pymol-users Mailing List for PyMOL Molecular Graphics System (Page 3)

Dear All,
I put off upgrading to Ubuntu 12.04 as this happens every time I upgrade with half my things (software). In any case...
I am no longer able to use the rendering plugin , which is a vlauble asset as I am at this moment in the midst of making some publication quality figures.
Additional, the standard ray trace option will only work if I use a white background, and zoom out further than would make a good image, ie a 300 amino protein about 1 inch square on an 8x8 inch window (visual field).
I tried standard things, such as updating pymol, manually installing pymol 1.5 , etc...and the same bug prevades.
As it is both the rendering types, I assume it is some change to memory utilized by the shaders, as it crashes everytime. I have a similar problem now with gimp as well, however the memory cap is easy to see and maxes out around 3-4 G before crashing, however there is a 16 G memory, along with 4G on the GPU so I do not know where the errors come from. I do not get the errors on VMD, however prefer Pymol for the ease of use and also the images are nice.
Any suggestions on how to fix this would be appriciated. I also posted a bug on ubuntu, but the responses of such are limited, ie a general posting on bugs rather than maillists...
Sincerely,
Stephan Lloyd Watkins

 Is there a way of mapping an object color to an ED map mesh.
 I am drawing a peptide coloured blue to red N-to C termini. I wanted to
 display the difference map for the peptide with the same colour mapping...
 Is there a way (trivial or not) that I can do this ??
 Many thanks
 Jon
 
Dr. Jonathan M. Grimes, 
NDM Senior Reseach Fellow
University Research Lecturer
Division of Structural Biology
Wellcome Trust Centre for Human Genetics
University of Oxford
Roosevelt Drive,
Oxford OX3 7BN, UK
Email: Jon...@st..., Web: www.strubi.ox.ac.uk 
Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547 

Greetings,
This is just a quick note to let you know that the server hosting the
PyMOLWiki has recently been upgraded. In general the site should be
faster. If you see any problems, please let me know.
If anyone is curious, the PyMOLWiki is still highly utilized. It's
been viewed over 9.6 million times and often gets more than 2,000
unique visitors each day.
Next, we've upgraded the open-source project page on SourceForge.
Please be aware that some links will have moved. Likewise, if you see
any problems, please let us know. The conversion will probably take a
little time, so please be patient.
Cheers,
-- Jason
--
Jason Vertrees, PhD
Director of Core Modeling Product Management
Schrödinger, Inc.
(e) Jas...@sc...
(o) +1 (603) 374-7120

Thanks Thomas.
That may or may not have worked, I can't tell. Usually after I load the
movie, I can "hide all" followed by "show sticks", and this will show me
sticks for all frames of the movie. When I do this now, I get sticks for
the first frame, but nothing shows up on later frames. Even if I go to a
later frame and type "show sticks", it's all hidden. Of course, if I have
to do it for each frame, it's already too much work. Any suggestions for
how to accomplish this?
Thanks!
Rye
On Thu, Dec 6, 2012 at 3:02 AM, Thomas Holder <sp...@us...
> wrote:
> Hi Rye,
>
> only "discrete" objects have per state bonding information. Try this:
>
> load multistate.pdb, discrete=1
>
> Hope that helps.
>
> Cheers,
> Thomas
>
> Rye Terrell wrote, On 12/05/12 18:20:
> > I'm loading a movie file now and it appears that the bonds determined in
> > the first frame are used throughout the entire movie, even if atoms move
> > further apart than the cutoff. Is my perception correct here? If so, can
> > I make the bonds be calculated for each frame?
>
> --
> Thomas Holder
> PyMOL Developer
> Schrödinger Contractor
>
>
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>

Hi Rye,
only "discrete" objects have per state bonding information. Try this:
load multistate.pdb, discrete=1
Hope that helps.
Cheers,
 Thomas
Rye Terrell wrote, On 12/05/12 18:20:
> I'm loading a movie file now and it appears that the bonds determined in
> the first frame are used throughout the entire movie, even if atoms move
> further apart than the cutoff. Is my perception correct here? If so, can
> I make the bonds be calculated for each frame?
-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

I'm loading a movie file now and it appears that the bonds determined in
the first frame are used throughout the entire movie, even if atoms move
further apart than the cutoff. Is my perception correct here? If so, can I
make the bonds be calculated for each frame?
On Tue, Dec 4, 2012 at 11:43 AM, Rye Terrell <rye...@ry...>wrote:
> Not sure what I was doing wrong before, but that worked like a charm!
> Thanks.
>
> Also, pyMol is really sweet. I've been bugging my group to use it for a
> few days now. :D
>
> Cheers,
> Rye
>
>
> On Tue, Dec 4, 2012 at 11:40 AM, Jason Vertrees <
> jas...@sc...> wrote:
>
>> Hi Rye,
>>
>> set connect_cutoff, 0.5
>>
>> load 1.xyz
>>
>> produces different bonding than if you left the connect_cutoff value
>> to its default, 0.35. Set it to 0.85 and then load the file and you'll
>> see the Unknown atoms in the middle bonded as well.
>>
>> Cheers,
>>
>> -- Jason
>>
>> On Tue, Dec 4, 2012 at 11:33 AM, Rye Terrell <rye...@ry...>
>> wrote:
>> >
>> > Hi Jason,
>> >
>> > Thanks for the tip. I still couldn't get it to work. I'll google around
>> some
>> > more, but here's the file. Thanks for any help.
>> >
>> > Cheers,
>> > Rye
>> >
>> >
>> > On Mon, Dec 3, 2012 at 4:34 PM, Jason Vertrees
>> > <jas...@sc...> wrote:
>> >>
>> >> Hi Rye,
>> >>
>> >> How about connect_cutoff in Å? There's also connect_mode
>> >> (http://www.pymolwiki.org/index.php/Connect_mode).
>> >>
>> >> If you send me a copy of your file I can look at it.
>> >>
>> >> Cheers,
>> >>
>> >> -- Jason
>> >>
>> >> On Mon, Dec 3, 2012 at 4:03 PM, Rye Terrell <rye...@ry...
>> >
>> >> wrote:
>> >> > I have a silicon bulk system. Pymol indicates that a handful of the
>> >> > atoms
>> >> > are bonded to each other. Many bonds are not indicated. Is there some
>> >> > value
>> >> > I can adjust that will make pymol indicate that more atoms are
>> bonded? I
>> >> > usually do this by setting some cutoff radius, but googling around
>> has
>> >> > yielded no results. I see that there is a way to bond atom pairs
>> >> > manually,
>> >> > but that would be incredibly tedious given the number of bonds there
>> >> > should
>> >> > be.
>> >> >
>> >> > Thanks for any help!
>> >> > Rye
>> >> >
>> >> >
>> >> >
>> ------------------------------------------------------------------------------
>> >> > Keep yourself connected to Go Parallel:
>> >> > BUILD Helping you discover the best ways to construct your parallel
>> >> > projects.
>> >> > http://goparallel.sourceforge.net
>> >> > _______________________________________________
>> >> > 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
>> >
>> >
>>
>>
>>
>> --
>> Jason Vertrees, PhD
>> Director of Core Modeling Product Management
>> Schrödinger, Inc.
>>
>> (e) Jas...@sc...
>> (o) +1 (603) 374-7120
>>
>
>

Hi all -
I'm working on generating some interactive 3D figures, and have found that PyMOL is able to write .obj and .wrl files, which is nice. However, I would like to be able to use COLLADA (.dae) format. I have found tools (MeshLab and Blender, for example) that can convert among various formats, but the process is somewhat convoluted and tedious, and so far I've been unable to replicate the lighting, view, and scale of the PyMOL session in the resulting scene entirely, and certainly not without without a lot of manual adjustment in these programs.
I don't know much about the internal data structures in PyMOL, but I wonder how complicated it would be to write a direct COLLADA exporter into PyMOL's save command (e.g. `save my_scene.dae`). There is a module called pycollada that seems to be fairly well documented and might be useful.
In the meantime, I'd be interested in hearing about other solutions any of you may have worked out for converting .wrl files to .dae format, especially those that can be automated. Thanks in advance.
Cheers,
Jared
--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
550 First Ave MSB 398
New York, NY 10016
212-263-7898
http://kong.med.nyu.edu/

Not sure what I was doing wrong before, but that worked like a charm!
Thanks.
Also, pyMol is really sweet. I've been bugging my group to use it for a few
days now. :D
Cheers,
Rye
On Tue, Dec 4, 2012 at 11:40 AM, Jason Vertrees <
jas...@sc...> wrote:
> Hi Rye,
>
> set connect_cutoff, 0.5
>
> load 1.xyz
>
> produces different bonding than if you left the connect_cutoff value
> to its default, 0.35. Set it to 0.85 and then load the file and you'll
> see the Unknown atoms in the middle bonded as well.
>
> Cheers,
>
> -- Jason
>
> On Tue, Dec 4, 2012 at 11:33 AM, Rye Terrell <rye...@ry...>
> wrote:
> >
> > Hi Jason,
> >
> > Thanks for the tip. I still couldn't get it to work. I'll google around
> some
> > more, but here's the file. Thanks for any help.
> >
> > Cheers,
> > Rye
> >
> >
> > On Mon, Dec 3, 2012 at 4:34 PM, Jason Vertrees
> > <jas...@sc...> wrote:
> >>
> >> Hi Rye,
> >>
> >> How about connect_cutoff in Å? There's also connect_mode
> >> (http://www.pymolwiki.org/index.php/Connect_mode).
> >>
> >> If you send me a copy of your file I can look at it.
> >>
> >> Cheers,
> >>
> >> -- Jason
> >>
> >> On Mon, Dec 3, 2012 at 4:03 PM, Rye Terrell <rye...@ry...>
> >> wrote:
> >> > I have a silicon bulk system. Pymol indicates that a handful of the
> >> > atoms
> >> > are bonded to each other. Many bonds are not indicated. Is there some
> >> > value
> >> > I can adjust that will make pymol indicate that more atoms are
> bonded? I
> >> > usually do this by setting some cutoff radius, but googling around has
> >> > yielded no results. I see that there is a way to bond atom pairs
> >> > manually,
> >> > but that would be incredibly tedious given the number of bonds there
> >> > should
> >> > be.
> >> >
> >> > Thanks for any help!
> >> > Rye
> >> >
> >> >
> >> >
> ------------------------------------------------------------------------------
> >> > Keep yourself connected to Go Parallel:
> >> > BUILD Helping you discover the best ways to construct your parallel
> >> > projects.
> >> > http://goparallel.sourceforge.net
> >> > _______________________________________________
> >> > 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
> >
> >
>
>
>
> --
> Jason Vertrees, PhD
> Director of Core Modeling Product Management
> Schrödinger, Inc.
>
> (e) Jas...@sc...
> (o) +1 (603) 374-7120
>

Hi Rye,
set connect_cutoff, 0.5
load 1.xyz
produces different bonding than if you left the connect_cutoff value
to its default, 0.35. Set it to 0.85 and then load the file and you'll
see the Unknown atoms in the middle bonded as well.
Cheers,
-- Jason
On Tue, Dec 4, 2012 at 11:33 AM, Rye Terrell <rye...@ry...> wrote:
>
> Hi Jason,
>
> Thanks for the tip. I still couldn't get it to work. I'll google around some
> more, but here's the file. Thanks for any help.
>
> Cheers,
> Rye
>
>
> On Mon, Dec 3, 2012 at 4:34 PM, Jason Vertrees
> <jas...@sc...> wrote:
>>
>> Hi Rye,
>>
>> How about connect_cutoff in Å? There's also connect_mode
>> (http://www.pymolwiki.org/index.php/Connect_mode).
>>
>> If you send me a copy of your file I can look at it.
>>
>> Cheers,
>>
>> -- Jason
>>
>> On Mon, Dec 3, 2012 at 4:03 PM, Rye Terrell <rye...@ry...>
>> wrote:
>> > I have a silicon bulk system. Pymol indicates that a handful of the
>> > atoms
>> > are bonded to each other. Many bonds are not indicated. Is there some
>> > value
>> > I can adjust that will make pymol indicate that more atoms are bonded? I
>> > usually do this by setting some cutoff radius, but googling around has
>> > yielded no results. I see that there is a way to bond atom pairs
>> > manually,
>> > but that would be incredibly tedious given the number of bonds there
>> > should
>> > be.
>> >
>> > Thanks for any help!
>> > Rye
>> >
>> >
>> > ------------------------------------------------------------------------------
>> > Keep yourself connected to Go Parallel:
>> > BUILD Helping you discover the best ways to construct your parallel
>> > projects.
>> > http://goparallel.sourceforge.net
>> > _______________________________________________
>> > 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
>
>
-- 
Jason Vertrees, PhD
Director of Core Modeling Product Management
Schrödinger, Inc.
(e) Jas...@sc...
(o) +1 (603) 374-7120

Hi Rye,
How about connect_cutoff in Å? There's also connect_mode
(http://www.pymolwiki.org/index.php/Connect_mode).
If you send me a copy of your file I can look at it.
Cheers,
-- Jason
On Mon, Dec 3, 2012 at 4:03 PM, Rye Terrell <rye...@ry...> wrote:
> I have a silicon bulk system. Pymol indicates that a handful of the atoms
> are bonded to each other. Many bonds are not indicated. Is there some value
> I can adjust that will make pymol indicate that more atoms are bonded? I
> usually do this by setting some cutoff radius, but googling around has
> yielded no results. I see that there is a way to bond atom pairs manually,
> but that would be incredibly tedious given the number of bonds there should
> be.
>
> Thanks for any help!
> Rye
>
> ------------------------------------------------------------------------------
> Keep yourself connected to Go Parallel:
> BUILD Helping you discover the best ways to construct your parallel
> projects.
> http://goparallel.sourceforge.net
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
--
Jason Vertrees, PhD
Director of Core Modeling Product Management
Schrödinger, Inc.
(e) Jas...@sc...
(o) +1 (603) 374-7120

I have a silicon bulk system. Pymol indicates that a handful of the atoms
are bonded to each other. Many bonds are not indicated. Is there some value
I can adjust that will make pymol indicate that more atoms are bonded? I
usually do this by setting some cutoff radius, but googling around has
yielded no results. I see that there is a way to bond atom pairs manually,
but that would be incredibly tedious given the number of bonds there should
be.
Thanks for any help!
Rye

Hi Joel,
thanks for the report. This will be fixed in the next PyMOL release.
Cheers,
 Thomas
Joel Tyndall wrote, On 12/03/12 02:53:
> Hi Jason/all,
> 
> Possible bug. When measuring distances around coordinated metals, I then
> wanted to change the colour of the resulting dashed line. The colour
> change would only appear when you turn the object off (or another).
> Happens with RNA and protein.
> 
> Cheers
> J
> 
> _________________________________
> 
> Joel Tyndall, PhD
> 
> Senior Lecturer in Medicinal Chemistry
> National School of Pharmacy
> University of Otago
> PO Box 56 Dunedin 9054
> New Zealand 
> Skype: jtyndall
> 
> Ph: +64 3 479 7293
-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

Hi Jason/all,
Possible bug. When measuring distances around coordinated metals, I then wanted to change the colour of the resulting dashed line. The colour change would only appear when you turn the object off (or another). Happens with RNA and protein.
Cheers
J
_________________________________
Joel Tyndall, PhD
Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall
Ph: +64 3 479 7293