Coot ,Pymol or Mumbo are all software can be used to mutate residues of PDB.
Rotamers can adjust by Coot and you can use Mumbo to do energy
minimisation .As for Pymol ,the powerful fig maker ,is not good choice
to do this .
Maybe Chimera is another choice . But I have not use it before. So
Hi Hongmin,
That should need some docking softwares or the structures of the complex.
ta
liu
Hongmin Zhang wrote:
Thanks! I think we still can't tell if the mutant would disturb ligand
binding or not.
Best!
Hongmin
On Wed, Dec 3, 2008 at 2:15 PM, Juergen Bosch [EMAIL PROTECTED]
mailto:[EMAIL
Hi there
Assuming you have a model of the complex you are interested in
tinkering with, try submitting it to the Rosetta Alanine Scanning
servery thing.
http://robetta.bakerlab.org/alascansubmit.jsp
By default, it mutates each residue in the interface to ala, does some
local minimisation (side
Wim Burmeister wrote:
Dear all,
I have a 3 A structure refined with REFMAC which gives consistently
average atomic B-factors of 40 A2, whereas the B factor from a Wilson
plot is about 60 A2. Is there any explanation for such a discrepancy?
There are no obvious problems:
No twinning,
Dear Wim,
I suppose that the solvent content would influence the Wilson plot and
also the distribution of atoms in the unit cell, I would not be too
alarmed about the discrepancy.
Interestingly, the Wilson plot of the Fcalc values is about 60 A2 as for
Fobs in the output dataset.
As far
Then I think it is the problem of fitting the TF parameters into low
resolution data.
REFMAC tries to use the lowest ( 9A) data to get the solvent B factor
and then after applying that correction to get an overall B.
Many Wilson plot programs only use the data from 4A out, with the belief
that
This reminds me of a potential problem with low resolution data that
you might have: if any strong reflection (or a couple of them) is only
partially measured, because it is in the half-shadow of the beamstop,
then the measured intensity is too small, which in turn results in a
too low
Eventually you will have to make the mutant for a reviewer. So in
silico will only give you perhaps some ideas but there's no way of
avoiding wetlab.
Jürgen
On 2 Dec 2008, at 22:38, Hongmin Zhang wrote:
Thanks! I think we still can't tell if the mutant would disturb
ligand binding or not.
Hi,
another possibility to avoid the problems Dirk is mentioning: mask the
beamstop correctly during data processing. Usually, each data
processing package has some tools for doing this (and sometimes even
an automatic procedure might actually work ... but I wouldn't rely on
it without checking).
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I should have given the precision that the problem remains unaffected
by a change of the resolution range (even if I use for example only 4.5
to 3 A resolution).
I am not using TLS and the data are quite isotropic. Rcryst values are
as expected for such a structure.
Anopther 3.5 A dataset does
And this is what I call just in time publication:
Davis et al. RosettaLigand Docking with Full Ligand and Receptor
Flexibility. J Mol Biol (2008) pp.
available online today.
Jürgen
On 3 Dec 2008, at 01:47, David Briggs wrote:
Hi there
Assuming you have a model of the complex you are
I want to impose restraints during REFMAC refinement on the tortion angles
that control the tilting of an OH group from a plane in a ligand bound to
the protein. A few things that confused me:
1. In library cif file, should I just increase or decrease the
tor.value_angle_esd if I want to
If you want to restrain the OH group to a plane, you need to include it
in the plane definition, and not the torsion definition.
Thanks
Abhinav
Stanford Synchrotron Radiation Laboratory
Joint Center for Structural Genomics
Mail Stop 99
Phone: (650) 926-2992
Fax: (650) 926-3292
Can anyone tell me where to purchase 1-butyl-2-methyl imidazolium chloride? I'd
like to try it as an ionic liquid as suggested on the Hampton website Tips
from RAMC.
Thanks so much!
Ronnie
Hi,
I've just double-checked this on my installation (6.0.99e still, but
shouldn't make a difference), and this command works.
I think that you've ended up with an older version of Phaser coming first
in your path. The syntax of the PACK command has changed (to allow it to
behave in a way
Hi all,
I am new to the process of refinement, so excuse me in advance if I
don't provide all the necessary details.
I collected three data sets of a particular protein in complex with
three different substrates (one protein bound to one substrate for
each structure). One of the
Dear Members,
I am getting crystals of my protein. The secondary structure prediction implies
that it has N-terminal with high degree of loop regions. I also get some
mountable crystals yielding weak diffraction pattern(10 A). The quality of the
crystals can also be assumed from its texture
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