Dear all,
I am working on a data-set (2.3A) and the space group problem bothers me a
lot.The space group of the data-set could be C2221 or P212121, since our
protein functions as a dimer, and P212121 gives two molecular in the asym-uint,
I think P212121 is more reasonable than C2221.However
Not sure if this helps, but MAPMAN contains options to make 1D and 2D
projections - see http://xray.bmc.uu.se/usf/mapman_man.html#S45
Many moons ago, I also wrote a script to generate general projections (e.g.,
onto the plane of an aromatic ring) using various USF programs - you may want
to
This was one of the things that Indonesia was written for (a long time ago, in
a galaxy far, far away), although I'm not sure if it will still run. If you're
desperate, see http://xray.bmc.uu.se/~dennis/
--Gerard
On Fri, 26 Nov 2010, Muhammed bashir Khan wrote:
Dear All;
I have
If you have LSQMAN, this is trivial - read your superimposed files and use the
RMsd_calc command - http://xray.bmc.uu.se/usf/lsqman_man.html#S59
--Gerard
On Tue, 23 Nov 2010, Huiying Li wrote:
Another question on RMSD:
I have two structures of the same protein superposed with the LSQ
Original Message
Subject:Re: [ccp4bb] Space group and R/Rfree value
Date: Wed, 01 Dec 2010 09:44:06 -0700
From: Maia Cherney ch...@ualberta.ca
To: Xiaopeng Hu huxp...@mail.sysu.edu.cn
References:
643947201.129232.1291191478190.javamail.r...@zmbx0.sysu.edu.cn
It is not at all unusual for a biological homodimer to sit on a
crystallographic two-fold symmetry axis. It is also not unusual
for such a dimer to sit entirely in the asymmetric unit. This
cannot be used to identify the space group.
The space group is determined by the diffraction data.
We did something like this with esprit.
You get the sequence alignments from Psiblast or whatever you fancy,
then edit in the structural alignment into the txt file it generates.
Messy but successful..
Eleanor
On 12/01/2010 03:44 PM, Gerard DVD Kleywegt wrote:
This was one of the things that
Hi all
I'm trying to figure out rotation matricies for ncs averaging in DM.
Except the conventions have got me confused.
The following input script for pdbset correctly maps monomer A to
monomer B.
rotate -
invert -
-0.4654 -0.0974 -0.8797 -
0.8789 -0.1689 -0.4462 -
Oops
It pays to view the pdbset log as it gives the right matrix.
F
On Dec 1, 2010, at 10:41 AM, Francis E Reyes wrote:
Hi all
I'm trying to figure out rotation matricies for ncs averaging in DM.
Except the conventions have got me confused.
The following input script for pdbset
Hi
I'm not sure if anyone has mentioned this yet, but if you use
hklview to view the mtz file (assuming you're working in ccp4-
land), you can probably get a better handle on the systematic
absences than by looking at the original images.
I'm told there are other tools available to
Wouldnt it be easier (in case anyone didnt suggest it yet) to look at
the parity analysis from e.g. dataman or probably phenix.xtriage to tell
you if you have pseudosymmetry (if you processed it in P212121) -- in
C1 you obvioulsy already assume _real_ centering.
visually inspecting maybe
Hi all:
I am trying to purify a protein that was expressed in a baculovirus
system. The protein elutes in the flow through in a DE52 column. Further
gel filtration gives an enriched protein but we see that some medium
components tag along (weight and activity data do not match). Another
On the DEAE, try lower ionic strength or slightly higher pH,
try DEAE-Sepharose instead of cellulose, to get it to stick
Try a cation exchange column like carboxymethyl- or phospho-
cellulose; at slightly acidic pH if necessary.
eab
Narayanan Ramasubbu wrote:
Hi all:
I am trying to purify a
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