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:[log in to unmask]] 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
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