psfgen for DNA

From: Nicholas M Glykos (
Date: Mon Mar 21 2005 - 10:20:49 CST

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 ?


            Dr Nicholas M. Glykos, Department of Molecular 
        Biology and Genetics, Democritus University of Thrace,
    Dimitras 19, 68100 Alexandroupolis, GREECE, Fax ++302551030613
     Tel ++302551030620 (77620),

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