VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon May 07 2018 - 16:49:44 CDT

Yes, that should work...

Best,
  John

On Mon, May 07, 2018 at 11:31:37PM +0200, Daniel Möller wrote:
> Hi,
> thanks. I'll test in the next days.
>
> Could I use the clipplane for truncatted CPK or VMD, too. So I don't have
> the black cut edge?
>
> Sincerely
>
> Daniel Möller
>
>
> -----Ursprüngliche Nachricht-----
> Von: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] Im Auftrag von
> John Stone
> Gesendet: Montag, 7. Mai 2018 21:41
> An: Daniel Möller
> Cc: vmd-l_at_ks.uiuc.edu
> Betreff: Re: vmd-l: A fill for "bodies" build out of surfacs
>
> Hi,
> You can do this with VMD if you render the resulting image with POV-Ray,
> as described in the VMD images and movies tutorial here:
>
> http://www.ks.uiuc.edu/Training/Tutorials/vmd-imgmv/imgmv/tutorial-html/node
> 2.html#SECTION00026000000000000000
>
> In addition to the "mol clipplane" command, there's an interactive
> "clipping plane tool" available in the Extensions | Visualization menu
> that should be able to set the solid clipping plane mode also.
>
> Best,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Mon, May 07, 2018 at 12:12:40PM +0200, Daniel Möller wrote:
> > Hi,
> >
> >
> >
> > I saw in publications pictures of cut proteins only displayed as
> surface,
> > where the inside of this body is filled with the surface color
> (excluding
> > shadows and similar fancy stuff).
> >
> > So its looks like you just cut a completely filled body (see:
> > [1]https://onlinelibrary.wiley.com/doi/full/10.1002/anie.201412070 Fig.
> 15
> > a)
> >
> > In VMD you've a black nothingness or the other side of the surface with
> > every fancy stuff, you are using.
> >
> >
> >
> > So my question are:
> >
> > Is it possible to get the same full body look in VMD? And if yes, how?
> >
> >
> >
> > Sincerely
> >
> >
> >
> > Daniel Möller
> >
> >
> >
> > --
> >
> > ------------------------
> >
> > Dipl. Biochem. Daniel Möller
> >
> >
> >
> > Bio-physical Chemistry
> >
> > Institute of Biochemie
> >
> > Unversity Greifswald
> >
> > Felix-Hausdorff-Strasse 4
> >
> > 17489 Greifswald, Germany
> >
> >
> >
> > Tel +49 3834 420 4406 (new)
> >
> >
> >
> >
> [2]https://biochemie.uni-greifswald.de/institut/forschung/forschung-in-den-a
> rbeitskreisen/ordner-aks-lehrstuehle/biophysikalische-chemie/
> >
> >
> >
> >
> >
> > References
> >
> > Visible links
> > 1.
> https://urldefense.proofpoint.com/v2/url?u=https-3A__onlinelibrary.wiley.com
> _doi_full_10.1002_anie.201412070&d=DwMFAw&c=OCIEmEwdEq_aNlsP4fF3gFqSN-E3mlr2
> t9JcDdfOZag&r=JBqQLS7jZ5whrB0hXJY8MNYcfDrh8UhlGJ2ANxoi8s0&m=k86GaYv5UtzgAgiz
> a8185oHU9-vkaDYRTrv6JzHjAkk&s=y6QseRqUYDaNeT4LdyKJSPup3mrzXY5lV7b_wKQ0Se0&e=
> > 2.
> https://urldefense.proofpoint.com/v2/url?u=https-3A__biochemie.uni-2Dgreifsw
> ald.de_institut_forschung_forschung-2Din-2Dden-2Darbeitskreisen_ordner-2Daks
> -2Dlehrstuehle_biophysikalische-2Dchemie_&d=DwMFAw&c=OCIEmEwdEq_aNlsP4fF3gFq
> SN-E3mlr2t9JcDdfOZag&r=JBqQLS7jZ5whrB0hXJY8MNYcfDrh8UhlGJ2ANxoi8s0&m=k86GaYv
> 5UtzgAgiza8185oHU9-vkaDYRTrv6JzHjAkk&s=SglyqPw55Aj8gGXrVFfGpKCOoDo-MFtHu83jq
> IHuUYw&e=
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/
>
> 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/