I was always a big fan of "lego loop" in O for building loops into dotted lines. Phoebe
---- Original message ---- >Date: Wed, 15 Oct 2008 16:20:26 +0100 >From: Eleanor Dodson <[EMAIL PROTECTED]> >Subject: Re: [ccp4bb] Poor electron density - polyAla or PolyGly? >To: CCP4BB@JISCMAIL.AC.UK > >Joe Smith wrote: >> Hello, >> I have been building a protein model (resolution 2.2A) which has one >> small loop of 6 residues having poor density. I cannot see any side >> chain in this region but I can see relatively poor main-chain density >> which at least clearly indicate the loop conformation. I am trying my >> best to build polyAla chain in this region. But 3-4 residues end up >> coming in disallowed region of Ramachandran plot. I think the problem >> is - in this region i can not even build the main chain atoms with >> high confidence. >> Can I build polyGly in this region? or should I just leave this >> region? I just don't feel like leaving this region empty. >> Any suggestions in this regards is highly appreciated! >> regards >> Joe >> >> >> >You could try using coot real space refinement with ramachandran >restraints on.. > Eleanor Phoebe A. Rice Assoc. Prof., Dept. of Biochemistry & Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123 RNA is really nifty DNA is over fifty We have put them both in one book Please do take a really good look http://www.rsc.org/shop/books/2008/9780854042722.asp
