PDB dump format

ilya ily... at gmail.com
Sun Oct 12 08:22:19 UTC 2008

Thanks Teo.

PS Well, they do ask a lot of money for their products, but the viewer
is available freely.

On Oct 12, 2:52 am, Laino Teodoro <teodor... at gmail.com> wrote:
> On 12 Oct 2008, at 00:01, ilya wrote:
> > OK... may be it's stupid viewers (accelrys!!!) because they don't know
> > about symbol field, but it would be nice to correct this for fast
> > viewing (and make it more std complaint).
> > The easy solution it just print everything left aligned (although it's
> > not strict standard complaint, most viewers understand it)
> > The second solution is to parse the name (in case input specified not
> > in pdb) and print according to the std, but maybe it's complex and
> > redundant.
> you're right.. we don't fully map the standard in writing the PDB.
> Regarding the issue you mentioned, I think that left justify  
> everything is the way to go. In fact:
> 1) input names may not necessarily reflect the standard i.e. the  
> first two
> characters may not be necessarily connected to the element symbol..
> that's a quite common practice..
> 2) it's only about dumping of PDB and more than worry on accelrys I'm  
> worried
> about what the other viewers like VMD, molekel or molden do. It does  
> not make any
> sense to spend too much time just to make accelrys happy.
> Anyway, field 13:16 is now left justified (in CVS).
> in case it should not solve the issue, since they ask you quite a  
> consistent
> amount of money for their products I suggest you to fill in a  
> customer complain.
> Maybe they will discover the existence of the field in the column  
> 77-78 ;-)
> Teo

More information about the CP2K-user mailing list