[PyMOL] Error opening saved .pse file

Sushmita . Lahiri Mon, 31 Jan 2005 09:28:38 -0800

Hi,

I am trying to open a *.pse file and I keep getting the following error:



Error: 1
EOFError Exception in Tk callback
  Function: <bound method PMGApp.file_open of <pmg_tk.PMGApp.PMGApp instance
at 0x08EDA3A0>> (type: <type 'instancemethod'>)
  Args: ()
Traceback (innermost last):
  File "C:\Program Files\DeLano
Scientific\PyMOL/modules\Pmw\Pmw_1_2\lib\PmwBase.py", line 1747, in __call__
    return apply(self.func, args)
  File "C:\Program Files\DeLano Scientific\PyMOL/modules\pmg_tk\PMGApp.py",
line 411, in file_open
    cmd.load(ofile)
  File "C:\Program Files\DeLano
Scientific\PyMOL/modules\pymol\importing.py", line 528, in load
    cmd.set_session(io.pkl.fromFile(fname))
  File "C:\Program Files\DeLano Scientific\PyMOL/modules\chempy\pkl.py",
line 24, in fromFile
    result = cPickle.load(fp)
EOFError: 


Please help!!!


Thanks in advance,
-Sushmita


-----Original Message-----
From: [email protected]
[mailto:[email protected]]
Sent: Monday, January 31, 2005 1:59 AM
To: [email protected]
Subject: PyMOL-users digest, Vol 1 #802 - 2 msgs


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Today's Topics:

   1. RE: electron density map manipulation (dieter blaas)
   2. RE: electron density map manipulation (Warren DeLano)

--__--__--

Message: 1
From: "dieter blaas" <[email protected]>
To: [email protected]
Date: Fri, 28 Jan 2005 10:18:41 +0100
Subject: RE: [PyMOL] electron density map manipulation
Reply-to: [email protected]
CC: "Warren DeLano" <[email protected]>

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Thanx Warren, perfect! But when entering:

"> load map1.dsn6
> slice_new slice1,map1

I get the message:
Syntax Error: invalid syntax with a ^ pointing to the "1" in slice1
I have tried several permutations of the syntax, but always receive an 
error message!
 
On 27 Jan 2005 at 22:51, Warren DeLano wrote:

> > 1/ can I make a solid surface?
> 
> Solid (opaque) surface with isosurface command (just like isomesh)
> 
> > 2/ can I make volume slices?
> 
> Slices are possible:
> 
> load map1.dsn6
> slice_new slice1,map1
> ramp_new ramp1,map1
> color ramp1, slice1
> 
> Then ctrl-middle-click and drag to change slice contour coloring
> 
> > 3/ can I load the map in the same way I load pdb files 
> > without command line input and manipulate the parameters with 
> > the mouse?
> 
> Not yet.
> 
> > is it O.K. to answer in this way or should I send the mail to 
> > the mailing list?
> 
> The mailing list is preferable.
> 
> 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:[email protected]      
>  
> 
> > -----Original Message-----
> > From: dieter blaas [mailto:[email protected]] 
> > Sent: Thursday, January 27, 2005 9:20 PM
> > To: Warren DeLano
> > Subject: RE: [PyMOL] electron density map manipulation
> > 
> > Thanx a lot, this works! I have three additional questions:
> > 1/ can I make a solid surface?
> > 2/ can I make volume slices?
> > 3/ can I load the map in the same way I load pdb files 
> > without command line input and manipulate the parameters with 
> > the mouse?
> > 
> > is it O.K. to answer in this way or should I send the mail to 
> > the mailing list?
> > Dieter
> > 
> > 
> > On 27 Jan 2005 at 16:49, Warren DeLano wrote:
> > 
> > > Dieter,
> > > 
> > > Have you tried the isomesh and isosurf commands?
> > > 
> > > load map1.dsn6, map1
> > > isomesh mesh1, map1, 1.0
> > > 
> > > 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:[email protected]      
> > >  
> > > 
> > > > -----Original Message-----
> > > > From: [email protected] 
> > > > [mailto:[email protected]] On Behalf Of 
> > > > Dieter Blaas
> > > > Sent: Monday, January 24, 2005 6:54 AM
> > > > To: [email protected]
> > > > Subject: [PyMOL] electron density map manipulation
> > > > 
> > > > Hi, I have been trying to visualize a DN6 electron density 
> > > > map. Although it is read in apparently correctly nothing 
> > > > shows on the screen. Are there any particular parameters to 
> > > > be set? I can visualize it in SwisspdbViewer but I was unable 
> > > > to produce surface rendering. Can Pymol produce a surface at 
> > > > a particular cut-off value as can Amira?
> > > > Thanx for hints, Dieter
> > > > 
> > > > 
> > > > -------------------------------------------------------
> > > > This SF.Net email is sponsored by: IntelliVIEW -- Interactive 
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> > > > _______________________________________________
> > > > PyMOL-users mailing list
> > > > [email protected]
> > > > https://lists.sourceforge.net/lists/listinfo/pymol-users
> > > > 
> > > 
> > > 
> > 
> > 
> > 
> 
> 



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<?xml  version="1.0" ?><html>
<head>
<title></title>
</head>
<body>
<div align="left"><font face="Arial"><span style="font-size:10pt">Thanx
Warren, perfect! But when entering:</span></font></div>
<div align="left"><br/></div>
<div align="left"><font face="Arial"><span
style="font-size:10pt">&quot;</span></font><font face="Arial"
color="#7f0000"><span style="font-size:10pt">&gt; load
map1.dsn6</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; slice_new slice1,map1</span></font></div>
<div align="left"><br/>
</div>
<div align="left"><font face="Arial"><span style="font-size:10pt">I get the
message:</span></font></div>
<div align="left"><font face="Arial"><span style="font-size:10pt">Syntax
Error: invalid syntax with a ^ pointing to the &quot;1&quot; in
slice1</span></font></div>
<div align="left"><font face="Arial"><span style="font-size:10pt">I have
tried several permutations of the syntax, but always receive an 
error message!</span></font></div>
<div align="left"><font face="Arial"><span style="font-size:10pt">
</span></font></div>
<div align="left"><font face="Arial"><span style="font-size:10pt">On 27 Jan
2005 at 22:51, Warren DeLano wrote:</span></font></div>
<div align="left"><br/>
</div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; 1/ can I make a solid
surface?</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; Solid (opaque) surface with isosurface command
(just like isomesh)</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; 2/ can I make volume
slices?</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; Slices are possible:</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; load map1.dsn6</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; slice_new slice1,map1</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; ramp_new ramp1,map1</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; color ramp1, slice1</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; Then ctrl-middle-click and drag to change slice
contour coloring</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; 3/ can I load the map in the same way I
load pdb files </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; without command line input and manipulate
the parameters with </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; the mouse?</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; Not yet.</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; is it O.K. to answer in this way or should
I send the mail to </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; the mailing list?</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; The mailing list is
preferable.</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; Cheers,</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; Warren</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; --</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; Warren L. DeLano,
Ph.D.&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160
;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160; </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; Principal Scientist</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; . DeLano Scientific LLC&#160;
</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; . 400 Oyster Point Blvd., Suite
213&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;
</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; . South San Francisco, CA
94080&#160;&#160;&#160; </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; . Biz:(650)-872-0942&#160;
Tech:(650)-872-0834&#160;&#160;&#160;&#160; </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; . Fax:(650)-872-0273&#160;
Cell:(650)-346-1154</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; .
mailto:[email protected]&#160;&#160;&#160;&#160;&#160; </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt;&#160; </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; -----Original
Message-----</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; From: dieter blaas
[mailto:[email protected]] </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; Sent: Thursday, January 27, 2005 9:20
PM</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; To: Warren DeLano</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; Subject: RE: [PyMOL] electron density map
manipulation</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; Thanx a lot, this works! I have three
additional questions:</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; 1/ can I make a solid
surface?</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; 2/ can I make volume
slices?</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; 3/ can I load the map in the same way I
load pdb files </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; without command line input and manipulate
the parameters with </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; the mouse?</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; is it O.K. to answer in this way or should
I send the mail to </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; the mailing list?</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; Dieter</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; On 27 Jan 2005 at 16:49, Warren DeLano
wrote:</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; &gt; Dieter,</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; &gt; </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; &gt; Have you tried the isomesh and isosurf
commands?</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; &gt; </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; &gt; load map1.dsn6,
map1</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; &gt; isomesh mesh1, map1,
1.0</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; &gt; </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; &gt; Cheers,</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; &gt; Warren</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; &gt; </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; &gt; --</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; &gt; Warren L. DeLano,
Ph.D.&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160
;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160; </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; &gt; Principal
Scientist</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; &gt; </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; &gt; . DeLano Scientific LLC&#160;
</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; &gt; . 400 Oyster Point Blvd., Suite
213&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;
</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; &gt; . South San Francisco, CA
94080&#160;&#160;&#160; </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; &gt; . Biz:(650)-872-0942&#160;
Tech:(650)-872-0834&#160;&#160;&#160;&#160; </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; &gt; . Fax:(650)-872-0273&#160;
Cell:(650)-346-1154</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; &gt; .
mailto:[email protected]&#160;&#160;&#160;&#160;&#160; </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; &gt;&#160; </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; &gt; </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; &gt; &gt; -----Original
Message-----</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; &gt; &gt; From:
[email protected] </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; &gt; &gt;
[mailto:[email protected]] On Behalf Of
</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; &gt; &gt; Dieter Blaas</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; &gt; &gt; Sent: Monday, January 24, 2005
6:54 AM</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; &gt; &gt; To:
[email protected]</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; &gt; &gt; Subject: [PyMOL] electron density
map manipulation</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; &gt; &gt; </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; &gt; &gt; Hi, I have been trying to
visualize a DN6 electron density </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; &gt; &gt; map. Although it is read in
apparently correctly nothing </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; &gt; &gt; shows on the screen. Are there
any particular parameters to </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; &gt; &gt; be set? I can visualize it in
SwisspdbViewer but I was unable </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; &gt; &gt; to produce surface rendering. Can
Pymol produce a surface at </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; &gt; &gt; a particular cut-off value as can
Amira?</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; &gt; &gt; Thanx for hints,
Dieter</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; &gt; &gt; </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">&gt; &gt; &gt; &gt; </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
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Message: 2
From: "Warren DeLano" <[email protected]>
To: <[email protected]>,
        <[email protected]>
Subject: RE: [PyMOL] electron density map manipulation
Date: Sun, 30 Jan 2005 10:19:30 -0800

Dieter,

Slices are a relatively new feature only found in the beta versions:

http://delsci.com/beta
http://delsci.com/macbeta

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:[email protected]      
 

> -----Original Message-----
> From: [email protected] 
> [mailto:[email protected]] On Behalf Of 
> dieter blaas
> Sent: Friday, January 28, 2005 1:19 AM
> To: [email protected]
> Cc: Warren DeLano
> Subject: RE: [PyMOL] electron density map manipulation
> 
> Thanx Warren, perfect! But when entering:
> 
> "> load map1.dsn6
> > slice_new slice1,map1
> 
> I get the message:
> Syntax Error: invalid syntax with a ^ pointing to the "1" in 
> slice1 I have tried several permutations of the syntax, but 
> always receive an error message!
> On 27 Jan 2005 at 22:51, Warren DeLano wrote:
> 
> > > 1/ can I make a solid surface?
> > 
> > Solid (opaque) surface with isosurface command (just like isomesh)
> > 
> > > 2/ can I make volume slices?
> > 
> > Slices are possible:
> > 
> > load map1.dsn6
> > slice_new slice1,map1
> > ramp_new ramp1,map1
> > color ramp1, slice1
> > 
> > Then ctrl-middle-click and drag to change slice contour coloring
> > 
> > > 3/ can I load the map in the same way I load pdb files without 
> > > command line input and manipulate the parameters with the mouse?
> > 
> > Not yet.
> > 
> > > is it O.K. to answer in this way or should I send the mail to the 
> > > mailing list?
> > 
> > The mailing list is preferable.
> > 
> > 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:[email protected]      
> >  
> > 
> > > -----Original Message-----
> > > From: dieter blaas [mailto:[email protected]]
> > > Sent: Thursday, January 27, 2005 9:20 PM
> > > To: Warren DeLano
> > > Subject: RE: [PyMOL] electron density map manipulation
> > > 
> > > Thanx a lot, this works! I have three additional questions:
> > > 1/ can I make a solid surface?
> > > 2/ can I make volume slices?
> > > 3/ can I load the map in the same way I load pdb files without 
> > > command line input and manipulate the parameters with the mouse?
> > > 
> > > is it O.K. to answer in this way or should I send the mail to the 
> > > mailing list?
> > > Dieter
> > > 
> > > 
> > > On 27 Jan 2005 at 16:49, Warren DeLano wrote:
> > > 
> > > > Dieter,
> > > > 
> > > > Have you tried the isomesh and isosurf commands?
> > > > 
> > > > load map1.dsn6, map1
> > > > isomesh mesh1, map1, 1.0
> > > > 
> > > > 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:[email protected]      
> > > >  
> > > > 
> > > > > -----Original Message-----
> > > > > From: [email protected]
> > > > > [mailto:[email protected]] On Behalf Of 
> > > > > Dieter Blaas
> > > > > Sent: Monday, January 24, 2005 6:54 AM
> > > > > To: [email protected]
> > > > > Subject: [PyMOL] electron density map manipulation
> > > > > 
> > > > > Hi, I have been trying to visualize a DN6 electron 
> density map. 
> > > > > Although it is read in apparently correctly nothing 
> shows on the 
> > > > > screen. Are there any particular parameters to be set? I can 
> > > > > visualize it in SwisspdbViewer but I was unable to produce 
> > > > > surface rendering. Can Pymol produce a surface at a 
> particular 
> > > > > cut-off value as can Amira?
> > > > > Thanx for hints, Dieter
> > > > > 
> > > > > 
> > > > > -------------------------------------------------------
> > > > > This SF.Net email is sponsored by: IntelliVIEW -- Interactive 
> > > > > Reporting Tool for open source databases. Create drag-&-drop 
> > > > > reports. Save time by over 75%! Publish reports on the web.
> > > > > Export to DOC, XLS, RTF, etc.
> > > > > Download a FREE copy at http://www.intelliview.com/go/osdn_nl
> > > > > _______________________________________________
> > > > > PyMOL-users mailing list
> > > > > [email protected] 
> > > > > https://lists.sourceforge.net/lists/listinfo/pymol-users
> > > > > 
> > > > 
> > > > 
> > > 
> > > 
> > > 
> > 
> > 
> 
> 





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