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] 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 > WWW: www.genzentrum.lmu.de > *******************************************************
