[gmx-users] more questions on g_coar and g_anaeig

[Anton Feenstra]

Q.Z. wrote:

> Sorry. I should put all my related questions in one message.
> I wonder if anyone know how display C-alpha trace of a protein. I did 
> covariance analysis on C-alpha and got pdb files only containing CA's. 
> Many graphic programs do not show them. Should I do covariance on all 
> atomes instead? Thanks.

Most programs I know (like rasmol, molscript or Insight), recognize a
'Ca-only' structure and will show you a C-a trace or ribbon. There may
be a 'morph' option in one of the programs (or a separate program from
one of the Gromacs users), that will shape your whole protein to fit
onto the Ca coordinates...


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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