I have a ~4.3 angstrom data set of a trigonal crystal of a seven subunit
protein complex which I can scale in P3, P31, P32, P321, P3121 and P3221 with
similar statistics:
P3
Shell Lower Upper Average Average Norm. Linear Square
limitAngstrom I error stat. Chi**2 R-fac R
Hi Bill,
First of all I would try to completely uninstall (via fink) both ccp4 and
coot. In fact the problem is not the location of the programs per se, but
the conflict between different versions of the same program. Fink can
update the softwares, but not when you rebuild the whole system.
Anyway,
I decided to upgrade my MacBook Pro to OS X 8.0 (previously 10.6), and update
my coot and CCP4 programs at the same time (now seems like a bad idea). I use
the precompiled library from the Scott Lab, so I followed the directions on his
website. I did the following:
Installed new X11 (from Xqu
Hi Theresa,
You can use our free Discovery Studio Visualizer:
http://accelrys.com/products/discovery-studio/visualization-download.php
You can select the region of choice (in your case the transmembrane domain) and
create a surface around it (Structure -> Surface -> Add). Then in the Molecular
Dear CCP4 Users,
Following the release of ccp4 6.3.0, CCP4 core team sets up an update mechanism
for moderate modifications of Suite's components between the releases. It is
expected that updates will be essential for CCP4 maintenance and will make
patch releases less frequent or even redundant
Ikerbasque, the Basque Foundation for
Science (Europe), would like to inform you that we have
launched an international call to attract 20 senior
researchers to the Basque Country (permanent
p
I know this isn't exactly your question, but it doesn't really take that
long to clone, express, and purify things nowadays--a few days, even? Also,
won't you be doing this anyway? So why not cut out the middle-man? Or,
better still, in your cloning downtime, do the software stuff.
JPK
On Thu,
Hi Careina,
In answer to your first question you could also try the iPATCH server:
http://portal.stats.ox.ac.uk/userdata/proteins/i-Patch/home.pl
This takes two reference structures for proteins that interact, and combined
with multiple sequence alignments of their homologs attempts to predict
Like Tim says SORTMTZ expects a different format used for unmerged reflection
lists.
And I think this space in the filename causes the SCALEIT problem - linux
operating systems often treat spaces as filename terminators..
But the " … " marks around a file name are meant to override the space
Dear colleagues,
the registration deadline for the Murnau Conference 2012 on Structural Biology
of Molecular Transport is 7 September- TOMORROW!
Please take this last chance to register:
http://www.murnauconference.de/2012/registration.html.
Murnau Conference 2012 on Structural Biology of Molec
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Dear,
you should split the structure into several PDB-files and use the
program 'volume' on each.
Tim
On 09/06/2012 09:58 AM, Theresa Hsu wrote:
> Dear all
>
> I have two membrane protein structures. Is there any tool to
> calculte the volume of
Hi Careina,
For the first question, it sounds as though IBIS would do what you want:
http://www.ncbi.nlm.nih.gov/Structure/ibis/ibis.cgi. It will also try to
answer your second question, although sequences are compared to known
structures, so if your sequence is dissimilar to anything in the PDB i
Dear all
I have two membrane protein structures. Is there any tool to calculte the
volume of transmembrane domain and solublle domain separately for comparison?
Thank you.
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