Sushmita, This looks like a truncated session file, which happens if PyMOL was quit while it was still writing a session file. Unfortunately, there is no way to recover the contents of that session.
In order to avoid this problem in the future, please take care to insure that your session file has written completely before closing the PyMOL window. Obviously, it would be better if PyMOL could take care of this this for you, but right now it doesn't...sorry! 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 > sushmita.lah...@astrazeneca.com > Sent: Monday, January 31, 2005 9:28 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Error opening saved .pse file > > > 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 > > > Send PyMOL-users mailing list submissions to > pymol-users@lists.sourceforge.net > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.sourceforge.net/lists/listinfo/pymol-users > or, via email, send a message with subject or body 'help' to > pymol-users-requ...@lists.sourceforge.net > > You can reach the person managing the list at > pymol-users-ad...@lists.sourceforge.net > > When replying, please edit your Subject line so it is more > specific than "Re: Contents of PyMOL-users digest..." > > > 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 > Content-type: text/plain; charset=US-ASCII > Content-transfer-encoding: 7BIT > Content-description: Mail message body > > 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 > Content-type: text/html; charset=US-ASCII > Content-transfer-encoding: 7BIT > 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.          60;           > </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.          60;           > </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 > style="font-size:10pt">> > > > PyMOL-users > mailing list</span></font></div> <div align="left"><font > face="Arial" color="#7f0000"><span > style="font-size:10pt">> > > > > PyMOL-users@lists.sourceforge.net</span></font></div> > <div align="left"><font face="Arial" color="#7f0000"><span > style="font-size:10pt">> > > > > https://lists.sourceforge.net/lists/listinfo/pymol-users</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">> > > </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">> > </span></font></div> <div align="left"><br/> </div> <div > align="left"></div> </body> </html> > > --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 > > > > > > > > > > > > > > > > > > ------------------------------------------------------- > > > > > > 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 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > --__--__-- > > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > End of PyMOL-users Digest >
