VMD-L Mailing List

From: oguz gurbulak (gurbulakoguz_at_yahoo.com)
Date: Tue Jan 03 2012 - 03:09:43 CST

Thanks for all replies. I successfully generated a  a representation with Create Rep selection writing "segname water" into the selected atoms bar. ________________________________ From: Adrian Roitberg <roitberg_at_ufl.edu> To: oguz gurbulak <gurbulakoguz_at_yahoo.com> Sent: Monday, January 2, 2012 11:34 PM Subject: Re: vmd-l: represent water molecules under the graphical representation create a new one named 'water' and pick vdw as the representation type. Adrian On 1/2/12 2:07 PM, oguz gurbulak wrote: > I have three different segments in psf and pdb files. One of them is > water and I want to create a picture of my system in VMD. To have a more > clear picture I should use different representations for my different > segments. For instance, segment A and C will be lines , segment B ( > water ) will be VDW or ball like drawing method like ions. Is it > possible to generate a picture that is similar to that in VMD ? > Thanks for your help. > *From:* Axel Kohlmeyer <akohlmey_at_gmail.com> > *To:* oguz gurbulak <gurbulakoguz_at_yahoo.com> > *Cc:* "vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu> > *Sent:* Monday, January 2, 2012 7:42 PM > *Subject:* Re: vmd-l: represent water molecules > > On Mon, 2012-01-02 at 03:48 -0800, oguz gurbulak wrote: >  > Dear VMD users, >  > >  > >  > How can I represent water molecules ( or any segment in pdb file ) >  > with red balls ( ball representation ) in VMD ? > > there is no representation in VMD called "ball". > > you have to be a bit more specific what > you are looking for. > > please always keep in mind that the quality > of answers to a question depends very much > on the quality of the question. > > axel. > >  > >  > >  > >  > Thanks for your help. >  > >  > >  > >  > >  > >  > > > -- > Dr. Axel Kohlmeyer > akohlmey_at_gmail.com <mailto:akohlmey_at_gmail.com> http://goo.gl/1wk0 > College of Science and Technology, > Institute for Computational Molecular Science, > Temple University, Philadelphia PA, USA. > > > --                             Dr. Adrian E. Roitberg                                   Professor                 Quantum Theory Project, Department of Chemistry                             University of Florida                               roitberg_at_ufl.edu