Hi, There have been many discussions along these lines over the years. The problem is understood well. The favoured solution is the use of mmCIF (as posted several times on the BB). But I would rather leave it to those officially involved to comment on the pros and cons. On the practical side, pdbcur will work equally well with mmCIF files.
Cheers Martyn * * Dr. Martyn Winn * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * Tel: +44 1925 603455 (DL) or +44 1235 567865 (RcaH) * E-mail: martyn.w...@stfc.ac.uk<mailto:martyn.w...@stfc.ac.uk> Skype: martyn.winn * From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dirk Kostrewa Sent: 02 September 2013 09:38 To: ccp4bb Subject: Re: [ccp4bb] Fractional coordinate shift with two-character chain names? 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 <kostr...@genzentrum.lmu.de><mailto:kostr...@genzentrum.lmu.de> To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> 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:CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>] 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: kostr...@genzentrum.lmu.de<mailto:kostr...@genzentrum.lmu.de> >> WWW: www.genzentrum.lmu.de<http://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: kostr...@genzentrum.lmu.de<mailto:kostr...@genzentrum.lmu.de> WWW: www.genzentrum.lmu.de<http://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: kostr...@genzentrum.lmu.de<mailto:kostr...@genzentrum.lmu.de> WWW: www.genzentrum.lmu.de<http://www.genzentrum.lmu.de> *******************************************************
