[CP2K:1438] PDB dump format

Laino Teodoro teodor... at gmail.com
Sat Oct 11 22:52:04 UTC 2008

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  
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  
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 ;-)

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