[ccp4bb] refining nucleic acid structures: Refmac or CNS?

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

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   - Amino Acids

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Building peptide in density using coot.
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2008-09-03

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Subject: NY, Cancer Metastasis Post-Doctoral Position (fwd)
From: Steve Almo almo {- at -} MEDUSA {- dot -} BIOC {- dot -} AECOM {- dot -} YU {- dot -} EDU
Date: 2008-09-04

Subject: refining nucleic acid structures: Refmac or CNS?
From: Melody Lin xtalin2007 {- at -} GMAIL {- dot -} COM
Date: 2008-09-03

Dear all,

I was refining complex structures with a DNA oligo that have some
noncanonical bent regions in the middle, the resolutions are fairly good,
around 1.8-2.2A. I used both CNS and Refmac. I found (not surprisingly) that
with Refmac, I got a lot of unusual sugar puckers like C1'-exo that is
neighboring the "usual" C2'-endo for B-DNA even in the normal B-DNA region.
from reading past emails in the CCP4 archive, it seems Refmac5 doesn't
restrain sugar pucker while CNS punishes violations to normal sugar pucking
more than violations in bond lengths. I would like to get people's current
opinion about which is the better program to use to refine nucleic acid
structures? Refmac or CNS combined with modified parameter file that
includes alternate common sugar puckers(e.g. C3'-endo)?

Also, I have a naive/beginner's question on Refmac---since I have a modified
base in the structure, I had to provide Refmac with a dictionary file of
that base, but the phosphate joining this modified base and the next has
strange geometry. I know how to restrain the link bond length, but how does
one restrain the angle for the linking bond?

Thank you very much for your input/suggestions.

Best,
Melody

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Building peptide in density using coot.
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2008-09-03

Next message:
Subject: NY, Cancer Metastasis Post-Doctoral Position (fwd)
From: Steve Almo almo {- at -} MEDUSA {- dot -} BIOC {- dot -} AECOM {- dot -} YU {- dot -} EDU
Date: 2008-09-04