pymol-users Mailing List for PyMOL Molecular Graphics System

Andrea,

I don't know the technical reason, but I seem to remember that Warren 
advised users who wanted to use PyMOL functions from within a Python 
script to simply use PyMOL as your Python interpreter.

In other words, write your Python program, then do
  pymol -c myprog.py

(the -c flag causes the program to run in batch mode i.e. not to start the 
GUI)

Gareth


On Thu, 28 Apr 2005, Andrea Spitaleri wrote:

> After any answer,
> I have been looking on this list and googling around (sorry if I
> didn't before...)
> there is:
> # set path in order to use pymol modules
> export PYMOL_PATH=/usr/local/pymol/
> export PYTHONPATH=/usr/local/pymol/modules/
> 
> then type python to enter in the shell and:
> spit@darkstar:~> python
> Python 2.3.3 (#1, Feb  5 2005, 16:22:10)
> [GCC 3.3.3 (SuSE Linux)] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
> >>> import pymol
> Traceback (most recent call last):
>   File "<stdin>", line 1, in ?
>   File "/usr/local/pymol/modules/pymol/__init__.py", line 306, in ?
>     import _cmd
> ImportError: No module named _cmd
> >>>
> I found already that someone got the same error but none helps him, so
> I tought that this is a pymol bug, isn't ?
> 
> thanks again for any help
> 
> regards
> 
> andrea
> 
> 
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> 

-------------------------------------------------------------------------------
 Gareth Stockwell
 EMBL - European Bioinformatics Institute
 Wellcome Trust Genome Campus
 Hinxton
 Cambridge CB10 1SD                                         ga...@eb...
 Tel 01223 492548                               http://www.ebi.ac.uk/~gareth

After any answer,
I have been looking on this list and googling around (sorry if I
didn't before...)
there is:
# set path in order to use pymol modules
export PYMOL_PATH=3D/usr/local/pymol/
export PYTHONPATH=3D/usr/local/pymol/modules/

then type python to enter in the shell and:
spit@darkstar:~> python
Python 2.3.3 (#1, Feb  5 2005, 16:22:10)
[GCC 3.3.3 (SuSE Linux)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import pymol
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
  File "/usr/local/pymol/modules/pymol/__init__.py", line 306, in ?
    import _cmd
ImportError: No module named _cmd
>>>
I found already that someone got the same error but none helps him, so
I tought that this is a pymol bug, isn't ?

thanks again for any help

regards

andrea

Andreas,

> ><plug> 
> >You should probably have a look at the Macromolecular Structure
> >Database (msd.ebi.ac.uk) - it contains proposed biological assemblies,
> >calculated using an algorithm based on that used for PQS.  You can
> >download PDB-format files from the website.  
> ></plug>
> >  
> >
> So in what respect do you think pdb files from MSD will be better than PQS?
> Since they both come from the EBI, they should be more or less the 
> same,I assume -  it would be schizofrenic to provide a good and bad 
> version of quaternary structures...
> Well, I just discovered from your mail address, you would know!

I'm no expert in the details of either MSD or PQS, but I'd say the main
differences are

1. PQS files can contain the same problems that legacy PDB files do,
namely inconsistent naming of atoms and residues, possible duplication of
atom/residue numbers, incorrect stereochemistries etc.  Compilation of the
MSD includes numerous checks for these things, in order to ensure that the
data is internally consistent, e.g. that all residues named 'XYZ' refer to
the same chemical compound.

2. The transformations used to generate biological assemblies in PQS 
sometimes cause problems regarding ligands.  PQS tries to assign a parent 
chain to each ligand molecule, so that when protein chains are duplicated 
and have symmetry operations applied to them, the ligand molecules get the 
same treatment.  For whatever reason, this sometimes does not work - I 
have seen PQS files in which a ligand gets split in half, with some atoms 
being transformed to a new symmetry mate, and some staying where they 
are...  This should not happen in the MSD due to the checks mentioned 
above.

3. Apparently the algorithm used to generate MSD assemblies is not
*exactly* the same as that used in PQS, and I believe there is a greater
degree of manual curation applied to the results.  So the structures you
get from MSD should agree with biological intutition more often (though 
there is certainly no guarantee it will be 100% correct)

If you want to know more details, I'd suggest you contact the MSD team via
the address on their website.
	
Hope that helps,
Gareth



-------------------------------------------------------------------------------
 Gareth Stockwell
 EMBL - European Bioinformatics Institute
 Wellcome Trust Genome Campus
 Hinxton
 Cambridge CB10 1SD                                         ga...@eb...
 Tel 01223 492548                               http://www.ebi.ac.uk/~gareth

Hello,
   I am trying to get the billboarding effect to work on a callback 
object(which contains some cgo's and other stuff).  Billboarding is when 
an object is always facing the camera (i.e. the rotation part of the 
matrix is removed).  I am using a callback object so that I can insert 
rotate,translate commands every time the screen is updated. What is the 
best way to do this?

First, I was thinking I could just get the current view and remove the 
0-8 rotation matrix values. So I would:
original=get_view
reset
draw objects
transform_selection(new_matrix)
set_view(original)

this approach did not work...

Next,  I was thinking I could abstract the camera position from the 
get_view command, then using a dot product, get the angle between the 
camera and the object.  Now I could rotate along the cross-product of 
the camera vector and the object vector by the - dot product.  Thus 
reversing the camera rotation for that specific object. Do I have to 
first translate the object to the "origin of rotation" (the 9-12 values 
of get_view() ?)

Is there a better/already implemented way to do this?


Any help would be appreciated.
Thanks,
Dan Kulp

Hi Paula,

* Paula Salgado <pa...@st...> [2005-04-27 10:44] wrote:
> Hi,
>=20
> Is it possible to save an r3d file in pymol for exporting into other=20
> render programs like povray? I would like to test rendering in other=20
> programs...

I use the following script to save an input file for povray:


#---------------------- save as make_pov.py ----------------
# make_pov.py                                                              =
                        =20

=66rom pymol import cmd

def make_pov(file):
  """
  Do "run make_pov.py" from within pymol and then execute the script       =
                        =20
  with "make_pov povray.inp" to create the povray.inp file.                =
                     =20
=20
  make note of the dimensions written out by this script and use the
  same (or the same ratio) within povray:
  e.g. output (the "vol" lines only appear if spheres are present):
                                                                           =
                        =20
   PyMOL>make_pov('povray.inp')
    RayRenderPOV: w 1100 h 900 f   63.349 b  102.310
    RayRenderPOV: vol  -17.316   17.316  -14.168
    RayRenderPOV: vol   14.168   63.349  102.310
    RayRenderPovRay: processed 714 graphics primitives.
    Ray: total time: 0.03 sec. =3D 123885.9 frames/hour. (0.03 sec. accum.)
=20
  So for example, you would run povray with:
    povray +Ipovray.inp +W1100 +H900
  or
    povray +Ipovray.inp +W550 +H450
  """
  (header,data) =3D cmd.get_povray()
  povfile=3Dopen(file,'w')
  povfile.write(header)
  povfile.write(data)
  povfile.close()

cmd.extend('make_pov',make_pov)
#---------------------- end of make_pov.py ----------------

All the stuff between the """'s is just instructional comment.

Save this script as a file and do "run make_pov.py" from the PyMOL
command line, then you can type "make_pov povray.inp" to create the
povray.inp file.

Cheers,
Rob
--=20
Robert L. Campbell, Ph.D.                         <rl...@po...>
Senior Research Associate                            phone: 613-533-6821
Dept. of Biochemistry, Queen's University,             fax: 613-533-2497
Kingston, ON K7L 3N6  Canada       http://adelie.biochem.queensu.ca/~rlc
    PGP Fingerprint: 9B49 3D3F A489 05DC B35C  8E33 F238 A8F5 F635 C0E2

I am soooo impressed by Apple on that one:

The page with Warren's name was corrected 'as we speak'...!

Apple guys, since you are watching, why not add other Structural 
Biology software ?
CCP4, ARP/wARP, Coot all run in OSX ... (and ARP/wARP modules ARE 
optimized
for G5, in one instance outperforming the Linux version by being 20+ 
faster - lots of
EXPs and smart programming from Serge Cohen ...)

Happy that tomorrow we place the order for our new Xserve cluster !

Apologies for the non-Pymol interferences !!!

	Tassos


On 27 Apr 2005, at 21:41, Anastassis Perrakis wrote:

> ... and furthermore, HKL2000 was not a graphics and visualization 
> software last time I checked ...!
>
> 	Tassos
>
> On 27 Apr 2005, at 21:14, Jim Nettles wrote:
>
>>
>> Michael Love did some early Darwin ports. Thanks MIchael, and we do 
>> need to make sure Warren gets the appropriate limelight. Thanks 
>> Warren!
>>
>> Jim N.
>>
>> P.S. I'll send a note to my Apple person
>>
>>
>> On Apr 27, 2005, at 2:37 PM, Mark A Saper wrote:
>>
>>> Seems like Apple thinks that PyMOL was written by Michael Love!?
>>> Go to http://www.apple.com/science/software/lifescience.html towards 
>>> end of page.
>>> _________________________________
>>> Mark A. Saper, Ph.D.
>>> sa...@um...		(734) 764-3353		fax (734) 764-3323
>>> http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html
>>>
>>>
>>>
>>> -------------------------------------------------------
>>> SF.Net email is sponsored by: Tell us your software development 
>>> plans!
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>>> _______________________________________________
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>>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>
>>
>>
>> -------------------------------------------------------
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>
>
>
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Ha ha. Good point. I missed that.

	Jim N.

On Apr 27, 2005, at 3:41 PM, Anastassis Perrakis wrote:

> ... and furthermore, HKL2000 was not a graphics and visualization 
> software last time I checked ...!
>
> 	Tassos
>
> On 27 Apr 2005, at 21:14, Jim Nettles wrote:
>
>>
>> Michael Love did some early Darwin ports. Thanks MIchael, and we do 
>> need to make sure Warren gets the appropriate limelight. Thanks 
>> Warren!
>>
>> Jim N.
>>
>> P.S. I'll send a note to my Apple person
>>
>>
>> On Apr 27, 2005, at 2:37 PM, Mark A Saper wrote:
>>
>>> Seems like Apple thinks that PyMOL was written by Michael Love!?
>>> Go to http://www.apple.com/science/software/lifescience.html towards 
>>> end of page.
>>> _________________________________
>>> Mark A. Saper, Ph.D.
>>> sa...@um...		(734) 764-3353		fax (734) 764-3323
>>> http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html
>>>
>>>
>>>
>>> -------------------------------------------------------
>>> SF.Net email is sponsored by: Tell us your software development 
>>> plans!
>>> Take this survey and enter to win a one-year sub to SourceForge.net
>>> Plus IDC's 2005 look-ahead and a copy of this survey
>>> Click here to start!  http://www.idcswdc.com/cgi-bin/survey?id=105hix
>>> _______________________________________________
>>> PyMOL-users mailing list
>>> PyM...@li...
>>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>
>>
>>
>> -------------------------------------------------------
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>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>

...and, Ribbons was certainly not created by... Ribbons! (unless Mike 
Carson has started using a pseudonym, that is)
Oh boy...

Luca

Begin forwarded message:

> From: Anastassis Perrakis <a.p...@nk...>
> Date: April 27, 2005 15:41:46 EDT
> To: Jim Nettles <jn...@em...>
> Cc: Mark A Saper <sa...@um...>, Pymol 
> <pym...@li...>
> Subject: Re: [PyMOL] PyMOL author??
>
> ... and furthermore, HKL2000 was not a graphics and visualization 
> software last time I checked ...!
>
> 	Tassos
>
> On 27 Apr 2005, at 21:14, Jim Nettles wrote:
>
>>
>> Michael Love did some early Darwin ports. Thanks MIchael, and we do 
>> need to make sure Warren gets the appropriate limelight. Thanks 
>> Warren!
>>
>> Jim N.
>>
>> P.S. I'll send a note to my Apple person
>>
>>
>> On Apr 27, 2005, at 2:37 PM, Mark A Saper wrote:
>>
>>> Seems like Apple thinks that PyMOL was written by Michael Love!?
>>> Go to http://www.apple.com/science/software/lifescience.html towards 
>>> end of page.
>>> _________________________________
>>> Mark A. Saper, Ph.D.
>>> sa...@um...		(734) 764-3353		fax (734) 764-3323
>>> http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html
>>>
>>>
>>>
>>> -------------------------------------------------------
>>> SF.Net email is sponsored by: Tell us your software development 
>>> plans!
>>> Take this survey and enter to win a one-year sub to SourceForge.net
>>> Plus IDC's 2005 look-ahead and a copy of this survey
>>> Click here to start!  http://www.idcswdc.com/cgi-bin/survey?id=105hix
>>> _______________________________________________
>>> PyMOL-users mailing list
>>> PyM...@li...
>>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>
>>
>>
>> -------------------------------------------------------
>> SF.Net email is sponsored by: Tell us your software development plans!
>> Take this survey and enter to win a one-year sub to SourceForge.net
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>> _______________________________________________
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>>
>
>
>
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... and furthermore, HKL2000 was not a graphics and visualization 
software last time I checked ...!

	Tassos

On 27 Apr 2005, at 21:14, Jim Nettles wrote:

>
> Michael Love did some early Darwin ports. Thanks MIchael, and we do 
> need to make sure Warren gets the appropriate limelight. Thanks 
> Warren!
>
> Jim N.
>
> P.S. I'll send a note to my Apple person
>
>
> On Apr 27, 2005, at 2:37 PM, Mark A Saper wrote:
>
>> Seems like Apple thinks that PyMOL was written by Michael Love!?
>> Go to http://www.apple.com/science/software/lifescience.html towards 
>> end of page.
>> _________________________________
>> Mark A. Saper, Ph.D.
>> sa...@um...		(734) 764-3353		fax (734) 764-3323
>> http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html
>>
>>
>>
>> -------------------------------------------------------
>> SF.Net email is sponsored by: Tell us your software development plans!
>> Take this survey and enter to win a one-year sub to SourceForge.net
>> Plus IDC's 2005 look-ahead and a copy of this survey
>> Click here to start!  http://www.idcswdc.com/cgi-bin/survey?id=105hix
>> _______________________________________________
>> PyMOL-users mailing list
>> PyM...@li...
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>
>
> -------------------------------------------------------
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> Take this survey and enter to win a one-year sub to SourceForge.net
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>

Hi,

Is there an equivalent to the move_zone, move_objects command of O in PyMOL?
Thanks in advance,

Eva Vanamee

Michael Love did some early Darwin ports. Thanks MIchael, and we do 
need to make sure Warren gets the appropriate limelight. Thanks Warren!

Jim N.

P.S. I'll send a note to my Apple person


On Apr 27, 2005, at 2:37 PM, Mark A Saper wrote:

> Seems like Apple thinks that PyMOL was written by Michael Love!?
> Go to http://www.apple.com/science/software/lifescience.html towards 
> end of page.
> _________________________________
> Mark A. Saper, Ph.D.
> sa...@um...		(734) 764-3353		fax (734) 764-3323
> http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html
>
>
>
> -------------------------------------------------------
> SF.Net email is sponsored by: Tell us your software development plans!
> Take this survey and enter to win a one-year sub to SourceForge.net
> Plus IDC's 2005 look-ahead and a copy of this survey
> Click here to start!  http://www.idcswdc.com/cgi-bin/survey?id=105hix
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Seems like Apple thinks that PyMOL was written by Michael Love!?
Go to http://www.apple.com/science/software/lifescience.html towards 
end of page.
_________________________________
Mark A. Saper, Ph.D.
sa...@um...		(734) 764-3353		fax (734) 764-3323
http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html

Andreas,

I think you'll find that if you delete the binary nastiness at line 268 of 
the file

REMARK 300  THE BIOMOLECULE IS A MOLECULAR SPECIES OF TYPE ....

it will load OK.  This is clearly a bug in the PQS database. 

<plug> 
You should probably have a look at the Macromolecular Structure
Database (msd.ebi.ac.uk) - it contains proposed biological assemblies,
calculated using an algorithm based on that used for PQS.  You can
download PDB-format files from the website.  
</plug>

btw, quite an impressive structure when you do load it!

Gareth


On Wed, 27 Apr 2005, Andreas Henschel wrote:

> Hi,
> 
> I am using PyMOL with PQS files , which supposedly come in PDB format 
> but I encountered some
> problems with a few entries (eg. 1m90.mmol, 
> ftp://ftp.ebi.ac.uk/pub/databases/msd/pqs/macmol/1m90.mmol) on opening:
> 
> PyMOL>load 1m90.mmol
>  Executive: object "1m90.mmol" created.
> ExecutiveWindowZoom-Error: selection doesn't specify any coordinates.
> 
> And the display remains empty. Rasmol manages to display the file.
> These problems usually occur with big complexes. Any idea?
> 
> Many thanks
> Andreas
> 
> -- 
> Andreas Henschel
> Bioinformatics Group
> TU Dresden
> Tatzberg 47-51
> 01307 Dresden, Germany
> 
> Phone: +49 351 463 40063
> EMail: ah...@bi...
> 
> 
> 
> 
> -------------------------------------------------------
> SF.Net email is sponsored by: Tell us your software development plans!
> Take this survey and enter to win a one-year sub to SourceForge.net
> Plus IDC's 2005 look-ahead and a copy of this survey
> Click here to start!  http://www.idcswdc.com/cgi-bin/survey?id=105hix
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 

-------------------------------------------------------------------------------
 Gareth Stockwell
 EMBL - European Bioinformatics Institute
 Wellcome Trust Genome Campus
 Hinxton
 Cambridge CB10 1SD                                         ga...@eb...
 Tel 01223 492548                               http://www.ebi.ac.uk/~gareth

Hi,

I am using PyMOL with PQS files , which supposedly come in PDB format 
but I encountered some
problems with a few entries (eg. 1m90.mmol, 
ftp://ftp.ebi.ac.uk/pub/databases/msd/pqs/macmol/1m90.mmol) on opening:

PyMOL>load 1m90.mmol
 Executive: object "1m90.mmol" created.
ExecutiveWindowZoom-Error: selection doesn't specify any coordinates.

And the display remains empty. Rasmol manages to display the file.
These problems usually occur with big complexes. Any idea?

Many thanks
Andreas

-- 
Andreas Henschel
Bioinformatics Group
TU Dresden
Tatzberg 47-51
01307 Dresden, Germany

Phone: +49 351 463 40063
EMail: ah...@bi...

Hi,

Is it possible to save an r3d file in pymol for exporting into other 
render programs like povray? I would like to test rendering in other 
programs...

Thanks a lot!
Paula

Hi guys/girls
easy and quick question:
how can i import pymol modules in my python scripts?
ie. I want use translate...
do i need to import what?

thanks a lot

andrea

>
>
>for example if i type help show and all the manual appears how do I then
>clear the manual from the screen?
>
Try pressing the 'Esc'ape key while the Viewer window is active..
 

=== pym...@li... wrote (on 04/25/2005 08:19 
PM): ===

> Subject:
> [PyMOL] returning image to PyMol viewer
> From:
> Sebastien Gerega <sge...@ma...>
> Date:
> Tue, 26 Apr 2005 12:21:12 +1000
> To:
> pymol-users <pym...@li...>
>
>
>This is probably a very simple question but I have been unable to find an
>answer by just looking online. When I type commands which bring up text in
>the viewer window how do i return the molecular image.
>for example if i type help show and all the manual appears how do I then
>clear the manual from the screen?
>thx,
>Sebastien
>
>----------------------------------------------------------------
>This message was sent using IMP, the Internet Messaging Program.
>  
>

-- 
Cameron Mura
UCSD

Sebastien,

Hit the ESC key or Hide Text from the Setting menu.

Cheers,
Warren


--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080   =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Sebastien Gerega
> Sent: Monday, April 25, 2005 7:21 PM
> To: pymol-users
> Subject: [PyMOL] returning image to PyMol viewer
>=20
> This is probably a very simple question but I have been=20
> unable to find an answer by just looking online. When I type=20
> commands which bring up text in the viewer window how do i=20
> return the molecular image.
> for example if i type help show and all the manual appears=20
> how do I then clear the manual from the screen?
> thx,
> Sebastien
>=20
> ----------------------------------------------------------------
> This message was sent using IMP, the Internet Messaging Program.
>=20
>=20
> -------------------------------------------------------
> SF email is sponsored by - The IT Product Guide Read honest &=20
> candid reviews on hundreds of IT Products from real users.
> Discover which products truly live up to the hype. Start reading now.
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>=20

Dear Sebastien.

> answer by just looking online. When I type commands which bring up
> text in the viewer window how do i return the molecular image.

Just press the <Esc> key (escape). Be sure that the PyMOL viewer window
(the one with the molecule) is focussed/selected prior to pressing
escape (if not, then click on it once).

Kind Regards,

./ Kristoffer

This is probably a very simple question but I have been unable to find an
answer by just looking online. When I type commands which bring up text i=
n
the viewer window how do i return the molecular image.
for example if i type help show and all the manual appears how do I then
clear the manual from the screen?
thx,
Sebastien

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This message was sent using IMP, the Internet Messaging Program.

Yunbo,

PyMOL wasn't unicode or utf8 compliant -- try saving the file in a directory
path that only contains plain ordinary ASCII characters.  Alternatively, the
latest beta version might work for you since it runs in utf8 by default.

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                     
Principal Scientist

. DeLano Scientific LLC  
. 400 Oyster Point Blvd., Suite 213           
. South San Francisco, CA 94080    
. Biz:(650)-872-0942  Tech:(650)-872-0834     
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...      
 

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf Of 
> yunbo.song
> Sent: Saturday, April 23, 2005 8:48 AM
> To: pym...@li...
> Subject: [PyMOL] Error report when I saved image
> 
> Hi, all,
>  
> I got the Error feed back when I saved image using Pymol. My 
> Operations system: Windows2000.
> What's wrong here? thanks in advance!!  error report is in 
> the following.
>  
> yunbo
> Apr23
>  
> Error:1
> UnicodeEncodeError exception in Tk callbacke
>   Function:<bound method Normal.file_savepng of 
> <pmg_tk.skins.normal.Normal instance at 0x03165738>> 
> (type:<'instancementhod">) Args:() Traceback (innermost last):
> File"nicodeEncodeError Exception in Tk callback
>  Function: <bound method Normal.file_savepng of 
> <pmg_tk.skins.normal.Normal ins ance at 0x03165738>> (type: 
> <type 'instancemethod'>)
>  Args: ()
> raceback (innermost last):
>  File "D:\Program Files\DeLano 
> Scientific\PyMOL/modules\Pmw\Pmw_1_2\lib\PmwBase.py", line 
> 1747, in __call__
>    return apply(self.func, args)
>  File "D:\Program Files\DeLano 
> Scientific\PyMOL/modules\pmg_tk\skins\normal\__init__.py", 
> line 581, in file_savepng
>    self.cmd.png(sfile)
>  File "D:\Program Files\DeLano 
> Scientific\PyMOL/modules\pymol\exporting.py", line 97, in png
>    r = cmd._do("cmd._png('"+str(filename)+"')")
> nicodeEncodeError: 'ascii' codec can't encode characters in 
> position 34-35: ordinal not in range(128)
> 

Hi!

Is there a way in pymol to represent superposition  of two molecules
one as a stick and the other as a dotted line? The purpose is to show
a conformational change.

(mol 1 as sticks and mol2 as dotted lines).

Thanks!

Sona

Hi Nicolas,

I have the same SGI computer, Indigo 2 Impact 10000
running IRIX 6.5.22m (BTW upgrade to this release is free from=20
supportfolio at SGI, might have to install patch 5086 first)

I have stereo graphics emitter and glasses,
and stereo works fine,
i just double click a link on my desktop to pymol.com
pymol version 0.97.

then on menus bar
Display-Stero mode- quad buffered.

running at 1024x786_96s is display settings
on SGI grey speckled monitor.

Are all the cables connected properly for the emitter box?

Dan



On 23 Apr 2005, at 06:19, pym...@li...=20
wrote:

> Hello PYMOLers,
> =3D20
>     I've recently installed Pymol v0.97 on an SGI but the hardware=3D20
> stereo mode was not detected. Is there somebody successfully using=20
> PyMol=3D20
> with this mode on an SGI ? If yes, could you please help me to fix=20
> this=3D20
> problem?
> =3D20
> My SGI:
>     - Irix 64 Release 6.5
>     - Model Indigo 2 Impact 10000
>     - Main Mem: 128 MB
>     - CPU: 175 MHz
> =3D20
> Thanks a lot,
> =3D20
> Nicolas Ambert.
>
> --=3D20
Dr. Daniel James White BSc. (Hons.) PhD
Bioimaging Coordinator
Nanoscience Centre and
Department of Biological and Environmental science
Division of Molecular Recognition
Ambiotica C242
PO Box  35
University of Jyv=E4skyl=E4
Jyv=E4skyl=E4 FIN 40014
Finland
+358 14 260 4183 (work)
+358 468102840 (mobile)

http://www.chalkie.org.uk
da...@ch...
wh...@cc...

Hi, all,

I got the Error feed back when I saved image using Pymol. My Operations system: Windows2000.
What's wrong here? thanks in advance!!  error report is in the following.

yunbo
Apr23

Error:1
UnicodeEncodeError exception in Tk callbacke 
  Function:<bound method Normal.file_savepng of <pmg_tk.skins.normal.Normal instance at 0x03165738>> (type:<'instancementhod">) Args:()
Traceback (innermost last):
File"nicodeEncodeError Exception in Tk callback
 Function: <bound method Normal.file_savepng of <pmg_tk.skins.normal.Normal ins
ance at 0x03165738>> (type: <type 'instancemethod'>)
 Args: ()
raceback (innermost last):
 File "D:\Program Files\DeLano Scientific\PyMOL/modules\Pmw\Pmw_1_2\lib\PmwBase.py", line 1747, in __call__
   return apply(self.func, args)
 File "D:\Program Files\DeLano Scientific\PyMOL/modules\pmg_tk\skins\normal\__init__.py", line 581, in file_savepng
   self.cmd.png(sfile)
 File "D:\Program Files\DeLano Scientific\PyMOL/modules\pymol\exporting.py", line 97, in png
   r = cmd._do("cmd._png('"+str(filename)+"')")
nicodeEncodeError: 'ascii' codec can't encode characters in position 34-35: ordinal not in range(128)

Hi all:
	We've definitely seen that pymol incompatibilities with the
nvidia 7-series drivers on FC3 machines in my group.  It's clearly
platform dependent, consistent with some of the other comments provided
here.  For those looking to downgrade back to nvidia's 6629 driver,
it's worth noting that this does not compile on some of the newer
kernels (e.g. FC3 2.6.11-1.14 here), complicating their installation.
This can be handled with a fairly easy patch, well-described at:

http://www.nvnews.net/vbulletin/showthread.php?t=46676

We're nicely back in business after this step --- hope this might
be of use to some of you as well.

Sincerely,
Kevin

--
**********************************************************************
Kevin Gardner, Ph.D.                  Kev...@ut...
Associate Professor - Dept. of Biochemistry - UT Southwestern Med Ctr
214-645-6365/FAX: -6353                      http://freedom7.swmed.edu