[Jmol-users] dots surface

Hi, I noticed the dots surface (van der Waals) sometimes appears to be very sparse, particularly when the size of the displayed molecule is small. Also, in the case of Connolly surface, the reentrant surface is often shown as dark spots. Is there anyway to smooth them out? Frank

[Jmol-users] Re: Default colors by element

> >> Note also that PyMOL beta versions now match Jmol's colors >> element-for-element except for those few atomic colors previously >> defined >> in PyMOL (just C,N,O,H,S -- I think) > > For backwards compatibility with RasMol/Chime, Jmol supports the command > > set defaultColors rasmol > set def

Re: [Jmol-users] RE: [PyMOL] Default colors by element

> Note also that PyMOL beta versions now match Jmol's colors > element-for-element except for those few atomic colors previously defined > in PyMOL (just C,N,O,H,S -- I think) For backwards compatibility with RasMol/Chime, Jmol supports the command set defaultColors rasmol set defaultColors jmol

[Jmol-users] Re: corporate endorsement of Jmol

On [2005-Feb-03] Miguel <[EMAIL PROTECTED]> wrote: > Warren wrote: > > Miguel is right that companies can sometimes be sensitive to this > > information, especially early on. However, every company that makes an > > investment in deploying Jmol has a shared interest in seeing the project > > su

RE: [Jmol-users] Re: [Fwd: Change color definitions]

> Thank you very much for the reply. I'm experimenting the select feature > to change the color of atoms. From the link, > http://jmol.sourceforge.net/colors/, I was wondering if every single > element can be selected by name. I tested bromine, chlorine, etc. They > all worked. Yes, all eleme

[Jmol-users] RE: [PyMOL] Default colors by element

Note also that PyMOL beta versions now match Jmol's colors element-for-element except for those few atomic colors previously defined in PyMOL (just C,N,O,H,S -- I think) Changing those colors is simply a matter of changing the associated color name: set_color helium, [ 0.4, 0.3, 0.7] recolor Car

RE: [Jmol-users] Re: [Fwd: Change color definitions]

Thank you very much for the reply. I'm experimenting the select feature to change the color of atoms. From the link, http://jmol.sourceforge.net/colors/, I was wondering if every single element can be selected by name. I tested bromine, chlorine, etc. They all worked. > Frank wrote: > > I wa

[Jmol-users] corporate endorsement of Jmol

Warren wrote: > Miguel is right that companies can sometimes be sensitive to this > information, especially early on. However, every company that makes an > investment in deploying Jmol has a shared interest in seeing the project > succeed. I couldn't agree more. > Thus, if asked nicely, I bet t

[Jmol-users] Re: [Fwd: Change color definitions]

Frank wrote: > I was wondering if there's a way to change the default color scheme in > Jmol. I would like to use a scheme with carbon green, similar to the > default color palette in PyMOL. There is currently no way to do this on a default basis. The short-term workaround is to create a script

Re: [Jmol-users] display of multiple models

Jeremy wrote: > I hope my questions are easy but not too dumb. They are good questions. > I have searched the list > archives and not found the answers. My questions regard display of > multiple structures in the same applet, either a protein and ligand, or > a set of alternate conformations of

[Jmol-users] display of multiple models

Hi All, I hope my questions are easy but not too dumb. I have searched the list archives and not found the answers. My questions regard display of multiple structures in the same applet, either a protein and ligand, or a set of alternate conformations of the same molecule, or two overlayed mo