Dear Martyn, Pavel and other interested,
I think, an official extension by the PDB to two characters for the
chain names and 5 digits for residues would really help. I'm currently
working on a structure with 6x15 chains (through NCS) - it is huge and
only a few programs can handle this by extending the PDB format.
The last PDB format revision 3.3
<http://www.wwpdb.org/documentation/format33/sect9.html#ATOM> still only
allows one character for the chain name and four digits for the residue
number.
More bigger structures will be published in the future and an official
human-readable extended PDB format would really help.
Cheers,
Dirk.
Am 30.08.13 18:14, schrieb MARTYN SYMMONS:
Hold your horsemen!
Does not this option save us from 'formatagedon'?
We currently only have single letters or numbers for chains. But we
could easily agree to switch to double letters. And long chains can be
a sequence of letter number permutations such as A1, A2, A3 etc
(actually I notice single numbers are allowed for the PDB - although
are deprecated until all the letters have been used).
We could allow the first character to be a number as well - so 11 12
13 as a valid sequence.for a single polymer.
Conversely we could expand the atom identifier to include letters as
is the case with most computing identifiers - however not many
programs seem to pay attention to the atom 'numbers' in any case.
Cheers
Martyn
Martyn Symmons (not Winn)
Cambridge
------------------------------------------------------------------------
*From:* Dirk Kostrewa <[email protected]>
*To:* [email protected]
*Sent:* Friday, 30 August 2013, 15:36
*Subject:* Re: [ccp4bb] Fractional coordinate shift with two-character
chain names?
Hi Martyn,
excellent - this worked!
Many thanks!
Cheers,
Dirk.
Am 30.08.13 16:04, schrieb Martyn Winn:
> IIRC the CCP4 library (i.e. mmdb) can handle 2-character chain
names. There may be something specific in pdbset which interferes. You
can try pdbcur as an alternative. Something like:
>
> pdbcur xyzin toxd_AA.pdb xyzout toxd_out.pdb <<eof
> translate * frac 0 0.2 0
> end
> eof
>
> I just tried it on a little example, and it works for me.
>
> Cheers
> Martyn
>
>> -----Original Message-----
>> From: CCP4 bulletin board [mailto:[email protected]
<mailto:[email protected]>] On Behalf Of
>> Dirk Kostrewa
>> Sent: 30 August 2013 14:41
>> To: ccp4bb
>> Subject: [ccp4bb] Fractional coordinate shift with two-character chain
>> names?
>>
>> Dear CCP4ers,
>>
>> I want to apply a fractional coordinate shift along a polar b-axis with
>> coordinates that have non-standard two-character chain names, such as
>> "AA", "AB", and so forth. Unfortunately, neither the old USF moleman2
>> nor the actual CCP4 pdbset can handle these chain names. To my
>> knowledge, only COOT and PHENIX can cope with them.
>> Before I start writing my own little jiffy, is there a quick way to use
>> COOT or PHENIX to apply a fractional coordinate shift, or could you
>> tell me, which other program I can use in this special case?
>>
>> Best regards,
>>
>> Dirk.
>>
>> --
>>
>> *******************************************************
>> Dirk Kostrewa
>> Gene Center Munich
>> Department of Biochemistry
>> Ludwig-Maximilians-Universität München
>> Feodor-Lynen-Str. 25
>> D-81377 Munich
>> Germany
>> Phone: +49-89-2180-76845
>> Fax: +49-89-2180-76999
>> E-mail: [email protected] <mailto:[email protected]>
>> WWW: www.genzentrum.lmu.de
>> *******************************************************
--
*******************************************************
Dirk Kostrewa
Gene Center Munich
Department of Biochemistry
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone: +49-89-2180-76845
Fax: +49-89-2180-76999
E-mail: [email protected] <mailto:[email protected]>
WWW: www.genzentrum.lmu.de
*******************************************************
--
*******************************************************
Dirk Kostrewa
Gene Center Munich
Department of Biochemistry
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone: +49-89-2180-76845
Fax: +49-89-2180-76999
E-mail: [email protected]
WWW: www.genzentrum.lmu.de
*******************************************************
