pymol-users Mailing List for PyMOL Molecular Graphics System

Hi-

With much fear and trepidation, I've posted on the pymol wiki a set of
scripts that I've been using to extend the movie making capabilities of
pymol.  The package is called slerpy.  It adds a set of commands that
can be used to set up a series of views or scenes that are interpolated
to make a movie.  It can be used to convert a series of scenes to a
movie in a fairly straightforward way.  It also includes commands that
allow crossfades of pymol objects and interpolation of settings such as
transparency during transitions between views.  The full details are at:

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

Please feel free to email with questions or complaints.

Best regards,

Joel

Structural Biology
Wyeth Pharmaceuticals
617-665-5698

Christoph,
=20
The message "Could not find platform independent libraries <prefix> =
Consider
setting $PYTHONHOME to <prefix>[:<exec_prefix>]" indicates that Python =
is
not being initialized properly.  You may need to set PYTHONHOME =
explicitly
in the pymol startup script.=20

Cheers,
Warren

--
DeLano Scientific LLC
Subscriber Support Services
mailto:de...@de...
=20
Not yet a PyMOL Subscriber, but want to support the project? =20
Email sa...@de... to quote your lab, school, or employer. =20
Thank you for participating!

-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of =
Christoph
Kaiser
Sent: Friday, December 29, 2006 11:22 AM
To: pym...@li...
Subject: [PyMOL] Pymol installation probs on ubuntu

Hello,

sorry for mybe asking stupid beginner's questions, but that's actually =
what
i am ;-) i just tried to get pymol running on ubuntu. turns aout to ba a
problem.
i have python 2.4, 2.3 and 2.2 installed via the synaptic package =
manager,
but when i tried to add pymol - also by synaptic - i already got some =
probs,
as it was not able to find some moduels. i could fix this problem by
changing the environment variables in the python start script.

now i ran into the following prob, for which i can't find any solution:

christoph@Richterpc1:/usr/lib/python2.4/site-packages/pymol$ pymol Could =
not
find platform independent libraries <prefix> Consider setting =
$PYTHONHOME to
<prefix>[:<exec_prefix>] Traceback (most recent call last):
  File "/usr/lib/python2.4/site-packages/pymol/__init__.py", line 105, =
in ?
    import pymol
  File "/usr/lib/python2.4/site-packages/pymol/__init__.py", line 329, =
in ?
    import _cmd
ImportError: /usr/lib/python2.4/site-packages/pymol/_cmd.so: undefined
symbol: PyUnicodeUCS4_SetDefaultEncoding

can anyone help me to fix this problem?

Thanks a lot in advance
Christoph

* * * * * * * * * * * * * * * * * *
Christoph Kaiser

TU M=FCnchen
Department of Chemistry

Biotechnology Laboratory
Prof. Dr. Johannes Buchner

 mail:  chr...@ch...
 phone: +49 089 289 13 371



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Hello,

sorry for mybe asking stupid beginner's questions, but that's actually
what i am ;-)
i just tried to get pymol running on ubuntu. turns aout to ba a problem.
i have python 2.4, 2.3 and 2.2 installed via the synaptic package manager,
but when i tried to add pymol - also by synaptic - i already got some
probs, as it was not able to find some moduels. i could fix this problem
by changing the environment variables in the python start script.

now i ran into the following prob, for which i can't find any solution:

christoph@Richterpc1:/usr/lib/python2.4/site-packages/pymol$ pymol
Could not find platform independent libraries <prefix>
Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>]
Traceback (most recent call last):
  File "/usr/lib/python2.4/site-packages/pymol/__init__.py", line 105, in ?
    import pymol
  File "/usr/lib/python2.4/site-packages/pymol/__init__.py", line 329, in ?
    import _cmd
ImportError: /usr/lib/python2.4/site-packages/pymol/_cmd.so: undefined
symbol: PyUnicodeUCS4_SetDefaultEncoding

can anyone help me to fix this problem?

Thanks a lot in advance
Christoph

* * * * * * * * * * * * * * * * * *
Christoph Kaiser

TU München
Department of Chemistry

Biotechnology Laboratory
Prof. Dr. Johannes Buchner

 mail:  chr...@ch...
 phone: +49 089 289 13 371

Pernille,

The algorithm PyMOL uses to generate outlines is discrete and based on
actual pixels.  Thus the maximum thickness is one pixel, but you can get a
thinner outline by increasing the antialiasing setting to simply render more
pixels:

set antialias, 2

--
DeLano Scientific LLC
Subscriber Support Services
mailto:de...@de...
 
Not yet a PyMOL Subscriber, but want to support the project?  
Email sa...@de... to quote your lab, school, or employer.  
Thank you for participating!

-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of Pernille
Haste Andersen
Sent: Thursday, December 21, 2006 6:49 AM
To: pym...@li...
Subject: [PyMOL] Outline in cartoon mode

Hello Everybody,

I am working on some cartoon representations of my proteins and would like
to adjust the line width of the outline to make it look even more elegant in
the ray trace mode 3.

I haven't been able to find a setting that successfully does that. Can
anyone help me?
(I know about the antialias options and the setting line_width doesn't seem
to help.)

A merry Christmas to everyone, and thanks for keeping such a nice
mailinglist!
Happy PyMoling in 2007,

Pernille

-- 


Pernille Haste Andersen, M. Sc., Ph D. student

Immunological Bioinformatics group,
Center for Biological Sequence Analysis, BioCentrum-DTU,Technical University
of Denmark, Bld. 208, DK-2800 LYNGBY, DENMARK
Tel:(+45) 45256127
E-mail : pa...@cb...


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Hello Everybody,

I am working on some cartoon representations of my proteins and would 
like to adjust the line width of the outline to make it look even more 
elegant in the ray trace mode 3.

I haven't been able to find a setting that successfully does that. Can 
anyone help me?
(I know about the antialias options and the setting line_width doesn't 
seem to help.)

A merry Christmas to everyone, and thanks for keeping such a nice 
mailinglist!
Happy PyMoling in 2007,

Pernille

-- 

Pernille Haste Andersen, M. Sc., Ph D. student

Immunological Bioinformatics group,
Center for Biological Sequence Analysis,
BioCentrum-DTU,Technical University of Denmark,
Bld. 208, DK-2800 LYNGBY, DENMARK
Tel:(+45) 45256127
E-mail : pa...@cb...

label selection, model+"-"+resn+resi
 


  _____  

From: pym...@li...
[mailto:pym...@li...] On Behalf Of Rafael
Najmanovich
Sent: Tuesday, December 19, 2006 3:04 AM
To: pym...@li...
Subject: [PyMOL] cmd.label, custom labels, script


Hi There, 

Is there a way to display custom labels from within scripts?

I need to display labels which include the object-name - this is not
possible using cmd.label it seems.
I can define a string as:
lab = "%s-%s%s" % (objn,resn,resi)
where objn is a variable that contains the object-name. I'd like to display
this string and I ask if there is some way to display these strings in the
same way/position as cmd.label normally would.

Thanks for your help.

r.

Dr. Rafael Najmanovich
European Bioinformatics Institute
Wellcome Trust Genome Campus
Cambridge CB10 1SD
United Kingdom

rafael.najmanovich at ebi.ac.uk - www.ebi.ac.uk/~rafi
+44-1223-492599 (voice) +44-7786-968257(mobile) +44-1223-494468 (fax)

> Perhaps Warren can post to the mailing list the clear text table of space
group names that are acceptable. 

PyMOL still uses Ralf Gross-Kunstleve's old sglite toolkit for decoding
spacegroups.  Thus, there is no static list of acceptable forms.  However,
included below are the most of the strings from sgsymbols.c.  It is probably
safe to assume that these strings will be recognized literally, but sglite
can handle some other common forms (e.g. "P212121" for "P 21 21 21").

Cheers,
Warren

P 1        
P -1       
P 1 2 1    
P 1 1 2    
P 2 1 1    
P 1 21 1   
P 1 1 21   
P 21 1 1   
C 1 2 1    
A 1 2 1    
I 1 2 1    
A 1 1 2    
B 1 1 2    
I 1 1 2    
B 2 1 1    
C 2 1 1    
I 2 1 1    
P 1 m 1    
P 1 1 m    
P m 1 1    
P 1 c 1    
P 1 n 1    
P 1 a 1    
P 1 1 a    
P 1 1 n    
P 1 1 b    
P b 1 1    
P n 1 1    
P c 1 1    
C 1 m 1    
A 1 m 1    
I 1 m 1    
A 1 1 m    
B 1 1 m    
I 1 1 m    
B m 1 1    
C m 1 1    
I m 1 1    
C 1 c 1    
A 1 n 1    
I 1 a 1    
A 1 a 1    
C 1 n 1    
I 1 c 1    
A 1 1 a    
B 1 1 n    
I 1 1 b    
B 1 1 b    
A 1 1 n    
I 1 1 a    
B b 1 1    
C n 1 1    
I c 1 1    
C c 1 1    
B n 1 1    
I b 1 1    
P 1 2/m 1  
P 1 1 2/m  
P 2/m 1 1  
P 1 21/m 1 
P 1 1 21/m 
P 21/m 1 1 
C 1 2/m 1  
A 1 2/m 1  
I 1 2/m 1  
A 1 1 2/m  
B 1 1 2/m  
I 1 1 2/m  
B 2/m 1 1  
C 2/m 1 1  
I 2/m 1 1  
P 1 2/c 1  
P 1 2/n 1  
P 1 2/a 1  
P 1 1 2/a  
P 1 1 2/n  
P 1 1 2/b  
P 2/b 1 1  
P 2/n 1 1  
P 2/c 1 1  
P 1 21/c 1 
P 1 21/n 1 
P 1 21/a 1 
P 1 1 21/a 
P 1 1 21/n 
P 1 1 21/b 
P 21/b 1 1 
P 21/n 1 1 
P 21/c 1 1 
C 1 2/c 1  
A 1 2/n 1  
I 1 2/a 1  
A 1 2/a 1  
C 1 2/n 1  
I 1 2/c 1  
A 1 1 2/a  
B 1 1 2/n  
I 1 1 2/b  
B 1 1 2/b  
A 1 1 2/n  
I 1 1 2/a  
B 2/b 1 1  
C 2/n 1 1  
I 2/c 1 1  
C 2/c 1 1  
B 2/n 1 1  
I 2/b 1 1  
P 2 2 2    
P 2 2 21   
P 21 2 2   
P 2 21 2   
P 21 21 2  
P 2 21 21  
P 21 2 21  
P 21 21 21 
C 2 2 21   
A 21 2 2   
B 2 21 2   
C 2 2 2    
A 2 2 2    
B 2 2 2    
F 2 2 2    
I 2 2 2    
I 21 21 21 
P m m 2    
P 2 m m    
P m 2 m    
P m c 21   
P c m 21   
P 21 m a   
P 21 a m   
P b 21 m   
P m 21 b   
P c c 2    
P 2 a a    
P b 2 b    
P m a 2    
P b m 2    
P 2 m b    
P 2 c m    
P c 2 m    
P m 2 a    
P c a 21   
P b c 21   
P 21 a b   
P 21 c a   
P c 21 b   
P b 21 a   
P n c 2    
P c n 2    
P 2 n a    
P 2 a n    
P b 2 n    
P n 2 b    
P m n 21   
P n m 21   
P 21 m n   
P 21 n m   
P n 21 m   
P m 21 n   
P b a 2    
P 2 c b    
P c 2 a    
P n a 21   
P b n 21   
P 21 n b   
P 21 c n   
P c 21 n   
P n 21 a   
P n n 2    
P 2 n n    
P n 2 n    
C m m 2    
A 2 m m    
B m 2 m    
C m c 21   
C c m 21   
A 21 m a   
A 21 a m   
B b 21 m   
B m 21 b   
C c c 2    
A 2 a a    
B b 2 b    
A m m 2    
B m m 2    
B 2 m m    
C 2 m m    
C m 2 m    
A m 2 m    
A b m 2    
B m a 2    
B 2 c m    
C 2 m b    
C m 2 a    
A c 2 m    
A m a 2    
B b m 2    
B 2 m b    
C 2 c m    
C c 2 m    
A m 2 a    
A b a 2    
B b a 2    
B 2 c b    
C 2 c b    
C c 2 a    
A c 2 a    
F m m 2    
F 2 m m    
F m 2 m    
F d d 2    
F 2 d d    
F d 2 d    
I m m 2    
I 2 m m    
I m 2 m    
I b a 2    
I 2 c b    
I c 2 a    
I m a 2    
I b m 2    
I 2 m b    
I 2 c m    
I c 2 m    
I m 2 a    
P m m m    
P n n n    
P c c m    
P m a a    
P b m b    
P b a n    
P n c b    
P c n a    
P m m a    
P m m b    
P b m m    
P c m m    
P m c m    
P m a m    
P n n a    
P n n b    
P b n n    
P c n n    
P n c n    
P n a n    
P m n a    
P n m b    
P b m n    
P c n m    
P n c m    
P m a n    
P c c a    
P c c b    
P b a a    
P c a a    
P b c b    
P b a b    
P b a m    
P m c b    
P c m a    
P c c n    
P n a a    
P b n b    
P b c m    
P c a m    
P m c a    
P m a b    
P b m a    
P c m b    
P n n m    
P m n n    
P n m n    
P m m n    
P n m m    
P m n m    
P b c n    
P c a n    
P n c a    
P n a b    
P b n a    
P c n b    
P b c a    
P c a b    
P n m a    
P m n b    
P b n m    
P c m n    
P m c n    
P n a m    
C m c m    
C c m m    
A m m a    
A m a m    
B b m m    
B m m b    
C m c a    
C c m b    
A b m a    
A c a m    
B b c m    
B m a b    
C m m m    
A m m m    
B m m m    
C c c m    
A m a a    
B b m b    
C m m a    
C m m b    
A b m m    
A c m m    
B m c m    
B m a m    
C c c a    
C c c b    
A b a a    
A c a a    
B b c b    
B b a b    
F m m m    
F d d d    
I m m m    
I b a m    
I m c b    
I c m a    
I b c a    
I c a b    
I m m a    
I m m b    
I b m m    
I c m m    
I m c m    
I m a m    
P 4        
P 41       
P 42       
P 43       
I 4        
I 41       
P -4       
I -4       
P 4/m      
P 42/m     
P 4/n      
P 42/n     
I 4/m      
I 41/a     
P 4 2 2    
P 4 21 2   
P 41 2 2   
P 41 21 2  
P 42 2 2   
P 42 21 2  
P 43 2 2   
P 43 21 2  
I 4 2 2    
I 41 2 2   
P 4 m m    
P 4 b m    
P 42 c m   
P 42 n m   
P 4 c c    
P 4 n c    
P 42 m c   
P 42 b c   
I 4 m m    
I 4 c m    
I 41 m d   
I 41 c d   
P -4 2 m   
P -4 2 c   
P -4 21 m  
P -4 21 c  
P -4 m 2   
P -4 c 2   
P -4 b 2   
P -4 n 2   
I -4 m 2   
I -4 c 2   
I -4 2 m   
I -4 2 d   
P 4/m m m  
P 4/m c c  
P 4/n b m  
P 4/n n c  
P 4/m b m  
P 4/m n c  
P 4/n m m  
P 4/n c c  
P 42/m m c 
P 42/m c m 
P 42/n b c 
P 42/n n m 
P 42/m b c 
P 42/m n m 
P 42/n m c 
P 42/n c m 
I 4/m m m  
I 4/m c m  
I 41/a m d 
I 41/a c d 
P 3        
P 31       
P 32       
R 3        
P -3       
R -3       
P 3 1 2    
P 3 2 1    
P 31 1 2   
P 31 2 1   
P 32 1 2   
P 32 2 1   
R 3 2      
P 3 m 1    
P 3 1 m    
P 3 c 1    
P 3 1 c    
R 3 m      
R 3 c      
P -3 1 m   
P -3 1 c   
P -3 m 1   
P -3 c 1   
R -3 m     
R -3 c     
P 6        
P 61       
P 65       
P 62       
P 64       
P 63       
P -6       
P 6/m      
P 63/m     
P 6 2 2    
P 61 2 2   
P 65 2 2   
P 62 2 2   
P 64 2 2   
P 63 2 2   
P 6 m m    
P 6 c c    
P 63 c m   
P 63 m c   
P -6 m 2   
P -6 c 2   
P -6 2 m   
P -6 2 c   
P 6/m m m  
P 6/m c c  
P 63/m c m 
P 63/m m c 
P 2 3      
F 2 3      
I 2 3      
P 21 3     
I 21 3     
P m -3     
P n -3     
F m -3     
F d -3     
I m -3     
P a -3     
I a -3     
P 4 3 2    
P 42 3 2   
F 4 3 2    
F 41 3 2   
I 4 3 2    
P 43 3 2   
P 41 3 2   
I 41 3 2   
P -4 3 m   
F -4 3 m   
I -4 3 m   
P -4 3 n   
F -4 3 c   
I -4 3 d   
P m -3 m   
P n -3 n   
P m -3 n   
P n -3 m   
F m -3 m   
F m -3 c   
F d -3 m   
F d -3 c   
I m -3 m   
I a -3 d   
 
P121    
P1211   
C121    
P1m1    
P1c1    
C1m1    
C1c1    
P12/m1  
P121/m1 
C12/m1  
P12/c1  
P121/c1 
C12/c1  

P2    
P21   
B2    
C2    
Pm    
Pb    
Pc    
Bm    
Cm    
Bb    
Cc    
P2/m  
P21/m 
B2/m  
C2/m  
P2/b  
P2/c  
P21/b 
P21/c 
B2/b  
C2/c  

P2   
P21  
C2   
Pm   
Pc   
Cm   
Cc   
P2/m 
P21/m
C2/m 
P2/c 
P21/c
C2/c 


-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of Thomas Stout
Sent: Tuesday, December 19, 2006 1:28 PM
To: Qi Wang
Cc: pym...@li...
Subject: Re: [PyMOL] symmetry generation P21/n?



I have discovered that PyMOL is somewhat picky about the format of the name
of the space group.  The only way I have found to uncover which specific
form(s) of the space group name PyMOL is looking for is to search within the
binary (not a good solution).  For example, P-1 will fail while "P -1" is
acceptable.  Also, P212121 versus P 21 21 21 may or may not fail.  There are
- in general - more options for the more
(biologically) common space groups. Perhaps Warren can post to the mailing
list the clear text table of space group names that are acceptable. 

In the meantime, you might try variations on "P 21/n" such as "P21/n", "P 21
n", "P 1 21/n 1", et cetera....

-Tom


-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of Qi Wang
Sent: Tuesday, December 19, 2006 1:01 PM
To: pym...@li...
Subject: [PyMOL] symmetry generation P21/n?

Hi looks to me Pymol doesn't recogize the space group symbol P 21/n.
Is it a bug or this group symbol is obsolete? Thanks.

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This email (including any attachments) may contain material that is
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Thanks for the note. I found the very last variation P 1 21/n 1 works
as a substitution for P21/n. Don't know if this would be a normal
practice for other symbols, but it's certainly worth trying (in case
it doesn't work in the first place)!

On 12/19/06, Thomas Stout <ts...@ex...> wrote:
>
>
> I have discovered that PyMOL is somewhat picky about the format of the
> name of the space group.  The only way I have found to uncover which
> specific form(s) of the space group name PyMOL is looking for is to
> search within the binary (not a good solution).  For example, P-1 will
> fail while "P -1" is acceptable.  Also, P212121 versus P 21 21 21 may or
> may not fail.  There are - in general - more options for the more
> (biologically) common space groups. Perhaps Warren can post to the
> mailing list the clear text table of space group names that are
> acceptable.
>
> In the meantime, you might try variations on "P 21/n" such as "P21/n",
> "P 21 n", "P 1 21/n 1", et cetera....
>
> -Tom
>
>
> -----Original Message-----
> From: pym...@li...
> [mailto:pym...@li...] On Behalf Of Qi Wang
> Sent: Tuesday, December 19, 2006 1:01 PM
> To: pym...@li...
> Subject: [PyMOL] symmetry generation P21/n?
>
> Hi looks to me Pymol doesn't recogize the space group symbol P 21/n.
> Is it a bug or this group symbol is obsolete? Thanks.
>
> ------------------------------------------------------------------------
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> SourceForge.net's Techsay panel and you'll get the chance to share your
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> _______________________________________________
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>
> 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.
>
>

I have discovered that PyMOL is somewhat picky about the format of the
name of the space group.  The only way I have found to uncover which
specific form(s) of the space group name PyMOL is looking for is to
search within the binary (not a good solution).  For example, P-1 will
fail while "P -1" is acceptable.  Also, P212121 versus P 21 21 21 may or
may not fail.  There are - in general - more options for the more
(biologically) common space groups. Perhaps Warren can post to the
mailing list the clear text table of space group names that are
acceptable.=20

In the meantime, you might try variations on "P 21/n" such as "P21/n",
"P 21 n", "P 1 21/n 1", et cetera....

-Tom


-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of Qi Wang
Sent: Tuesday, December 19, 2006 1:01 PM
To: pym...@li...
Subject: [PyMOL] symmetry generation P21/n?

Hi looks to me Pymol doesn't recogize the space group symbol P 21/n.
Is it a bug or this group symbol is obsolete? Thanks.

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Hi looks to me Pymol doesn't recogize the space group symbol P 21/n.
Is it a bug or this group symbol is obsolete? Thanks.

Hi Rafael,

You can use

cmd.label(selection,'"objectname-"+resn+resi')

Do mind the quotes.., the label string is _eval_uated.
Of course, if objn = "objectname", it also works as

cmd.label(selection,'objn+"-"+resn+resi')

Cheers,

Tsjerk

On 12/19/06, Rafael Najmanovich <raf...@eb...> wrote:
>  Hi There,
>
>  Is there a way to display custom labels from within scripts?
>
>  I need to display labels which include the object-name - this is not
> possible using cmd.label it seems.
>  I can define a string as:
>  lab = "%s-%s%s" % (objn,resn,resi)
>  where objn is a variable that contains the object-name. I'd like to display
> this string and I ask if there is some way to display these strings in the
> same way/position as cmd.label normally would.
>
>  Thanks for your help.
>
>  r.
>
>
>
> Dr. Rafael Najmanovich
> European Bioinformatics Institute
> Wellcome Trust Genome Campus
> Cambridge CB10 1SD
> United Kingdom
>
> rafael.najmanovich at ebi.ac.uk - www.ebi.ac.uk/~rafi
> +44-1223-492599 (voice) +44-7786-968257(mobile) +44-1223-494468 (fax)
>
>
> -------------------------------------------------------------------------
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>


-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

Hi Michael,

try to set a low resolution in addition to the increased VdW radii.  Play
around with the following set of commands:

set gaussian_resolution, 9.0
# or whatever looks best
map_new mapName, gaussian, 3.0, object
# number is separation between grid lines, 1 is way too detailed for low
resolution
isosurface surfaceName, mapName, 1.0
# contour level, 3 looks good

This is what Warren helped me with when I tried to create an EM-like figure.


Andreas



On 12/19/06, Michael Lerner <mgl...@gm...> wrote:
>
> Hi,
>
> I want to show the electrostatic potential surface 10A away from a
> protein.  I used to do this by setting all of the vdw radii to 10A,
> but I'm wondering if there's a better way these days.  The surface I
> got by altering the vdw radii always looked really choppy and not so
> smooth.
>
> Thank you,
>
> -Michael Lerner
>

	Hi There,

	Is there a way to display custom labels from within scripts?

	I need to display labels which include the object-name - this is not  
possible using cmd.label it seems.
	I can define a string as:
	lab = "%s-%s%s" % (objn,resn,resi)
	where objn is a variable that contains the object-name. I'd like to  
display this string and I ask if there is some way to display these  
strings in the same way/position as cmd.label normally would.

	Thanks for your help.

	r.

Dr. Rafael Najmanovich
European Bioinformatics Institute
Wellcome Trust Genome Campus
Cambridge CB10 1SD
United Kingdom

rafael.najmanovich at ebi.ac.uk - www.ebi.ac.uk/~rafi
+44-1223-492599 (voice) +44-7786-968257(mobile) +44-1223-494468 (fax)

>
> A more succinct description might be found here
>


I didn't copy/paste the last link ... (still the morning here)

http://cholla.wustl.edu/baker/classes/nbcr/user-guide/x2686.html

doppelt olivia wrote:
> Hello,
> 
> I've been trying to load a grd file in pymol but, it doesn't work.
> Here is my file : test.grd
> 
> COMPLETE MINI MAP
> (17I5)
> 20.00000 1.25 1.25 90.00000 90.00000 90.00000
> 16 1 1
> 1 -8 8 -1 0 0 1
> 
> -6 14 0 -24 -31 -45 -48 -16 39 102 102 18 -38 -39 -42 -43 -44
> -31 -21 -56 -50 -30 17 103 106 107 2 -37 -32 -29 -29 -27 -32 -36
> -54 -54 20 95 90 74 62 11 -25 -25 -39 -50 -32 -19 -44 -51 -55
> -56 -2 81 110 54 -25 -47 -41 -28 -33 -24 -16 -51 -42 108 215 230
> 
> 
> This is exactly the INSIGHTII format, can you tell me if I need to
> change something or if I need to install some plugins in order for pymol
> to load this file ?
> 

Hi,
last time I checked the InsightII .grd format described a fortran binary
data file (see here for specs :
http://www-bio.unizh.ch/docu/acc_docs/doc/delphi/E_File_Formats.html#425695
)
I can confirm that the format described in the specs is read by pymol.



Seeing what your data look like, it might be easier for you to convert
it to the .dx file format (cf opendx) (... a quick script should do it).

The specs of the dx file format may be found here :
http://opendx.sdsc.edu/docs/html/pages/usrgu068.htm#HDRXMPLES

A more succinct description might be found here

HIH

Avell

Hi,

I want to show the electrostatic potential surface 10A away from a
protein.  I used to do this by setting all of the vdw radii to 10A,
but I'm wondering if there's a better way these days.  The surface I
got by altering the vdw radii always looked really choppy and not so
smooth.

Thank you,

-Michael Lerner

-- 
Biophysics Graduate Student
Carlson Lab, University of Michigan
http://www.umich.edu/~mlerner http://lernerclan.net

Hello,=0A=0AI've been trying to load a grd file in pymol but, it doesn't wo=
rk.=0AHere is my file : test.grd=0A=0A=0A COMPLETE MINI MAP=0A(17I5)   =0A2=
0.00000     1.25       1.25       90.00000    90.00000   90.00000      =0A1=
6      1       1              =0A 1   -8    8   -1    0    0    1=0A=0A=0A =
   -6   14    0  -24  -31  -45  -48  -16   39  102  102   18  -38  -39  -42=
  -43  -44=0A  -31  -21  -56  -50  -30   17  103  106  107    2  -37  -32  =
-29  -29  -27  -32  -36=0A  -54  -54   20   95   90   74   62   11  -25  -2=
5  -39  -50  -32  -19  -44  -51  -55=0A  -56   -2   81  110   54  -25  -47 =
 -41  -28  -33  -24  -16  -51  -42  108  215  230=0A  =0A=0A=0A=0AThis is e=
xactly the INSIGHTII format, can you tell me if I need to change something =
or if I need to install some plugins in order for pymol to load this file ?=
=0A=0Athe command I use is : =0Aload test.grd, grd=0A=0AThanks in advance,=
=0A =0AOlivia Doppelt=0A=0A=0A=0A=0A=09=0A=0A=09=0A=09=09=0A_______________=
____________________________________________________________ =0AD=E9couvrez=
 une nouvelle fa=E7on d'obtenir des r=E9ponses =E0 toutes vos questions ! =
=0AProfitez des connaissances, des opinions et des exp=E9riences des intern=
autes sur Yahoo! Questions/R=E9ponses =0Ahttp://fr.answers.yahoo.com

Whoops, I goofed that example! meant

set state, 1, obj1
set state, 3, obj2

-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of DeLano
Scientific
Sent: Friday, December 15, 2006 4:27 PM
To: 'S. Frank Yan'; pym...@li...
Subject: Re: [PyMOL] A suggestion on molecule selection

Frank,
 
set state, state-number, object-name

set state, obj1, 1
set state, obj2, 3

You can also use the freeze and thaw options in the object's action menu to
freeze an object into the current state independent of the global state.

Cheers,
Warren

________________________________

From: pym...@li...
[mailto:pym...@li...] On Behalf Of S. Frank Yan
Sent: Friday, December 15, 2006 4:08 PM
To: pym...@li...
Subject: [PyMOL] A suggestion on molecule selection



Hi,

 

When two SDF files, each of which contains multiple entries, are loaded, it
seems PyMOL can only display the same frames from the two objects.  It goes
like frame 1 in obj 1 and frame 1 in obj 2, and cannot do like frame 1 in
obj 1 and frame 3 in obj 2.  I was wondering if there is a way to get
around.

 

Thanks a lot,

Frank

 



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Dear all,
We found a very simple (and trivial) solution to the problem. We
rebooted winXP in safe-mode (logged in as adminstrator) and installed
pymol without any problem. Now it runs fine.
Best,
Joris

Joris Beld wrote:
> Dear all,
> Unfortunately this -and previous suggestions- do not fix the problem
> we encounter when installing pymol on our brand new Dell winXP/SP2
> systems.
> We tried the suggestions in the pymol-wiki, we tried the specific
> 16-bit Dell issue and we tried the shorter path method without any
> success. What happens now is that the installer doesn't start up at
> all, although the wowexec is loaded. The wowexec process just hangs
> till one logs out/reboots.
> Anyone another idea how to fix this? Thanks for the help!
> Best,
> Joris
> Hilvert Gruppe, ETH Zürich, Switzerland
>

Dear all,
Unfortunately this -and previous suggestions- do not fix the problem we
encounter when installing pymol on our brand new Dell winXP/SP2 systems.
We tried the suggestions in the pymol-wiki, we tried the specific 16-bit
Dell issue and we tried the shorter path method without any success.
What happens now is that the installer doesn't start up at all, although
the wowexec is loaded. The wowexec process just hangs till one logs
out/reboots.
Anyone another idea how to fix this? Thanks for the help!
Best,
Joris
Hilvert Gruppe, ETH Zürich, Switzerland


Angelo Favia wrote:
> Hi Warren and all,
>     I finally managed to solve my problem:
> here'e where I found the inspiration:
> http://discuss.pcmag.com/forums/1004327277/ShowPost.aspx
> "The setup utility  is a 16-bit app (as you have guessed), and it may 
> gag if the path to its home folder is too long"
>
> I simply moved the  installation files to a short path (namely C:\) and 
> renamed the directory containing the setup.exe of Pymol into "Pymol" (to 
> make the path even shorter) and the installation was successfull!!!
> Hope this can help somebody else in the list...
>
> A.
>
>
>
> Angelo Favia wrote:
>   
>> I've got a Dell D820.
>>     I tried but it didn't fix my problem...
>> I went for the soft solution first (partial removal of the "guilty" 
>> software) and for the hard one (total removal) then.
>> The same error appears...as nothing changed.
>>
>> A.
>>
>>
>> DeLano Scientific wrote:
>>   
>>     
>>> Joris,
>>>  
>>> Some Dell systems are uniquely afflicted -- according to another Dell 
>>> XP/SP2 owner:
>>>  
>>> "I found the solution, apparently the installer gets screwed up by 
>>> some software
>>> that Dell installs as part of their standard build.   The fix can be 
>>> found at:
>>>
>>> http://www.wave.com/support/CSC/CustomerService/Documents/DM-010.htm
>>>
>>> I followed the steps in the above url and PyMol installed without a 
>>> hitch.
>>>
>>> A detailed discussion on the topic can be found at:
>>>
>>> http://forum.installsite.net/index.php?s=03b224df496bbf806744f85d27c687e9&showtopic=14905&st=0&#entry41109"
>>>  
>>> Joris, do please follow up to the list if this solves your problem...
>>>  
>>> Cheers,
>>> Delsci
>>>  
>>> ------------------------------------------------------------------------
>>> *From:* pym...@li... 
>>> [mailto:pym...@li...] *On Behalf Of 
>>> *Joris Beld
>>> *Sent:* Thursday, December 14, 2006 7:11 AM
>>> *To:* pym...@li...
>>> *Subject:* Re: [PyMOL] installation trouble
>>>
>>> Dear all,
>>> We installed yesterday six brand new Dell PCs with winXPpro/SP2 (fully 
>>> updated) and encounter exactly the same error (and also...the 
>>> solutions in the pymol wiki didn't help us so far). Anyone a solution?
>>> Thanks in advance.
>>> Best,
>>> Joris Beld
>>> Hilvert Group, ETH Zürich
>>>
>>> Angelo D Favia wrote:
>>>     
>>>       
>>>> I already tried all of the solution at the website but they didn't work 
>>>> for me.
>>>> The error message still appears.
>>>>
>>>> A.
>>>>
>>>>
>>>> DeLano Scientific wrote:
>>>>   
>>>>       
>>>>         
>>>>> <" rel="nofollow">http://www.pymolwiki.org/index.php/Windows_Install>
>>>>>  
>>>>> -----Original Message-----
>>>>> From: pym...@li...
>>>>> [mailto:pym...@li...] On Behalf Of Angelo D
>>>>> Favia
>>>>> Sent: Monday, December 11, 2006 9:39 AM
>>>>> To: pym...@li...
>>>>> Subject: [PyMOL] installation trouble
>>>>>
>>>>> Hi all,
>>>>>    I'm trying to install the latest version of pymol on my laptop (Windows
>>>>> XP pro SP2) but there seem to be something wrong.
>>>>> I get the following error message in a window whose title is "Can't run
>>>>> 16-bit Windows program": "Cannot find file
>>>>> C:\***\pymol-0_99rc6-bin-win32\SETUP.EXE (or one of its components). 
>>>>> Check to ensure the path and filename are correct and that all required
>>>>> libraries are available."
>>>>> Any clue about this error??
>>>>> thanks
>>>>>
>>>>> angelo
>>>>>
>>>>> --
>>>>> Angelo D Favia, PhD
>>>>> www.ebi.ac.uk/~afavia
>>>>>
>>>>>
>>>>> -------------------------------------------------------------------------
>>>>> Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's
>>>>> Techsay panel and you'll get the chance to share your opinions on IT &
>>>>> business topics through brief surveys - and earn cash
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>>>>> _______________________________________________
>>>>> PyMOL-users mailing list
>>>>> PyM...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>>>>
>>>>>
>>>>> -------------------------------------------------------------------------
>>>>> Take Surveys. Earn Cash. Influence the Future of IT
>>>>> Join SourceForge.net's Techsay panel and you'll get the chance to share your
>>>>> opinions on IT & business topics through brief surveys - and earn cash
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>>>>> _______________________________________________
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>>>>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>>>>
>>>>>   
>>>>>     
>>>>>         
>>>>>           
>>>>   
>>>>       
>>>>         
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>>>
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>>>   
>>>     
>>>       
>>   
>>     
>
>
>   

Frank,
 
set state, state-number, object-name

set state, obj1, 1
set state, obj2, 3

You can also use the freeze and thaw options in the object's action menu to
freeze an object into the current state independent of the global state.

Cheers,
Warren

________________________________

From: pym...@li...
[mailto:pym...@li...] On Behalf Of S. Frank Yan
Sent: Friday, December 15, 2006 4:08 PM
To: pym...@li...
Subject: [PyMOL] A suggestion on molecule selection



Hi,

 

When two SDF files, each of which contains multiple entries, are loaded, it
seems PyMOL can only display the same frames from the two objects.  It goes
like frame 1 in obj 1 and frame 1 in obj 2, and cannot do like frame 1 in
obj 1 and frame 3 in obj 2.  I was wondering if there is a way to get
around.

 

Thanks a lot,

Frank

 

Hi,

=20

When two SDF files, each of which contains multiple entries, are loaded,
it seems PyMOL can only display the same frames from the two objects.
It goes like frame 1 in obj 1 and frame 1 in obj 2, and cannot do like
frame 1 in obj 1 and frame 3 in obj 2.  I was wondering if there is a
way to get around.

=20

Thanks a lot,

Frank

=20

Matt,

Three points:

(1) PyMOL's sculpting feature isn't a forcefield, so it is best to clean up
any pose you" sculpt" with a molecular mechanics forcefield minimization
afterwards (using external software, such as the Swiss PDB viewer).

(2) Unless bonding information is provided in the file, PyMOL connects atoms
based on distances.  Depending upon your perspective, this is either an
annoying limitation or a welcome warning that the structure you've loaded is
nonphysical (or at least, far from equilibrium).

(3) To save PDB files with explicit bonding and valences using the
"multi-CONECT" convention, "set pdb_conect_all" before saving the file.
Unfortunately, this feature may be broken or missing in noncurrent builds.

Cheers,
Warren


-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of Matt Wagner
Sent: Thursday, December 14, 2006 1:03 PM
To: pym...@li...
Subject: [PyMOL] Why does the sculpting feature not work?

Hi,

I constructed a model (.pdb format) and attempted to eliminated some of the
excessive contortions in the loop when opened in PYMOL.  I was using
"Auto-sculpting" to eliminate these contortions.  All looked great, but when
I saved my work to a .pdb file and opened it back up,
it contained broken, stretched, and ugly bonds!!.    Perhaps I have am
not using the right tool for this task?   When I open my model in
Swiss PDB Viewer, all is fine.  However, I need the graphics and great
picture quality that PYMOL creates.  Can you tell me a better approach to
eliminating contortions in loops in PYMOL or perhaps another program that I
should use with just as great graphics?


Matt Wagner
The Gogonea Group
Cleveland, OH 44106
216-875-9723

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Martin,

Just FYI, the gradient display in PyMOL you and I have been working on =
is
still too immature to be considered supportable or supported.  Indeed, =
prior
to your post, you were one of the few PyMOL users even aware of it.

For everyone else, I suppose I should announce that one of the many new
features pending for PyMOL 1.0 is the ability to display fieldlines in =
maps
such as illustrated here:  <" rel="nofollow">http://pymol.sf.net/pmimag/fieldlines.jpg>  =
The
bugs are still being worked out, but usage parallels that of isomesh =
with
ramp-based coloring by map potential.  If you have SVN source, then
"gradient ?" for usage.  Note that this feature will not be supported by
DeLano Scientific until after the 1.0 release.

As for your question, "mdo" movie commands should be limited to =
localized
state changes within PyMOL.  Performing I/O or running external system =
calls
(e.g. APBS) within a movie command is likely to not work, and may cause
trouble, such crashes or hangs.

The way to approach your need is to either precompute and preload all of
your maps into PyMOL states (impractical for 600 maps), or to write a =
Python
script which takes over from PyMOL in terms of sequencing, performing
electrostatics, calculations, and rendering the movie.

Cheers,
Warren


-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of Martin
H=F6fling
Sent: Friday, December 15, 2006 8:01 AM
To: pym...@li...
Subject: [PyMOL] surface coloring fails with gradient loaded

Hi there,

i am trying to render fieldlines and sf potential together in a movie.

The movie setup is like this:

import os
set gradient_spacing=3D5
load ProtOut.pdb,prot
load trajshort.xtc,prot
mset 1 -7
show surface
set surface_solvent=3D1
for a in range(1,7): cmd.mdo(a,"delete flines;delete dxmap;delete
dxmap2;delete rmp;delete rmp2;save prot.pdb,prot;os.system(\"pdb2pqr
--ff=3Damber prot.pdb prot.pqr&>log.txt\");os.system(\"apbs
apbs.in&>log.txt\");load apbsout.dx,dxmap;load =
apbsout.dx,dxmap2;ramp_new
rmp,dxmap, [-1.5,-0.75,0];ramp_new rmp2,dxmap,[-10,0,10];gradient
flines,dxmap,-10,10,prot,carve=3D15;color rmp,flines;set
surface_color=3Drmp,prot")

set ray_trace_frames=3D1
set cache_frames=3D1
mclear

Is there anything wrong on this setup?
the surface is always white. If i do a show surface in every frame, then =
it
seems to me as if the surface is calculated for all frames (600 in =
total).=20
This is too slow to do it on every step.

Any ideas?

Cheers
	Martin

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DEVDEV
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PyM...@li...
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Hi there,

i am trying to render fieldlines and sf potential together in a movie.

The movie setup is like this:

import os
set gradient_spacing=5
load ProtOut.pdb,prot
load trajshort.xtc,prot
mset 1 -7
show surface
set surface_solvent=1
for a in range(1,7): cmd.mdo(a,"delete flines;delete dxmap;delete 
dxmap2;delete rmp;delete rmp2;save 
prot.pdb,prot;os.system(\"pdb2pqr --ff=amber prot.pdb 
prot.pqr&>log.txt\");os.system(\"apbs apbs.in&>log.txt\");load 
apbsout.dx,dxmap;load apbsout.dx,dxmap2;ramp_new rmp,dxmap,
[-1.5,-0.75,0];ramp_new rmp2,dxmap,[-10,0,10];gradient 
flines,dxmap,-10,10,prot,carve=15;color rmp,flines;set 
surface_color=rmp,prot")

set ray_trace_frames=1
set cache_frames=1
mclear

Is there anything wrong on this setup?
the surface is always white. If i do a show surface in every frame, then it 
seems to me as if the surface is calculated for all frames (600 in total). 
This is too slow to do it on every step.

Any ideas?

Cheers
	Martin