut on cygwin but
> >> > I imagine that would be an even bigger chore to port LOL).
> >> >
> >> > If I can reconstruct, I apparently started with pymol-v1.5.0.1.tar and I 
> >> > think at some point I ran
> >> > autoreconf -l thinking I could go the "configure" route but then did 
> >> > python setup.py build and
> >> > install in separeate steps., This seemed to work but attempts to display 
> >> > the test pdb
> >> > files never displayed anything, I could not get any more menu's and one 
> >> > core was running
> >> > at 100 percent until I killed it.
> >> >
> >> > Going the confugre route, I think the first problem was with a bunch of 
> >> > undefined CGO things

Re: [PyMOL] Shader issues and automatic disabling (was Re: I just built pymol, comes up but hangs on any attempt...)

[Jason Vertrees]

Hi Ben,

>> If your machine does have shader issues and they don't automatically
>> disable, please let us know.
>
> What would be the symptoms/output if this is happening?
>
> I get occasional reports from our users with errors like this:
>
>   CShaderPrg_New-Error: vertex shader compilation failed name='default'; log 
> follows.
> infoLog=cI
>   PyMOLShader_NewFromFile-Warning: default shader files not found, loading 
> from memory.
>   CShaderPrg_Link-Error: Shader program failed to link name='default'; 
> GL_MAX_VARYING_FLOATS=124 log follows.
> $^?
>   CShaderPrg_New-Error: vertex shader compilation failed name='volume'; log 
> follows.
>
> They seem to be informational, since PyMOL seeems to run reasonably well even
> after outputting those messages, but I can't say for sure.
>
> The graphics start up message on the machine looks pretty normal to me:
>
>   Detected GLSL version 1.20.
>   OpenGL graphics engine:
>GL_VENDOR: NVIDIA Corporation
>GL_RENDERER: Quadro 4000/PCIe/SSE2
>GL_VERSION: 2.1.2 NVIDIA 304.37
>   Adapting to Quadro hardware.
>   Detected 24 CPU cores.  Enabled multithreaded rendering.


The key seems to be,

>   PyMOLShader_NewFromFile-Warning: default shader files not found, loading 
> from memory.

We load shaders from disk, but when they're not found we just read in
some basic default shaders from code, which is what this is doing. Did
you move or change $PYMOL_DATA?

Cheers,

-- Jason

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[PyMOL] Shader issues and automatic disabling (was Re: I just built pymol, comes up but hangs on any attempt...)

[Ben Eisenbraun]

Hi Jason,

> If your machine does have shader issues and they don't automatically
> disable, please let us know.

What would be the symptoms/output if this is happening?

I get occasional reports from our users with errors like this:

  CShaderPrg_New-Error: vertex shader compilation failed name='default'; log 
follows.
infoLog=cI
  PyMOLShader_NewFromFile-Warning: default shader files not found, loading from 
memory.
  CShaderPrg_Link-Error: Shader program failed to link name='default'; 
GL_MAX_VARYING_FLOATS=124 log follows.
$^?
  CShaderPrg_New-Error: vertex shader compilation failed name='volume'; log 
follows.

They seem to be informational, since PyMOL seeems to run reasonably well even 
after outputting those messages, but I can't say for sure.

The graphics start up message on the machine looks pretty normal to me:

  Detected GLSL version 1.20.
  OpenGL graphics engine:
   GL_VENDOR: NVIDIA Corporation
   GL_RENDERER: Quadro 4000/PCIe/SSE2
   GL_VERSION: 2.1.2 NVIDIA 304.37
  Adapting to Quadro hardware.
  Detected 24 CPU cores.  Enabled multithreaded rendering.

-ben

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Re: [PyMOL] 3D projector for low cost 3D Protein Cave

[mesters]

Hello stereophiles,

many thanks to Jason Vertrees, Roger Rowlett and Sabuj Pattanayek for 
sending me information about their 3D stereo beamer setup.


I recently purchased the following equipment and was not even sure it 
would work:


- Optoma GT750, 1280 x 720 pixel resolution, 3000 ansi lumen, short 
throw (< 2 meter distance = fantastic 120" wide picture), 3D ready, HD ready
- Lenovo w530, nvidia k1000m (with 192 cuda units), produces up to an 
amazing 1920 × 1080 pixel @ 120 HZ (!), VGA, mini display port
- ASUS VG278H (not the HE model!) including one pair of nvidia glasses, 
HDMI (blue-ray stereo content), VGA, DVI (720p @ 120Hz), build-in IR emitter


Concerning the mobile workstation (running windows 7 professional) and 
the ASUS display:
- if the monitor is connected by a simple mini display to HDMI adaptor, 
the resolution is 1920 × 1080 pixel @ 24 Hz, HD 3D is running at 1920 × 
1080 pixel @ 96 Hz (I assume because 2 x 24 Hz x 2 eyes = 96 Hz which is 
below the 120 Hz the monitor can handle).
PYMOL and COOT can be viewed in stereo making use of the build-in IR 
emitter and the nvidia glasses that came with the screen. The picture 
looks stable and better than what I remember from the good old CTR Monitors.
- The small k1000m has an amazing graphics power (equal to the old 
Quadro 2000) but I had to buy a really expensive adaptor ( Club3D /Mini 
DisplayPort to Active DVI/ Dual Link, /CAC/-/1151/) for displaying 1920 
× 1080 pixel @ 120 HZ on the 27 inch stereo screen. In this mode, the 
build-in IR emitter does not work. I needed to buy the nvidia glasses 
with IR emitter, which is connected to the USB port of the workstation. 
120 Hz picture is stable as a rock!


In summary for this part, I should have maybe better purchased a mobile 
workstation with a true DVI-D outlet (not even sure those exsist!?) and 
safe me spending 150 US$ for the adaptor (the cheaper ones will not 
work!). Although, those mobiels are probably much more expensive as I 
merely spend 1950 US$ for the quad core with 16 GB memory and 256 GB 
solid state drive.


Concerning the mobile workstation (running windows 7 professional) and 
the GT750 beamer:
- the beamer is a truely pleasant surprize for the money paid (800 US$). 
One can choose DLP link stereo (short white flash in between pictures) 
or IR emitter using the build-in vesa 3-pin connector that works with 
all the old IR emitters we have in the lab.
- at less than 2 meters distance the beamer displays a fantastic 120" 
wide stereo picture (the bigger the picture the better the 3D effect)
- using the DLP linked glasses from optoma there is no ghosting at all 
in the stereo pictures displayed and this setup works great for group 
meetings and small class room setting as the glasses are not that 
expensive compared to the IR models.


So, finally the low cost 3D Protein Cave (and the monitor) is up and 
running under windows 7 professional.


- Jeroen -

p.s. this particualr setup works for me and I did not try it under 
linux. The k1000m graphics card has no 3-pin vesa stereo connector which 
is required for displaying 3D content under linux (see nvidia website). 
But I have some hope that the beamer could work using the DLP link option...





Am 13.06.12 19:48, schrieb mesters:

Hi,

I am planing to purchase/build a LOW-COST "3D Protein Cave" consisting 
of a 3D capable projector (720p @ 120Hz or DLP 3D Ready?) and a 
windows 7 computer with a quadro 2000 card. However, I am a bit 
sceptic about the sync problem causing ghosting.


Main Questions:

1) Is anyone out there succesfully operating a 3D projektor (with true 
stereoscopic 3D at 720p @ 120Hz) that has ist own 3-pin vesa out (!) 
to drive the nvidia emitter (like modern 3D-TVs do)? This would be the 
best solution to avoid ghosting (i.e. the output device drives the 
glasses, not the video card)!


2) Is anyone out there succesfully running a 3D projektor using the 
DLP Link option (white flash in between images to sync the glasses). 
Is this technique being used at all (for true stereoscopic 3D software 
such as Pymol, Coot, Yasara, etc.) by anyone?


Optional:

3) What about the new 3D Monitors with a build-in IR emitter. Do those 
work well for 3D steroscopic viewing with software like Pymol?


Any input is welcome, I do not want to spend a lot of money to find 
out it does not work after all


Jeroen.


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Re: [PyMOL] Shader issues and automatic disabling (was Re: I just built pymol, comes up but hangs on any attempt...)

[Ben Eisenbraun]

Hi Jason,

> The key seems to be,
> 
> >   PyMOLShader_NewFromFile-Warning: default shader files not found, loading 
> > from memory.
> 
> We load shaders from disk, but when they're not found we just read in
> some basic default shaders from code, which is what this is doing. Did
> you move or change $PYMOL_DATA?

Ah, I bet this is because they are running it via X-forwarding over an
ssh tunnel. I'm pretty certain that one of the reports came from a user
running PyMOL this way, and I can duplicate the error messages running over
a tunnel.

Is this actually going to break anything?

Thanks.

-ben

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Re: [PyMOL] Shader issues and automatic disabling (was Re: I just built pymol, comes up but hangs on any attempt...)

[Jason Vertrees]

Ben,

> Ah, I bet this is because they are running it via X-forwarding over an
> ssh tunnel. I'm pretty certain that one of the reports came from a user
> running PyMOL this way, and I can duplicate the error messages running over
> a tunnel.
>
> Is this actually going to break anything?

Yes -- volumes won't render correctly and the high-performance and
-quality graphics won't be enabled. However, you should still have
basic rendering and functionality.

Cheers,

-- Jason

-- 
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PyMOL Product Manager
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(o) +1 (603) 374-7120

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[PyMOL] ray_trace_mode 1

[Arne Dieckmann]

Hi all, 

I would like to use ray_trace_mode 1 to render some structures. However, I am 
also using isomeshes within the same picture and do not want them to have a 
black outline. Is there any way to have the black outline only for specified 
objects or to make them transparent in isomeshes? 


Cheers, 
Arne


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Re: [PyMOL] Shader issues and automatic disabling (was Re: I just built pymol, comes up but hangs on any attempt...)

[Ben Eisenbraun]

Hi Jason,

> > Ah, I bet this is because they are running it via X-forwarding over an
> > ssh tunnel. I'm pretty certain that one of the reports came from a user
> > running PyMOL this way, and I can duplicate the error messages running over
> > a tunnel.
> >
> > Is this actually going to break anything?
> 
> Yes -- volumes won't render correctly and the high-performance and
> -quality graphics won't be enabled. However, you should still have
> basic rendering and functionality.

Is there a suggested workaround?

I wonder how the shaders are actually loaded. In my local test case, the
PyMOL directory is hosted on NFS and automounted to/from the same location,
so in theory no matter which side is trying the fopen (or whatever), it
should be able to find the file on disk at the same path.

Thanks for your help.

-ben

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Re: [PyMOL] ray_trace_mode 1

[Jason Vertrees]

Hi Arne,

Unfortunately, ray_trace_mode is a global setting. You get the gain on
all objects. I agree is looks poor on isomeshes. We should consider
making ray_trace_gain object/atom level.

Cheers,

-- Jason

On Fri, Oct 5, 2012 at 2:26 PM, Arne Dieckmann  wrote:
> Hi all,
>
> I would like to use ray_trace_mode 1 to render some structures. However, I am 
> also using isomeshes within the same picture and do not want them to have a 
> black outline. Is there any way to have the black outline only for specified 
> objects or to make them transparent in isomeshes?
>
>
> Cheers,
> Arne
>
>
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Re: [PyMOL] 3D projector for low cost 3D Protein Cave

[Sabuj Pattanayek]

On Fri, Oct 5, 2012 at 3:48 PM, Bradford R. Battey, Jr.
 wrote:
> On Oct 5, 2012, at 4:33 PM, Sabuj Pattanayek  wrote:
>
>> We've tried the Asus VG278H with the built-in emitter and the nvidia
>> 3d vision v2 goggles (one pair included with the monitor) in Linux and
>> it works without the need for an expensive quadro with the 3 pin mini

> Hi Sabuj,
> How is this configured?  We're in the process of trying to get three 
> workstations put together and obtaining the older 3D monitors is being 
> problematic.  From the driver readme, I don't see where 3D Stereo over HDMI 
> is supported.  Many thanks!

The monitor comes with HDMI, VGA, and DVI inputs. We've only connected
to it using dual link DVI (using the cable it comes with which
supports 120Hz @ 1080p) from the video cards we've tested, currently a
quadro 370 and a quadro 3700 . Plan on testing a GTX 680 with it soon
but probably won't be testing the mini hdmi to hdmi link. xorg.conf
needs to be set to option stereo 10 as usual.

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