From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Mon Mar 21 2005 - 11:51:21 CST
The nucleic selection is a macro with the definition hardcoded into vmd.
It may not be flexible enough to understand all "patched" resnames
Brian
PS you will get more publicity on the vmd-l_at_ks.uiuc.ed
email list
On Mon, 21 Mar 2005, Nicholas M Glykos wrote:
>
> Dear All,
>
> A quick question :
>
> We use psfgen to prepare a DNA system. When we apply the 5TER patch with
> something like
>
> ....
> segment A {
> first 5TER
> last 3TER
> pdb A.pdb
> }
> ....
>
> and then view the resulting pdb & psf files using VMD and selecting "all"
> atoms, all looks fine. But if we select "nucleic" the termini disappear as
> if not recognised as being 'nucleic'. If instead of '5TER' we use the
> '5PHO' patch, the termini are recognised by the "nucleic" selection.
> Is this a feature of VMD (interpreting the word 'nucleic' sensus
> strictus), or we are missing something here ?
>
> Thanks,
> Nicholas
>
>
> --
>
>
> Dr Nicholas M. Glykos, Department of Molecular
> Biology and Genetics, Democritus University of Thrace,
> Dimitras 19, 68100 Alexandroupolis, GREECE, Fax ++302551030613
> Tel ++302551030620 (77620), http://www.mbg.duth.gr/~glykos/
>
************************************************
Brian Bennion, Ph.D.
Bioscience Directorate
Lawrence Livermore National Laboratory
P.O. Box 808, L-448 bennion1_at_llnl.gov
7000 East Avenue phone: (925) 422-5722
Livermore, CA 94550 fax: (925) 424-6605
************************************************
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