On 11/02/2010 02:36 PM, Buz Barstow wrote:
Dear All,
I'm looking for a software program to produce, given a 3D atomic structure of a
molecule, a linear map showing the surface accessibility of residues in a
protein structure.
Would any one know of a program that can produce this sort of map.
*REMINDER**
Biological Structures Group BCA Winter Meeting
Wednesday 15th December 2010
University of Reading
Hosted by the School of Biological Sciences
***
Registration details can be found at:
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Dear All,
Thanks for your suggestions! I ended up using the areaimol program in ccp4.
My next question:
Given a list of accessible surface area, is there a generally accepted value of
ASA above which a residue classifies as a surface residue, while below this
number it is an interior residue?
Thanks very much for all of the helpful suggestions!
The most useful solution for us was a python script provided by Ed
Pozharski at the ccp4wiki link below, which reads a .sca file and
produces a table with both and / for a user-defined
number of shells.
http://strucbio.biologie.uni-konstan
That depends on what you are trying to do. Maybe the best strategy is
to use fuzzy logic, whereby a residue which has 30% of it's Gly-X-Gly
ASA buried has the "surfaceness" of 0.7.
On Wed, 2010-11-03 at 09:55 -0400, Buz Barstow wrote:
> Dear All,
>
> Thanks for your suggestions! I ended up usin
Dear All,
Thank you for the replies sorry about the delay in my reply. Here is
some more information, for those of you that are interested, to try fill
in some gaps.
The data was collected on our home source with osmic vairmax-HF optics
and an RAXISIV++ detector. We are investigating whether
Dear David,
Many thanks indeed for this movie and the extra info.
It is quite captivating!
The 'strange spot' features do seem progress to other regions of
reciprocal space at approximately constant diffraction resolution in
an anti-clockwise manner.but I am still digesting your movie
Beh
CCP4'ers,
Are 9 datasets the maximum for an mtz file? or a single run of cad?
The manual (http://www.ccp4.ac.uk/html/cad.html) seems to suggest that
9 is the limit per cad run but not for a given mtz.
F
-
Francis E. Reyes M.Sc.
215 UCB
Universi
Hello,
9 mtz files are the limit of CAD, one things you can do is to modify the
source file , that is wrote in fortran, or write a bash script or that
run iteratively the CAD script and change the MTZ files.
R.
On 03/11/2010 18:11, Francis E Reyes wrote:
CCP4'ers,
Are 9 datasets the maximu
Hi Francis,
the limit ist for CAD. You can put as much datasets as you want in one mtz,
but you have to run cad than stepwise. Be careful with the column labels.
Duplicate labels lead to problems.
Christian
Am Mittwoch 03 November 2010 18:11:34 schrieb Francis E Reyes:
> CCP4'ers,
>
> Are 9 d
Is it known/can you divulge the nature/structure of the macromolecules in
the crystal? Is it protein, nucleic acid, other? Does the structure have
periodicity to it?
JPK
- Original Message -
From: "David Goldstone"
To:
Sent: Wednesday, November 03, 2010 10:53 AM
Subject: Re: [ccp4b
Yes, CAD is limited to 9 input files. I seem to remember I once tried to
increase the limit, but got into problems (it is not just a case of
increasing MAXFILES). It is far simpler and safer to run CAD
iteratively.
But an MTZ file can hold more. The current limits are:
#define MXTALS 100
#d
OK! John prompted me to look more carefully at the images and they
don't seem to be consistent with any optics or detector effect.
Attached a Blowup (almost as strange as Antonioni's 1966 film with this
name) of one of the areas. As others have pointed out already, the
features are not round halo
I have a version which I modified a while back to handle up to 999
files simultaneously, and which I can send to anyone privately on
request, as long as you accept the entire risk of using it (and you
should probably also heed Martyn's warning!). It has probably
diverged from the distributed versi
Hi Buz,
Sorry to respond a little late, but if you are still tinkering with surface
accessibility calculations, you can use the following web server that will
calculate the "diffusion accessibility" of each atom in your input .pdb file:
http://nihserver.mbi.ucla.edu/diff_acc/
"Diffusion access
I don't think it looks like satellite spots at all--it looks more like a
flat diffuse scattering background or perhaps a diffuse ring, with some
strange blanking/clearing of a circle around the spot. Perhaps it is a
result of having not just the usual convolution of the molecule with the
lattic
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