Am 29 Jul 2012 um 18:53 hat Tatyana Sysoeva geschrieben:
Hi!
I heard a couple of times that use of cacodylate buffers in crystallization
is bad, and not only
because of the compound toxicity.
As I understood, presence of the cacodylate in a protein crystal will cause a
particular
Dear all,
I have a refine structure with 8 ncs copies and several hundreds of
water molecules (which was put in one chain). Now I try to separate
these molecules by renaming to the chain id of each adjacent protein
molecule. I know RCSB can do this during deposition process. Do anyone
know a
Dear Tatyana,
We once had a project where the crystallization
condition contained cacodylate. The crystals diffracted
to 1.9A and survived reasonably well under the beam
(maybe there was indeed some colour change upon
exposure, I do not remember exactly).
We were working with drug soaks. The
Dear experts,
Thank you for your helpful input. I think it's clear now to conclude that
the alternative conformations exist on both Phe and Tyr residues.
Counter level = 1 sigma
http://i50.tinypic.com/anzfrn.png
Counter level = 0.7 sigma - the alternative conformation of Phe can be
confirmed.
Dear Zhiyi,
I think that sortwater (http://www.ccp4.ac.uk/html/sortwater.html), will do
something along what you want. Remember to read the documentation ;-)
Best regards,
Folmer
2012/7/30 Zhiyi Wei ustcwebri...@gmail.com
Dear all,
I have a refine structure with 8 ncs copies and several
Dear all,
I am currently trying to refine co-crystallized ligand structures at 2.8-3.4 Å
resolution. After initial molecular replacement the density in the maps, both
2Fo-Fc and Fo-Fc looks good and the ligand seams to have
bound. However after running Refmac directly on the output files the
Dear Damian,
The initial map after molecular replacement and BEFORE atomic refinement is
maybe not the highest quality map, but definitively the map with the least
model bias. If you see good density for you inhibitors in those maps, they
almost certainly will have bound. In that case I would
Without wishing to re-ignite previous discussions on this topic
(perhaps FLAME ... /FLAME tags would be in order!), I would point
out that this and similar confusion with other space groups has arisen
largely from a failure of some programmers (and users!) to fully
comprehend the important
Hi there,
at this point I'm confused, at least with respect to one thing.
If I have a solved a structure in spacegroup #155, with a=b and different from
c, and alpha=beta=90, gamma=120, this would be reported as R32 in the
international tables. However programs refers to it as H32.
What should
Hi Sebastiano
How programs refer to it is irrelevant for the purposes of
publication! If you want to be precise and stick to the ITC
convention on nomenclature it's space group R32 in the setting
R32:h, since as I explained it's only the standard symbol R32 which
is generally shown in the main
That is perfectly clear.
What was confusing me was indeed (mostly) the PDB CRYST1 record.
I guess I will go for R32:h.
Thanks a lot,
ciao,
s
On Jul 30, 2012, at 6:36 PM, Ian Tickle wrote:
Hi Sebastiano
How programs refer to it is irrelevant for the purposes of
publication! If you want to
Dear Ian,
I made a modest contribution to this discussion a long time ago, and I
will only limit myself to one point.
I think you may be confusing setting and lattice mode. A change of
setting is performed by an integer matrix with determinant 1 (a unimodular
matrix) whereas a change
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