Hi -
"ARP/wARP Loops" (from the ccp4i interface) could also be tried. What
it will do is build a few "trees" of Ca's in non-negative density and
in conformations consistent with penta-peptide conformations from the
PDB, then build the residues in Ramachandran allowed conformations,
and then "rank" the solutions according to density and present the
most likely ones.
(Details in Joosten et al, Acta D, 2008 - http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18391408
)
Having said this, it might as well be a good idea to leave these out -
at least for now. Have you finished the rest of the structure? Build
waters, possible ions and ligands, care of your rotamers, etc ... When
all else is finished the loop might look clearer.
Tassos
From: Joe Smith <[EMAIL PROTECTED]>
To: CCP4BB@JISCMAIL.AC.UK
Sent: Wednesday, 15 October, 2008 4:11:01 PM
Subject: [ccp4bb] Poor electron density - polyAla or PolyGly?
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
