This may be worth to mention in this context: http://cci.lbl.gov/hybrid_36/
Pavel On Fri, Aug 30, 2013 at 9:14 AM, MARTYN SYMMONS < [email protected]> wrote: > 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]] 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] > >> 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 > ******************************************************* > > >
