As far as I know clustalw/x can provide you with a list of scores per
residue. You can easily feed the score into the B-value column with perl
or other command line tools. I did this a couple of years ago, not being a
scripting guru it took maybe one hour and was fun.
--
Tim Gruene
Institut fu
Just in case somebody else want to prepare a S-hexylglutathione solution.Bryan suggested me to gently warm it up (37 celsius degrees is enough).But also I got these suggestions,I crystallized some GSTs with that compound several years ago.I found that the trick was to solublise it by adding NaOH an
A python script to do just that is below.
Cheers,
Stephen
== Start of script ==
#!/usr/bin/python
import os
import string
import sys
if len(sys.argv) != 3:
print 'Set the B factor column to reflect sequence conservation from CLUSTALX'
print 'Usage: colour_sequence '
sys.exit(1)
PDB_file
Dear all
I am trying one DPC bound peptide.Can anyone suggest me which
precipitant and additives I should add.Thanx in advance.
Shivesh
Hi Iain,
Here's a perlscript that takes as arguments:
clustalw_aln_file reference_seq_name pdb_file min_B max_B
and calculates a consensus score as the fraction most represented amino acid
in a column, where min_B=100% and max_B=0%.
Multiple chains are handled as long as the reference sequence in
Dear All,
We are looking for an electron microscopist, structural biologist,
computational image processor or biochemist for structural studies of
yeast prion fibrils using cryo-EM and single-particle image processing.
This is a really exciting project, and potentially an ideal post for a
cr
First of all, I would like to thank you for your comments.
After consideration of all your comments, I conclude that there are
three possibilities.
1.) search for some particularly poorly-behaved regions using
parvati-server
a.) refining the occupancy of that atoms and/or
b.) tightening
Iain,
Like Dante said, you can use the ConSurf server to easily generate your
pdb with a conservation score in the b-factor column and then use the
script color_b.py (http://adelie.biochem.queensu.ca/~rlc/work/pymol/) to
make the figure with pymol.
Marcos
Iain Kerr wrote:
I'm trying to co
Hey all,
let me give this discussion a little kick and see if it spins into outer
space.
How many reflections do people use for cross-validation? Five per cent is a
value that I read often in papers. Georg Zocher started with 5% but lowered
that to 1.5% in the course of refinement. We've had
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Extended Deadline: Monday 5th February 9am
There will be beamtime available at the ESRF for MX data collection with
a setup that allows online monitoring of UV/VIS spectral changes of the
crystal during the X-ray diffraction experiment. Users
Hi all,
I only wish to draw your attention to the fact that the
Henderson-Hasselbach equation (as used in the paper you cite) is only
valid if you use zwitterionic buffers. Otherwise, with other buffers,
especially phosphate and multi-acids (e.g. succinate, citrate and so
on), any calculation
On Wednesday 31 January 2007 06:10, Georg Zocher wrote:
> First of all, I would like to thank you for your comments.
>
> After consideration of all your comments, I conclude that there are
> three possibilities.
>
> 1.) search for some particularly poorly-behaved regions using
> parvati-server
Hello everybody!
I would like to know how to calculate how much accessible surface area is
lost upon binding a determined carbohydrate to ConA lectin using SURFACE or
AREAiMOL from CPP4.
Thanks in advance for your help!
Sincerely,
--
Taianá Maia de Oliveira
Laboratório de Moléculas Biologicamen
Hello everybody!
I would like to know how to calculate how much accessible surface area is
lost upon binding a determined carbohydrate to ConA lectin using SURFACE or
AREAiMOL from CPP4.
Thanks in advance for your help!
Sincerely,
--
Taianá Maia de Oliveira
Laboratório de Moléculas Biologicament
I've just remembered another approach that I've heard suggested,
although I don't know anyone who has tried it.
Dissolve plenty of the small molecule in paraffin or silicone oil, and
use this mixture to cover the drop. This can be used with regular vapor
diffusion or (probably better) micro
OK, figured it out with help from the suggestions. Thanks !
PROTSKIN, given a PDB file and a CLUSTALW alignment does a fine job of
modifying the B-factor column into % identity (or similarity)
Two problems I encountered:
1. A residue we mutated not matching up with the corresponding sequence
Hello everybody!
I would like to know how to calculate how much accessible surface area is
lost upon binding a determined carbohydrate to ConA lectin using SURFACE or
AREAiMOL from CPP4.
Thanks in advance for your help!
Sincerely,
--
Taianá Maia de Oliveira
Laboratório de Moléculas Biologicament
As I see it, the size of the test set is a question of the desired
precision of the free R. At the point of test set selection there is
variability between the many possible choices: you could happen to pick
a test set with a spuriously low free R or one with an unfortunately
high free R. The
I would agree mostly with what Dale said, and point out that it applies as
well to the SigmaA estimation that is a necessary part of ML refinement.
When we were developing the ML targets that went into CNS, we did a number
of tests to see how many cross-validation reflections were needed. The
f
Hi Shivesh,
Have you tried dropping your MPD concentration (ie. by increments of
~5%)? Changing the pH may also result in larger crystals.
JP
On 1/30/07, shivesh kumar <[EMAIL PROTECTED]> wrote:
Dear all
Sorry for unrelated query.I have crystallized a protein which is at 40% of
MPD.But the p
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