UPDB

Malcolm Gillies gillies@cmcind.far.ruu.nl
Mon, 31 Aug 1998 13:58:17 +0200


> Malcolm Gillies <gillies@cmcind.far.ruu.nl> wrote:
>> What did you have in mind with regard to support of the various
>> mutations of the PDB format which are read and written by various
>> modelling programs? Most of the misery I've had to deal with has
>> been a result of the quirks of the PDB handling in programs such
>> as Insight, Sybyl, DelPhi, GRASP etc.
>
> Can you give me some information about the syntax differences used
> by those programs?  Not semantics (like how atom names are done)
> because I don't attempt to address that at my level of code.  I'm
> only worried about a column delimited file format with a small set
> of fixed data types.

Unfortunately Insight's behaviour doesn't seem to be documented
properly anywhere. I'll have to do some experiments, as it's got me
completely confused.

From memory, the problem is with handling atom name information in
columns 12 and 16, and with three letter vs four letter residue names
(the fourth letter being used to indicate ionisation state, and capping).

The other programs I mentioned are more straightforward in this respect;
my main problem is getting them to talk to Insight.

Sybyl supports a number of different PDB variants; the main problem there
is with semantic differences in atom naming and chain cappin, as you
suggest.

>> number of significant characters in the atom and residue names,
>
> I knew about, and can handle, the 3 vs. 4 character residue names.
> I haven't heard about the same for atom names.  Is there a five
> character atom name used some where?  Or are you talking about
> the difference between " CA " and "CA  "?

Well, more the difference between

2HH2
 HH2
 HH22

But I'd have to check back to be certain exactly which column the
names fall into.

>   Since I am trying to be as complete as I can, can you tell me
> about those types of variations?

I will try to reverse-engineer what Insight is doing, and get back to
you.

cheers,

Malcolm