RE: [PyMOL] electron density map manipulation

[Warren D. <wa...@de...>]

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:wa...@de...      
 

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf Of 
> dieter blaas
> Sent: Friday, January 28, 2005 1:19 AM
> To: pym...@li...
> 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:wa...@de...      
> >  
> > 
> > > -----Original Message-----
> > > From: dieter blaas [mailto:die...@un...]
> > > 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:wa...@de...      
> > > >  
> > > > 
> > > > > -----Original Message-----
> > > > > From: pym...@li...
> > > > > [mailto:pym...@li...] On Behalf Of 
> > > > > Dieter Blaas
> > > > > Sent: Monday, January 24, 2005 6:54 AM
> > > > > To: pym...@li...
> > > > > 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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> > > 
> > > 
> > 
> > 
> 
>