pymol-users Mailing List for PyMOL Molecular Graphics System

On Tue, Jun 30, 2009 at 2:24 PM, Buz Barstow <bu...@ma...> wrote:

> I have a very large library (almost 1000) of similar genetic
> sequences, for which I would like to generate homology models. Does
> anyone know of a way to automate requests to a homology modeling
> server, such as SWISS-Model through pymol, or alternatively through
> python?


I believe Modeller uses Python - never tried it myself, though.  There is a
server for Modeller but academic users can download the program itself.

There is in fact an API for using SWISS-Model from a Perl script (which
could probably be converted to Python, or wrapped by a Python script), which
I used years ago for a similar project.  As far as I know this is
unpublished, probably because they don't want people to trash their server,
but they were happy to supply it when I contacted the site maintainer.  They
asked that I limit the frequency of my requests, however.  I would recommend
emailing them.  (I have no idea how Modeller compares to SWISS-Model, but I
suspect it's more rigorous, especially when sequence homology is remote.)

There are other ways to go about this - bioinformaticists have been abusing
online databases and servers like this for years - but it's considered bad
etiquette to do this without permission (and some groups explicitly forbid
this use).

-Nat

Hi All,

I have a very large library (almost 1000) of similar genetic  
sequences, for which I would like to generate homology models. Does  
anyone know of a way to automate requests to a homology modeling  
server, such as SWISS-Model through pymol, or alternatively through  
python?


Thanks! and all the best,

--Buz

The difference?  $769.99 - $354.99 = $415 exactly.

 

But seriously, this is a question for Dell, not pymol-users.

 

For what it is worth, mid $300's is the current per-unit pricing for the
ZM-M220W display - but they originally hit the market at a 2-3X higher
price, so one of those links is probably old.

 

Cheers,

Warren

 

 

________________________________

From: Lihua Wang [mailto:mo...@gm...] 
Sent: Tuesday, June 30, 2009 11:44 AM
To: pym...@li...
Subject: [PyMOL] ZM-M220W and TRIMON ZM-M220W

 

Hi PyMOL users:

 

I am looking into stereo 3D on LCD monitors. What is the difference
between  ZM-M220W and TRIMON  ZM-M220W?

 

 

http://accessories.us.dell.com/sna/products/Displays/productdetail.aspx?
c=us&l=en&s=hied&cs=RC956904&sku=A2550610
<http://accessories.us.dell.com/sna/products/Displays/productdetail.aspx
?c=us&l=en&s=hied&cs=RC956904&sku=A2550610> 

 

and

 

http://accessories.us.dell.com/sna/products/Displays/productdetail.aspx?
c=us&l=en&s=hied&cs=RC956904&sku=A1997135
<http://accessories.us.dell.com/sna/products/Displays/productdetail.aspx
?c=us&l=en&s=hied&cs=RC956904&sku=A1997135> 

 

Thanks!

 

Hi PyMOL users:


I am looking into stereo 3D on LCD monitors. What is the difference between
ZM-M220W and TRIMON  ZM-M220W?





http://accessories.us.dell.com/sna/products/Displays/productdetail.aspx?c=us&l=en&s=hied&cs=RC956904&sku=A2550610



and



http://accessories.us.dell.com/sna/products/Displays/productdetail.aspx?c=us&l=en&s=hied&cs=RC956904&sku=A1997135



Thanks!

Ah! taqeven is a list and I am cycling through the list to translate 
each member.  I incorrectly thought the problem was in the vector 
format, not the variable.

The final working version is:

cmd.translate("[3.3,0,0]", "%s"%taqeven[y]) where y is the position in 
the list i am cycling through.

thank you Andreas.
thank you Warren.

best
zach cp





On 06/29/2009 01:26 PM, Andreas Förster wrote:
> Assuming taqeven is the name of the object you want to translate, use
>
> cmd.translate("[3.3,0,0]", "taqeven")
>
>
> Andreas
>
>
>
> zach powers wrote:
>> Hi,
>>
>> I have been having some trouble with teh cmd.translate syntax/
>>
>>
>> I have tried variations on the following:
>>
>>      cmd.translate("[3.3,0,0]", "%s"%taqeven)
>>
>> including
>>      cmd.translate('[3.3,0,0]', "%s"%taqeven)
>>
>> and
>>
>> cmd.translate("3.3,0,0", "%s"%taqeven)
>>
>>
>> I still always get the following error message:
>> Error: bad vector.
>> Traceback (most recent call last):
>>    File "/usr/lib/python2.6/site-packages/pymol/parsing.py", line 
>> 455, in run_file
>>      execfile(file,global_ns,local_ns)
>>    File "../Desktop/02_test.py", line 66, in <module>
>>      cmd.translate("3.3,0,0", "%s"%taqeven)
>>    File "/usr/lib/python2.6/site-packages/pymol/editing.py", line 
>> 1464, in translate
>>      raise pymol.CmdException
>>
>>
>> I am sure this is a simple syntax issue but I am unsure of how to 
>> write the vector into the cmd.tranlate format.
>>
>> any help would be appreciated.
>>
>> thanks
>> zach cp
>>
>> ------------------------------------------------------------------------------ 
>>
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>

Assuming taqeven is the name of the object you want to translate, use

cmd.translate("[3.3,0,0]", "taqeven")


Andreas



zach powers wrote:
> Hi,
> 
> I have been having some trouble with teh cmd.translate syntax/
> 
> 
> I have tried variations on the following:
> 
>      cmd.translate("[3.3,0,0]", "%s"%taqeven)
> 
> including
>      cmd.translate('[3.3,0,0]', "%s"%taqeven)
> 
> and
> 
> cmd.translate("3.3,0,0", "%s"%taqeven)
> 
> 
> I still always get the following error message:
> Error: bad vector.
> Traceback (most recent call last):
>    File "/usr/lib/python2.6/site-packages/pymol/parsing.py", line 455, 
> in run_file
>      execfile(file,global_ns,local_ns)
>    File "../Desktop/02_test.py", line 66, in <module>
>      cmd.translate("3.3,0,0", "%s"%taqeven)
>    File "/usr/lib/python2.6/site-packages/pymol/editing.py", line 1464, 
> in translate
>      raise pymol.CmdException
> 
> 
> I am sure this is a simple syntax issue but I am unsure of how to write 
> the vector into the cmd.tranlate format.
> 
> any help would be appreciated.
> 
> thanks
> zach cp
> 
> ------------------------------------------------------------------------------
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
> 

-- 
         Andreas Förster, Research Associate
         Paul Freemont & Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
             http://www.msf.bio.ic.ac.uk

Hi,

I have been having some trouble with teh cmd.translate syntax/


I have tried variations on the following:

     cmd.translate("[3.3,0,0]", "%s"%taqeven)

including
     cmd.translate('[3.3,0,0]', "%s"%taqeven)

and

cmd.translate("3.3,0,0", "%s"%taqeven)


I still always get the following error message:
Error: bad vector.
Traceback (most recent call last):
   File "/usr/lib/python2.6/site-packages/pymol/parsing.py", line 455, 
in run_file
     execfile(file,global_ns,local_ns)
   File "../Desktop/02_test.py", line 66, in <module>
     cmd.translate("3.3,0,0", "%s"%taqeven)
   File "/usr/lib/python2.6/site-packages/pymol/editing.py", line 1464, 
in translate
     raise pymol.CmdException


I am sure this is a simple syntax issue but I am unsure of how to write 
the vector into the cmd.tranlate format.

any help would be appreciated.

thanks
zach cp

PyMOLers,

I just finished a script that I think is pretty cool.  It finds the
interface residues between two protein chains.  The script can easily be
modified to fit the slightly different literature-based versions, but
this script implements the general idea upon which most are based:

http://www.pymolwiki.org/index.php/InterfaceResidues

I hope someone finds this useful.

Cheers,

-- Jason

-- 

Jason Vertrees, PhD

Dartmouth College : jv...@cs...
Boston University : ja...@bu...

PyMOLWiki : http://www.pymolwiki.org/

Have you heard?

You Mom Is Open Source! <" rel="nofollow">http://winkleman.com/exhibition/view/1628> 

No, that is not some veiled condemnation of maternal virtue, but rather
the provocative title of Shane Hope <http://www.shanehope.info> 's
latest Solo Exhibition at the Winkleman Gallery
<http://www.winkleman.com>  in New York City.

Shane is a modern artist (a digital surrealist?) who applies PyMOL and
other open-source tools as traditional artists employ pencil or
paintbrush. Not to be missed from his current expo are two works with
familiar titles for PyMOL users:

   ray_trace_mode=2
<" rel="nofollow">http://winkleman.com/artist/seriesworkview/1406/376/10324/2> 

and 

   cartoon_trace_atoms=1
<" rel="nofollow">http://winkleman.com/artist/seriesworkview/1406/376/10326/2> 

though my personal favorite is his 

   Junk DNA Sculptural Ontogenesis
<" rel="nofollow">http://winkleman.com/artist/seriesworkview/1406/376/10327> 

 

Shane's other recent "mol mods" can be browsed
<" rel="nofollow">http://winkleman.com/artist/seriesview/1406/376>  online. 

 

Congratulations to Shane Hope on this latest exhibition! 

 

Cheers,

Warren

 

http://shanehope.info <" rel="nofollow">http://shanehope.info/> 

 

http://www.winkleman.com <" rel="nofollow">http://www.winkleman.com/> 

 

Actually, I now see that if I had read the PyMOLwiki page for "label_color" instead of just for "label", I would have seen the syntax noting that "object" is a field...

My bad...  I may still add such an example to the "label" page since there is so much other material there as well...

-Tom

-----Original Message-----
From: Warren DeLano [mailto:wa...@de...] 
Sent: Wednesday, June 24, 2009 11:05 AM
To: Thomas Stout; pym...@li...
Subject: RE: [PyMOL] is font_color universal?

Tom,

# per-object:

set label-color, color-name, object-name

# per-atom:

set label-color, color-name, selection

# for example

fragment arg

label all, name

set label_color, yellow, arg

set label_color, red, elem c

# note that the other label settings may not work below the per-object level

Cheers,
Warren


________________________________________
From: Thomas Stout [mailto:ts...@ex...]
Sent: Wednesday, June 24, 2009 10:59 AM
To: pym...@li...
Subject: [PyMOL] is font_color universal?

 
Hi All -- 
 
In my reading of the documentation/wiki and experimenting with settings, it looks like "font_color" is universal, meaning that you can only have one font color for ALL objects in a session file -- correct? 
 
I was hoping to have different color labels for different objects, so if anybody knows how to manage that (without resorting to Photo$hop), I'd be very interested to hear!  (I'd like the labels to be the same color as the alpha-Carbon to which they are attached)
 
Cheers,
Tom
 
 

This email (including any attachments) may contain material
that is confidential and privileged and is for the sole use of
the intended recipient. Any review, reliance or distribution by
others or forwarding without express permission is strictly
prohibited. If you are not the intended recipient, please
contact the sender and delete all copies.
Exelixis, Inc. reserves the right, to the extent and under
circumstances permitted by applicable law, to retain, monitor
and intercept e-mail messages to and from its systems.

Fantastic!  That's exactly what I was looking for...

Is that true to all versions of PyMOL?  I will update the Wiki accordingly if so

Thanks as always, Warren
-Tom 

-----Original Message-----
From: Warren DeLano [mailto:wa...@de...] 
Sent: Wednesday, June 24, 2009 11:05 AM
To: Thomas Stout; pym...@li...
Subject: RE: [PyMOL] is font_color universal?

Tom,

# per-object:

set label-color, color-name, object-name

# per-atom:

set label-color, color-name, selection

# for example

fragment arg

label all, name

set label_color, yellow, arg

set label_color, red, elem c

# note that the other label settings may not work below the per-object level

Cheers,
Warren


________________________________________
From: Thomas Stout [mailto:ts...@ex...]
Sent: Wednesday, June 24, 2009 10:59 AM
To: pym...@li...
Subject: [PyMOL] is font_color universal?

 
Hi All -- 
 
In my reading of the documentation/wiki and experimenting with settings, it looks like "font_color" is universal, meaning that you can only have one font color for ALL objects in a session file -- correct? 
 
I was hoping to have different color labels for different objects, so if anybody knows how to manage that (without resorting to Photo$hop), I'd be very interested to hear!  (I'd like the labels to be the same color as the alpha-Carbon to which they are attached)
 
Cheers,
Tom
 
 

This email (including any attachments) may contain material
that is confidential and privileged and is for the sole use of
the intended recipient. Any review, reliance or distribution by
others or forwarding without express permission is strictly
prohibited. If you are not the intended recipient, please
contact the sender and delete all copies.
Exelixis, Inc. reserves the right, to the extent and under
circumstances permitted by applicable law, to retain, monitor
and intercept e-mail messages to and from its systems.

Tom,

# per-object:

set label-color, color-name, object-name

# per-atom:

set label-color, color-name, selection

# for example

fragment arg

label all, name

set label_color, yellow, arg

set label_color, red, elem c

# note that the other label settings may not work below the per-object level

Cheers,
Warren


________________________________________
From: Thomas Stout [mailto:ts...@ex...] 
Sent: Wednesday, June 24, 2009 10:59 AM
To: pym...@li...
Subject: [PyMOL] is font_color universal?

 
Hi All -- 
 
In my reading of the documentation/wiki and experimenting with settings, it looks like "font_color" is universal, meaning that you can only have one font color for ALL objects in a session file -- correct? 
 
I was hoping to have different color labels for different objects, so if anybody knows how to manage that (without resorting to Photo$hop), I'd be very interested to hear!  (I'd like the labels to be the same color as the alpha-Carbon to which they are attached)
 
Cheers,
Tom
 
 

 
Hi All -- 
 
In my reading of the documentation/wiki and experimenting with settings,
it looks like "font_color" is universal, meaning that you can only have
one font color for ALL objects in a session file -- correct? 
 
I was hoping to have different color labels for different objects, so if
anybody knows how to manage that (without resorting to Photo$hop), I'd
be very interested to hear!  (I'd like the labels to be the same color
as the alpha-Carbon to which they are attached)
 
Cheers,
Tom
 
 

This email (including any attachments) may contain material
that is confidential and privileged and is for the sole use of
the intended recipient. Any review, reliance or distribution by
others or forwarding without express permission is strictly
prohibited. If you are not the intended recipient, please
contact the sender and delete all copies.
Exelixis, Inc. reserves the right, to the extent and under
circumstances permitted by applicable law, to retain, monitor
and intercept e-mail messages to and from its systems.

> Message: 3
> Date: Mon, 15 Jun 2009 13:04:35 -0400
> From: David Borland <bo...@re...>
> Subject: [PyMOL] disappearing data
> To: pym...@li...
> Message-ID: <4A3...@re...>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> Often, when zooming in and out, the molecule I am looking at will 
> disappear.  Looks like this happens mostly upon zooming out (or scaling 
> the object down--not sure exactly how this is implemented) when the 
> frame rate is relatively low (large molecule/rendering 
> surfaces/stereo/etc.).  I can type "zoom all," which will fix things, 
> however it can be quite annoying to have to do this often, and it seems 
> like this should be a relatively easy fix.  Any thoughts?  Thanks,
> 
> David


David,

Are you on Mac OS X?  If so, try updating your X11.  I had the same
problems and that got rid of them.  It didn't get rid of focus-stealing
or slow GUI updates, but it did fix the blanking data.

HTH,

-- Jason

-- 

Jason Vertrees, PhD

Dartmouth College : jv...@cs...
Boston University : ja...@bu...

PyMOLWiki : http://www.pymolwiki.org/

Hi,

I'm writing a wizard that consists of a bunch of files in a folder. I want 
the folder name to be the name of the wizard. Will this work?
Do I need a file in the folder with the same name as the folder (wizard name)?
Are wizard file and class names case sensitive (for the wizard command to 
work)?
Can I place the folder in some arbitrary location and use PYTHONPATH (on linux 
AND windows) to point to it? I want this for testing, hopefully and 
eventually the module will find its way to the wizard or contrib folder.
Does pymol check contrib for wizards?
Is the biopython license acceptable for distributing wizards as part of 
pymol?

Is it possible to unlink the views in grid mode (i.e. independent 
rotation/translation of objects in each box)?

Please bear with me, I may have more questions.

Thanks,
Indraneel

> Message: 4
> Date: Tue, 16 Jun 2009 15:19:13 -0600
> From: Bradley Hintze <bra...@ag...>
> Subject: [PyMOL] Select Residus on Surface
> To: pym...@li...
> Message-ID:
> 	<393...@ma...>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Is there a way to select only surface residues?

Bradly,

Good timing: this was very recently discussed on this list.  It was so
useful we turned it into a script which is now deposited on the PyMOLWiki,

  http://www.pymolwiki.org/index.php/FindSurfaceResidues


The script should have all the information you need.

Cheers,

-- Jason

-- 

Jason Vertrees, PhD

Dartmouth College : jv...@cs...
Boston University : ja...@bu...

PyMOLWiki : http://www.pymolwiki.org/

Hari & Others,

At this moment, the LCD flat panel to buy for use with PyMOL is the Zalman M220W (scan-line interleaved, passive stereo 3D).

Unfortunately, last week's nVidia driver updates do not contain the expected support for 120 Hz LCDs from Samsung and ViewSonic.  However, my personal belief and conviction is that they will be supported in the near future, and that they will work with PyMOL -- at least under Windows XP and Vista.

Furthermore, having personally tested the stereo 3D capabilities of both the Samsung and ViewSonic displays with nVidia 3D Vision emitter and glasses, the Samsung 2233RZ is so much better at generating a clean, nearly ghost-free stereo 3D effect, that I plan to strongly recommend the Samsung 2233RZ over the ViewSonic VX2265wm, if (when) nVidia releases their stereo-3D-capable OpenGL drivers for 120Hz LCDs.  

Whereas the Samsung's 3D effect is equal to, if not better than a CRT, the ViewSonic is clearly inferior to both -- at least in my experience, using nVidia 3D Vision glasses.  Hopefully ViewSonic's future 120 Hz products will be more competitive!

So recap:

If you need stereo 3D-capable today, then buy a Zalman M220W http://pymol.org/zalman .  That display will work with Mac, Windows, and Linux, without need of any special graphics card.  You give up half the vertical resolution, but hey -- it works today, and it works quite well.

However, if you expect to need a stereo 3D capable LCD in the future, then plan on buying a 120Hz Samsung 2233RZ with the nVidia 3D Vision glasses and an updated Quadro graphics card.  This will give you same high-quality, full-resolution 3D effect as a Crystal Eyes-based CRT setup.  But please do wait until the critical drivers are released before spending any money, and realize that you may be stuck using Windows for the time being.

Cheers,
Warren

> -----Original Message-----
> From: hari jayaram [mailto:ha...@gm...] 
> Sent: Monday, June 22, 2009 7:16 AM
> To: PyM...@li...; CO...@ji...
> Subject: Re: [PyMOL] Caution - 120 Hz LCDs: Not CRT killers yet...
> 
> Hi
> I am wondering if there is a linux nvidia driver update or 
> any other hack that allows Crystal Eyes 3 stereo products to  
> work with the LCD 120Hz flat panel monitors.
> 
> I should have read Warrens warning post  (Dated Jan 23 , 2009 
> [ccp4bb] Caution - 120 Hz LCDs: Not CRT killers yet) , before 
> purchasing the Viewsonic VX2265wm 120Hz LCD. But my CRT died 
> last week and since I was addicted to pymol/coot-in stereo ( 
> with Crystal Eyes 3 ) ,  I rushed out and bought this 120 Hz 
> LCD monitor.
> 
> Of course things dont work . And I am wondering if there is 
> any update from nvidia or any other workaround  that allows 
> me to get stereo on this setup.
> 
> Monitor : Viewsonic FuHzion VX2265wm 120Hz Graphics card: 
> Quadro FX 4600
> OS: Ubuntu Linux X86_64 - Hardy Heron 8.04 Stereo glasses: 
> Crystal Eyes 3 with 3pin mini din connector
> 
> 
> Thanks for your help in advance
> Hari Jayaram
> Brandeis University
> 
> 
> 
> On Tue, Feb 10, 2009 at 1:54 PM, Warren DeLano 
> <wa...@de...> wrote:
> >
> > Donnie,
> >
> > This tripped me up for a while too, but I think the stereo 
> DIN is an 
> > output (for projector, & Z-screens, etc.) not an input.  
Suffice it to 
> > say that the nVidia USB dongle does not work (in my hands, with or 
> > without USB power) as a VESA-based emitter the way we 
> apparently both 
> > hoped it would!
> >
> > Cheers,
> > Warren
> >
> > > -----Original Message-----
> > > From: Donnie Berkholz [mailto:dbe...@ge...]
> > > Sent: Tuesday, February 10, 2009 9:49 AM
> > > To: Warren DeLano
> > > Cc: PyM...@li...
> > > Subject: Re: [PyMOL] Caution - 120 Hz LCDs: Not CRT killers yet...
> > >
> > > On 23:26 Thu 22 Jan     , Warren DeLano wrote:
> > > > I tested out the Samsung Syncmaster 2233RZ / NVIDIA 3D Vision 
> > > > bundle today ($599 for a 120 Hz LCD display with one 
> pair of glasses).
> > >
> > > > I was very much hoping that this new display would nevertheless 
> > > > also work with existing nVidia Quadro-based Mac or 
> Linux systems 
> > > > with existing emitters and glasses running existing 
> OpenGL software.
> > Sadly,
> > > > this does not seem to be the case due at least in part 
> to the fact
> > that
> > > > the phase of the sync signal coming out of the Quadro card does 
> > > > not match the update phase of the LCD display.  In 
> addition, light 
> > > > from
> > the
> > > > display itself seems to corrupt the sync signal for 
> StereoGraphics 
> > > > glasses.
> > >
> > > Hi Warren,
> > >
> > > Did you happen to try the new glasses + emitter with a CRT? I am 
> > > particularly curious whether this works on Linux, or whether it 
> > > needs some sort of USB driver stubs so that Linux knows 
> what to do 
> > > with
> > these
> > > devices.
> > >
> > > It comes with a stereo-DIN cable so it seems like it could work, 
> > > provided the emitter can get power via USB and the glasses can 
> > > charge via USB.
> > >
> > > If the new glasses can work with a CRT, then at least we 
> could buy 
> > > stereo bundles now and use all of the parts of them in 
> some sort of 
> > > Frankenstein setup pending support for LCD stereo.
> > >
> > > --
> > > Thanks,
> > > Donnie
> > >
> > > Donnie Berkholz
> > > Developer, Gentoo Linux
> > > Blog: http://dberkholz.wordpress.com
> >
> >
> >
> > 
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> 
> 
> 
> 

Hi
I am wondering if there is a linux nvidia driver update or any other
hack that allows Crystal Eyes 3 stereo products to  work with the LCD
120Hz flat panel monitors.

I should have read Warrens warning post  (Dated Jan 23 , 2009 [ccp4bb]
Caution - 120 Hz LCDs: Not CRT killers yet) , before purchasing the
Viewsonic VX2265wm 120Hz LCD. But my CRT died last week and since I
was addicted to pymol/coot-in stereo ( with Crystal Eyes 3 ) ,  I
rushed out and bought this 120 Hz LCD monitor.

Of course things dont work . And I am wondering if there is any update
from nvidia or any other workaround  that allows me to get stereo on
this setup.

Monitor : Viewsonic FuHzion VX2265wm 120Hz
Graphics card: Quadro FX 4600
OS: Ubuntu Linux X86_64 - Hardy Heron 8.04
Stereo glasses: Crystal Eyes 3 with 3pin mini din connector


Thanks for your help in advance
Hari Jayaram
Brandeis University



On Tue, Feb 10, 2009 at 1:54 PM, Warren DeLano <wa...@de...> wrote:
>
> Donnie,
>
> This tripped me up for a while too, but I think the stereo DIN is an
> output (for projector, & Z-screens, etc.) not an input.  Suffice it to
> say that the nVidia USB dongle does not work (in my hands, with or
> without USB power) as a VESA-based emitter the way we apparently both
> hoped it would!
>
> Cheers,
> Warren
>
> > -----Original Message-----
> > From: Donnie Berkholz [mailto:dbe...@ge...]
> > Sent: Tuesday, February 10, 2009 9:49 AM
> > To: Warren DeLano
> > Cc: PyM...@li...
> > Subject: Re: [PyMOL] Caution - 120 Hz LCDs: Not CRT killers yet...
> >
> > On 23:26 Thu 22 Jan     , Warren DeLano wrote:
> > > I tested out the Samsung Syncmaster 2233RZ / NVIDIA 3D Vision bundle
> > > today ($599 for a 120 Hz LCD display with one pair of glasses).
> >
> > > I was very much hoping that this new display would nevertheless also
> > > work with existing nVidia Quadro-based Mac or Linux systems with
> > > existing emitters and glasses running existing OpenGL software.
> Sadly,
> > > this does not seem to be the case due at least in part to the fact
> that
> > > the phase of the sync signal coming out of the Quadro card does not
> > > match the update phase of the LCD display.  In addition, light from
> the
> > > display itself seems to corrupt the sync signal for StereoGraphics
> > > glasses.
> >
> > Hi Warren,
> >
> > Did you happen to try the new glasses + emitter with a CRT? I am
> > particularly curious whether this works on Linux, or whether it needs
> > some sort of USB driver stubs so that Linux knows what to do with
> these
> > devices.
> >
> > It comes with a stereo-DIN cable so it seems like it could work,
> > provided the emitter can get power via USB and the glasses can charge
> > via USB.
> >
> > If the new glasses can work with a CRT, then at least we could buy
> > stereo bundles now and use all of the parts of them in some sort of
> > Frankenstein setup pending support for LCD stereo.
> >
> > --
> > Thanks,
> > Donnie
> >
> > Donnie Berkholz
> > Developer, Gentoo Linux
> > Blog: http://dberkholz.wordpress.com
>
>
>
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Zach,

Can you wait a week or two?   This sort of thing is about to get 100X easier in PyMOL...

Cheers,
Warren

-----Original Message-----
From: Charlop-Powers, Zachary [mailto:Zac...@ms...]
Sent: Thu 6/18/2009 10:11 PM
To: pym...@li...
Subject: [PyMOL] Animation/ Matrix Question
 
Hi,

I would like to create a movie where my molecules are moving at the same time that the camera is moving in/around/though them. 

I have been using Slerpy to get the movement effects that i would like but I would also like to make the molecules undergo translation/rotation functions relative to one another. Slerpy also has this capability but limited for what I would like to do.  Using the  Slerpy 'saction' command I can have the option to change elements in the scene but then Slerpy will interpolate 50 frames until the next shot and I don't get to coordinate my molecular movements with my camera movements. I can approach this if I shorten the default frame number in slerpy (take steps of 5 or something like that) but then I don't get to take advantage of Slerpy's smooth camera motion. 

Although there may be many ways to do what I would like to do, does anyone have any experience with outputting the view matrix  (get_view)  for each of slerpy's camera positions? If so,  I could do a dry run with Slerpy, use get_view to output the view matrix and then combine each view with a rotate/translate function in order to get the effect I am looking for. The only problem is that I haven't figured out how to do that. Perhaps someone on this list already has?

Hmmm. I think the most logical way would be if there were some script that could get_view for each frame of the final movie. Any help/suggestions would be greatly appreciated.

best,
zach cp

Thank You Warren; Pymol is a great program and the PyMolWiki has become a fantastic resource for newbies.

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All -

Good morning. I was wondering if anybody could help me with rendering a A
to B transition in DNA. When I render it in cartoon mode, the tube
connecting the P-P on the DNA backbone is discontinuous (mainly at the
transitions between A and B DNA).

Any suggestions?

Many thanks
Ben

Hi,

I would like to create a movie where my molecules are moving at the same time that the camera is moving in/around/though them. 

I have been using Slerpy to get the movement effects that i would like but I would also like to make the molecules undergo translation/rotation functions relative to one another. Slerpy also has this capability but limited for what I would like to do.  Using the  Slerpy 'saction' command I can have the option to change elements in the scene but then Slerpy will interpolate 50 frames until the next shot and I don't get to coordinate my molecular movements with my camera movements. I can approach this if I shorten the default frame number in slerpy (take steps of 5 or something like that) but then I don't get to take advantage of Slerpy's smooth camera motion. 

Although there may be many ways to do what I would like to do, does anyone have any experience with outputting the view matrix  (get_view)  for each of slerpy's camera positions? If so,  I could do a dry run with Slerpy, use get_view to output the view matrix and then combine each view with a rotate/translate function in order to get the effect I am looking for. The only problem is that I haven't figured out how to do that. Perhaps someone on this list already has?

Hmmm. I think the most logical way would be if there were some script that could get_view for each frame of the final movie. Any help/suggestions would be greatly appreciated.

best,
zach cp

Thank You Warren; Pymol is a great program and the PyMolWiki has become a fantastic resource for newbies.

Is there a way to select only surface residues?

-- 
Bradley J. Hintze
B.S. Biochemistry
Utah State University
801-712-8799

Often, when zooming in and out, the molecule I am looking at will 
disappear.  Looks like this happens mostly upon zooming out (or scaling 
the object down--not sure exactly how this is implemented) when the 
frame rate is relatively low (large molecule/rendering 
surfaces/stereo/etc.).  I can type "zoom all," which will fix things, 
however it can be quite annoying to have to do this often, and it seems 
like this should be a relatively easy fix.  Any thoughts?  Thanks,

David

Looks like you need to install the appropriate python-dev package (or
otherwise point setup.py to the appropriate include directory if you
build python from source).



Vivek Ranjan wrote:
> I downloaded the latest pymol by using the following command:
> 
> svn co https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol pymol
> 
> Then, while running the command "python setup.py install", I
> encountered the following:
> 
> In file included from layer5/main.h:35,
>                  from layer0/Block.c:20:
> layer0/os_python.h:28:19: error: Python.h: No such file or directory
> In file included from layer0/Block.c:20:
> layer5/main.h:45: error: expected ‘)’ before ‘*’ token
> layer5/main.h:46: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
> ‘__attribute__’ before ‘*’ token
> error: command 'gcc' failed with exit status 1
> 
> Any help ??
> 
> Thanks,
> 
> Vivek
> 
> ------------------------------------------------------------------------------
> Crystal Reports - New Free Runtime and 30 Day Trial
> Check out the new simplified licensing option that enables unlimited
> royalty-free distribution of the report engine for externally facing 
> server and web deployment.
> http://p.sf.net/sfu/businessobjects
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

I downloaded the latest pymol by using the following command:

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

Then, while running the command "python setup.py install", I
encountered the following:

In file included from layer5/main.h:35,
                 from layer0/Block.c:20:
layer0/os_python.h:28:19: error: Python.h: No such file or directory
In file included from layer0/Block.c:20:
layer5/main.h:45: error: expected ‘)’ before ‘*’ token
layer5/main.h:46: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
‘__attribute__’ before ‘*’ token
error: command 'gcc' failed with exit status 1

Any help ??

Thanks,

Vivek