Re: [ccp4bb] PDB SEGID Case Sensitivity

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

- CCP4BB

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: PDB SEGID Case Sensitivity
From: James Stroud xtald00d {- at -} GMAIL {- dot -} COM
Date: 2010-02-03

Next message:
Subject: Re: PDB SEGID Case Sensitivity
From: James Stroud xtald00d {- at -} GMAIL {- dot -} COM
Date: 2010-02-03

Subject: Re: PDB SEGID Case Sensitivity
From: Ethan Merritt merritt {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2010-02-03

On Wednesday 03 February 2010 15:59:26 James Stroud wrote:
> Hello All,
>
> In typically comical fashion, the PDB specification 3.2 at http://www.wwpdb.org/documentation/format32/sect9.html
> leaves out columns 67-76 for ATOM and HETATM records.
>
> Since I can only conclude that SEGIDs must be one of those "grey
> areas", I thought I'd make a multiple choice survey and go with the
> quorum opinion.
>
> Please respond with the most correct answer so I know how to proceed:
>
>
> What is the general status of case sensitivity of SEGID in PDB
> file formats?

"Don't ask; don't tell"

PDB sanction of SEGID has been an on-again off-again thing.

In 1999 they said:
] We propose to discontinue support for this identifier in files
] that are processed and released into the archive. No format
] changes are proposed here, we will simply place blanks in any
] SEGID fields.

So far as I know, the PDB/RCSB folks do not even look at these columns.
So it comes down to a question of individual non-PDB programs.
Which program were you wondering about?

> 1. Gee, I thought that it was specified to be case sensitive.
> 2. Well, someone once told me that it was specified to be
> case insensitive but I can't remember who that was.
> 3. I thought it was specified to be something too but
> most programs largely ignore specifications in my experience.
> 4. Specifications are for sissies, real crystallographers
> don't depend on them.
>
>
> Thank you in advance for taking the time to participate.
>
> James
>

--
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: PDB SEGID Case Sensitivity
From: James Stroud xtald00d {- at -} GMAIL {- dot -} COM
Date: 2010-02-03

Next message:
Subject: Re: PDB SEGID Case Sensitivity
From: James Stroud xtald00d {- at -} GMAIL {- dot -} COM
Date: 2010-02-03