Dear Quing,
My first suggesting is a no-brainer: try to get better data. At 4.3Å model
building and refinement will remain painful, whatever you try. Getting better
data includes improving your crystals (ligands, additives etc.) and the
cryoconditions. You could also try to collect data on say
Seeing Herman's message reminds me that I forgot to send this reply to the BB
as well.
Herman makes many of the same points, and a very good additional point that you
want to examine whether the molecular replacement solution in the lower
symmetry space group actually has the higher symmetry.
On 17 Jul 2012, at 22:34, William G. Scott wrote:
On Jul 17, 2012, at 6:25 AM, Felix Frolow wrote:
I will wait for fink version if it will be one… :-\
Does anyone use or want this anymore?
Apologies for reanimating this long-dead discussion, but did you reach a
conclusion about putting
Search for homologous binding partners with close or remote homologies
with your own sequences can also be addressed from the InterEvol database
http://biodev.cea.fr/interevol/
It seems you can upload the sequences there :
http://biodev.cea.fr/interevol/interevalign.aspx
Hope this can help
On 09/06/2012 07:48 PM, Qing Luan wrote:
I built a molecular replacement model
What is the model based on (i.e. how much sequence identity you have)?
Did you try something other than CNS (specifically for twinning detection)?
Did you check the patterson map and/or self-rotation for off-origin
And also - I presume p6 does not work?
On 09/06/2012 07:48 PM, Qing Luan wrote:
which I can scale in P3, P31, P32, P321, P3121 and P3221 with similar
statistics:
Hi Qing -
Just a couple of observations on your story, without a real solution:
- Your space group is almost certainly P31 2 1. Your scaling statistics
and Phaser results point to this - if your true space group was P31,
then your statistics would be noticeably (even dramatically) worse in
Hi Matt,
You may be right, but how do you distuinguish you between a
crystallographic 2-fold and perfect twinning? A solution that refines to
an Rfree of 55.6% is not exactly a textbook example of a correct
solution. Poor data, low-resolution and twinning/pseudosymmetry can
cause all kinds of
Just a comment
- Your space group is almost certainly P31 2 1. Your scaling statistics
results point to this - if your true space group was P31,
then your statistics would be noticeably (even dramatically) worse in
the higher symmetry space group.
I've seen a dramatic counter-example to
Dear All,
The Ho lab at the Institute of Biological Chemistry of Academia Sinca in Taiwan
seeks a motivated structural biologist at post-doctoral level with interest in
structure and activity studies of pharmaceutically important enzymes.
The laboratory currently works on the
Matt,
On 09/07/2012 09:56 AM, Matthew Franklin wrote:
I'm also a bit dubious about the 4.3 A limit; your useful data may be
ending around 4.6 instead, despite the high I/sigma numbers.
Why? I would rather suggest Qing extends resolution to where
I/sigma~1. Other than Rmerge, I don't see
Dear Ed -
I agree with you, and I felt a little funny giving that advice, since I
know that Rmerge is rather outdated as a resolution cutoff. What I was
really reacting to was the slope of I versus resolution; if you look at
Qing's Scalepack table, you can see that average I plateaus in the
Dear CCP4BBers
we have an opening for an EMBL Interdisciplinary Postdoc (EIPOD)
position to develop data collection procedures for the new
high-precision diffactrometer on the P14 beamline
at EMBL Hamburg. Beamline P14 will be fully tunable and have a
sub-10-micron focus and is equipped with
Dear Colleagues,
Please pass this ad on to any interested candidates.
Thanks and best wishes,
John
--
John Rubinstein
Molecular Structure and Function Program
The Hospital for Sick Children
555 University Avenue, Rm. 3330
Toronto, ON
Canada
M5G 1X8
Tel: (+001) 416-813-7255
Fax: (+001)
Dear Colleagues,
Please pass this ad on to any interested candidates.
Thanks and best wishes,
John
--
John Rubinstein
Molecular Structure and Function Program
The Hospital for Sick Children
555 University Avenue, Rm. 3330
Toronto, ON
Canada
M5G 1X8
Tel: (+001) 416-813-7255
Fax: (+001)
I have a buried active site and would like to determine if there is room
for a water molecule in various mutants. Does anyone know of a good
program to calculate this? I have heard of GRID and VOID but have never
used them.
Thanks.
--
Yarrow Madrona
Graduate Student
Molecular Biology and
All:
Sorry for the non-CCP4 question. But please help!!
I have to install jre 1.5_22 on my mac to have the COEUS (MIT software
premium). My computer already has java 1.6
How to install the old version. If this old is not on the computer, then the
install commands do not work.
Thanks a lot
Hi Yarrow,
You can use the likes of areaimol to calculate the surface accessible area,
with or without accounting for crystal symmetry:
http://www.ccp4.ac.uk/html/areaimol.html
There are other alternatives, but I hope that helps,
Rob
On 8 Sep 2012, at 00:37, Yarrow Madrona wrote:
I have a
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