VMD-L Mailing List

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Wed Feb 02 2011 - 22:45:23 CST

That's why the command is called pdbalias - it only affects reading a
sequence or coordinates from a PDB file. If you have the data in some
other form it's possible to do these substitutions another way.

For a sequence in a Tcl list:
   foreach i [lsearch -all $seq HIS] { lset seq $i HSD }

For a structure in VMD:
   set sel [atomselect top "resname ILE name CD1"]
   $sel set name CD
   $sel delete

Note that pdbalias handles swapping names, which would require some care
in the above methods (do both searches before assigning new names).

Implementing pdbalias residue for the residue command would be trivial.

Implementing pdbalias atom for the coord command is trickier because if
you alias an atom in an aliased residue there is no record of the original
residue name like you have when reading the same pdb file. (The coord
command just takes segname, resid, and atomname.) So doing:

   pdbalias atom HIS CD1 CD
   pdbalias residue HIS HSD

would work when reading from a pdb file but for the coord command you
would need to use the resname that matches the topolgy file (this would
also work for the pdb file, since that code searches both ways):

   pdbalias atom HSD CD1 CD

So the question is, what's your use case where you need pdbalias to apply
to residue and coord commands and you can cope with the above anomaly?

-Jim

On Wed, 2 Feb 2011, Seth Tanner wrote:

> Dear psfgen developers,
>
> I want to point out a minor but still an important detail that lacks
> in the psfgen1.4 implementation.
>
> The program gives the users the ability to define their sequences on
> their own. However there are 'alias' commands working only if the
> sequence or the coordinates are supplied from a PDB file. That is, the
> following code is not usable when you use information external to a
> PDB file.
> ******************
> pdbalias atom ILE CD1 CD
> pdbalias residue HIS HSD
> ******************
> I hope this utility would be available in the next version.
>
> Thanks for reading,
>
> Seth
>