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: pymol-users-requ...@lists.sourceforge.net
[mailto:pymol-users-requ...@lists.sourceforge.net]
Sent: Monday, January 31, 2005 1:59 AM
To: pymol-users@lists.sourceforge.net
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" <dieter.bl...@univie.ac.at>
To: pymol-users@lists.sourceforge.net
Date: Fri, 28 Jan 2005 10:18:41 +0100
Subject: RE: [PyMOL] electron density map manipulation
Reply-to: dieter.bl...@univie.ac.at
CC: "Warren DeLano" <war...@delanoscientific.com>
--Alt-Boundary-8494.13938296
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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:war...@delsci.com
>
>
> > -----Original Message-----
> > From: dieter blaas [mailto:dieter.bl...@univie.ac.at]
> > 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:war...@delsci.com
> > >
> > >
> > > > -----Original Message-----
> > > > From: pymol-users-ad...@lists.sourceforge.net
> > > > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
> > > > Dieter Blaas
> > > > Sent: Monday, January 24, 2005 6:54 AM
> > > > To: pymol-users@lists.sourceforge.net
> > > > 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
> > > > PyMOL-users@lists.sourceforge.net
> > > > https://lists.sourceforge.net/lists/listinfo/pymol-users
> > > >
> > >
> > >
> >
> >
> >
>
>
--Alt-Boundary-8494.13938296
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Content-description: Mail message body
<?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">"</span></font><font face="Arial"
color="#7f0000"><span style="font-size:10pt">> load
map1.dsn6</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> 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 "1" 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">> > 1/ can I make a solid
surface?</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> 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">> </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > 2/ can I make volume
slices?</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> Slices are possible:</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> load map1.dsn6</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> slice_new slice1,map1</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> ramp_new ramp1,map1</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> color ramp1, slice1</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> 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">> </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > 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">> > 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">> > the mouse?</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> Not yet.</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > 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">> > the mailing list?</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> The mailing list is
preferable.</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> Cheers,</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> Warren</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> --</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> Warren L. DeLano,
Ph.D.            
;         </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> Principal Scientist</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> . DeLano Scientific LLC 
</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> . 400 Oyster Point Blvd., Suite
213          
</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> . South San Francisco, CA
94080    </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> . Biz:(650)-872-0942 
Tech:(650)-872-0834     </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> . Fax:(650)-872-0273 
Cell:(650)-346-1154</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> .
mailto:war...@delsci.com      </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">>  </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > -----Original
Message-----</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > From: dieter blaas
[mailto:dieter.bl...@univie.ac.at] </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > Sent: Thursday, January 27, 2005 9:20
PM</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > To: Warren DeLano</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > Subject: RE: [PyMOL] electron density map
manipulation</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > 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">> > 1/ can I make a solid
surface?</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > 2/ can I make volume
slices?</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > 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">> > 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">> > the mouse?</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > 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">> > the mailing list?</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > Dieter</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > 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">> > </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > Dieter,</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > Have you tried the isomesh and isosurf
commands?</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > load map1.dsn6,
map1</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > isomesh mesh1, map1,
1.0</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > Cheers,</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > Warren</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > --</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > Warren L. DeLano,
Ph.D.            
;         </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > Principal
Scientist</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > . DeLano Scientific LLC 
</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > . 400 Oyster Point Blvd., Suite
213          
</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > . South San Francisco, CA
94080    </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > . Biz:(650)-872-0942 
Tech:(650)-872-0834     </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > . Fax:(650)-872-0273 
Cell:(650)-346-1154</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > .
mailto:war...@delsci.com      </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > >  </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > > -----Original
Message-----</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > > From:
pymol-users-ad...@lists.sourceforge.net </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > >
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > > Dieter Blaas</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > > Sent: Monday, January 24, 2005
6:54 AM</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > > To:
pymol-users@lists.sourceforge.net</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > > Subject: [PyMOL] electron density
map manipulation</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > > </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > > 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">> > > > 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">> > > > 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">> > > > 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">> > > > 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">> > > > a particular cut-off value as can
Amira?</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > > Thanx for hints,
Dieter</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > > </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > > </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > >
-------------------------------------------------------</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > > This SF.Net email is sponsored
by: IntelliVIEW -- Interactive </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > > Reporting Tool for open source
databases. Create drag-&-drop </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > > reports. Save time by over 75%!
Publish reports on the web. </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > > Export to DOC, XLS, RTF,
etc.</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > > Download a FREE copy at
http://www.intelliview.com/go/osdn_nl</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > >
_______________________________________________</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
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--Alt-Boundary-8494.13938296--
--__--__--
Message: 2
From: "Warren DeLano" <war...@delanoscientific.com>
To: <dieter.bl...@univie.ac.at>,
<pymol-users@lists.sourceforge.net>
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:war...@delsci.com
> -----Original Message-----
> From: pymol-users-ad...@lists.sourceforge.net
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
> dieter blaas
> Sent: Friday, January 28, 2005 1:19 AM
> To: pymol-users@lists.sourceforge.net
> 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:war...@delsci.com
> >
> >
> > > -----Original Message-----
> > > From: dieter blaas [mailto:dieter.bl...@univie.ac.at]
> > > 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:war...@delsci.com
> > > >
> > > >
> > > > > -----Original Message-----
> > > > > From: pymol-users-ad...@lists.sourceforge.net
> > > > > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
> > > > > Dieter Blaas
> > > > > Sent: Monday, January 24, 2005 6:54 AM
> > > > > To: pymol-users@lists.sourceforge.net
> > > > > 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
> > > > >
> > > > >
> > > > > -------------------------------------------------------
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> > > > > _______________________________________________
> > > > > PyMOL-users mailing list
> > > > > PyMOL-users@lists.sourceforge.net
> > > > > https://lists.sourceforge.net/lists/listinfo/pymol-users
> > > > >
> > > >
> > > >
> > >
> > >
> > >
> >
> >
>
>
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