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Dear ZhiYi,
It seems that this subject comes times to times to either the ccp4bb or
straight to me, yet I raised this question some years ago. I could count
several people with the same situation; that makes me wonder how frequently
this happens and, above all, how frequently people do take care to make the
job the best possible.
Going to your question: as it was raised at that time and as I could
notice (with the program version at that time), there is an issue with
refmac such that it increases the B-factor of one of the molecules and
pushes it ouside of the density, even if their occupancies sum <=1. The
solution I found was to use CNS with the capabilities to turn on and off the
interactions. That allowed me to refine well my molecules, sharing positions
(occ sum = 1). On the other hand, refmac has the TLS tool, im my humble
opinion, a MUST for anyone who cares on providing the best refined possible
model (at least to try it, and now I must say I will try the TLSMD server in
every structure I have in my hands) (this a question, "MUST's" I am yet for
some time to elaborate and propose to the ccp4bb...).
So, I made a huge labour on swapping between CNS (to refine the
overlapping ligands) and refmac (to use TLS, important for that structure);
although this labour, I feel myself confortable as to have made the most
possible to achieve the best final model. At describing this process in the
paper, one referee wrote "...akward description of the refinement method..."
and I hope that was due to my inabilities with the redaction on the english
language, yet concerning methodoly itself I cannot think of any other better
way. If there is so, please, educate me.
If you find difficulties to prepare the CNS files for turning on-off
interactions, let me know and I can try to dig this from my archives, as a
template for you.
Concerning occupancies, there is a crude general recommendation to
attribute values such that B-factors end up approx. the same, although there
might be distinct cases to analyse. I think other people can add more useful
comments on this.
Jorge
----- Original Message -----
From: "ZhiYi Wei" <[EMAIL PROTECTED]>
To: <[email protected]>
Sent: Thursday, September 15, 2005 12:11 PM
Subject: [ccp4bb]: Questions on ligand refinement
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Hi, all
How to refine two different ligands in the same position and figure out
their
occupancy? Which program will be better to deal with this situation, CNS
or
refmac? I know that some similar questions have been posted in bb, but I
can not
find any answers in detail.
Any answers will be appreciated.
