nze...@umn.edu]
Sent: Tuesday, January 22, 2013 9:21 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Superposing nucleic acids
Minimally, I believe you want to use P and C1'.
(This has been done by others, including Pabo and Pabo & Nekludova, J.Mol.
Biol., 301:597-694 (2000).
Minimally, I believe you want to use P and C1'.
(This has been done by others, including Pabo and Pabo & Nekludova,
J.Mol. Biol., 301:597-694 (2000).
I actually prefer to use all backbone atoms: P O5' C5' C4' O3' C3' C2'
C1' O1'
Barry Finzel
Medicinal Chemistry Department
2-160C Weaver-D
Dear Alan,
This depends very much on whether the structures are similar in the
helical conformations or not, and on what question you are trying to
address. If these are nearly identical structures, it really does not
matter much what atoms you use for superposition, as long as they lie
along the
Dear all - is there a convention for superposing nucleic acids duplexes
of unrelated sequence?
i.e. which atoms should be superposed : C4' of the sugar, P of the
backbone, O3'/O5' of the backbone, or some combination thereof?
Alan
--
Alan Cheung
Gene Center
Ludwig-Maximilians-University
Feo
