Hi,
I am currently refining some reasonably high (1.4-1.6 Å) resolution protein:RNA
complex structures and was trying the approach described in Schwartz et al.
Nat. Struct. Biol. 8 (2001) 761-765 where they divided each nucleotide into
three TLS groups – the ribose, the phosphorus atom plus
Hello Huw,
what happens when you remove the period '.' in the residue range description,
i.e., replace
RANGE 'B 3.' 'B 3.' P
with
RANGE 'B 3' 'B 3' P
?
Tim
On Thu, Jul 15, 2010 at 03:54:45PM +0100, Huw Jenkins wrote:
Hi,
I am currently refining some reasonably high
Hi,
Yes, zero origin is a sure sign that it hasn't identified the atoms in
the TLS group.
There is presumably some problem matching atom names, but am not sure
what. If you send me the files, I can have a play.
However, you might have problems with the group definitions anyway. I
seem to
On 15 Jul 2010, at 16:24, Tim Gruene wrote:
what happens when you remove the period '.' in the residue range description,
i.e., replace
RANGE 'B 3.' 'B 3.' P
with
RANGE 'B 3' 'B 3' P
No difference unfortunately.
Thanks,
Huw
--
Dr Huw Jenkins
Astbury Centre for
On 15 Jul 2010, at 16:28, Martyn Winn wrote:
Yes, zero origin is a sure sign that it hasn't identified the atoms in
the TLS group.
There is presumably some problem matching atom names, but am not sure
what. If you send me the files, I can have a play.
I thought that too but if I change the
On Thursday 15 July 2010, Huw Jenkins wrote:
Hi,
I am currently refining some reasonably high (1.4-1.6 Å) resolution
protein:RNA complex structures and was trying the approach described in
Schwartz et al. Nat. Struct. Biol. 8 (2001) 761-765 where they divided each
nucleotide into three
On 15 Jul 2010, at 17:06, Ethan Merritt wrote:
My gut feeling is that the best TLS description would be each base
(or base pair) in its own group, the use TLSMD to analyse and assign groups
for the backbone atoms. But again I have no actual experience with this,
so it's only a suggestion.
Dear Huw,
at 1.4-1.6A resolution I would actually try anisotropic refinement and tighten
the restraints a little in case the resolution is not quite high enough. You
can do this with refmac5, phenix.refine, and shelxl and you would not have to
worry about TLS groups anymore.
Cheers, Tim
On
Refinement with rigid-base TLS parameterization has been previously
explored:
Holbrook, Dickerson, Kim (1985) Acta Cryst B41, 255-262.
(the photocopy is located in the pile of dust that I maintain adjacent
to my desk)
Ethan Merritt wrote:
On Thursday 15 July 2010, Huw Jenkins wrote:
Hi,
On Thursday 15 July 2010 09:18:33 am Huw Jenkins wrote:
On 15 Jul 2010, at 17:06, Ethan Merritt wrote:
My gut feeling is that the best TLS description would be each base
(or base pair) in its own group, then use TLSMD to analyse and assign groups
for the backbone atoms. But again I
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