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.
Thanks! and all the best,
--Buz
t; which you could convert into the total fraction per residue with not too much
> effort.
>
> Is this what you are looking for?
>
> Cheers, Tim
>
> On Tue, Nov 02, 2010 at 10:36:56AM -0400, Buz Barstow wrote:
>> Dear All,
>>
>> I'm looking for a software
Dear all,
I am considering trying to crystallize a small peptide (around 15 amino acids).
The peptide is soluble in neutral water or buffer (pH 7.0) until at least 10 mM
(13 mg/mL), and adopts a turn conformation when bound to Zn.
What are your thoughts on attempting this?
If you think that i
Dear all,
I am trying to purify a metalloprotein (a hydrogenase) using affinity
chromatography.
I have produced two tagged versions of the enzyme: one with an N-terminal 6x
histidine affinity tag, and the other with a C-terminal 6x his-tag. The tagged
proteins are both tied to an IPTG-inducibl
Dear All,
I'm planning an experiment to study the oxidation of NADH by a
flavoprotein at cryogenic temperatures to facilitate collection of X-
ray diffraction data.
In planning this experiment, I have seen a few obstacles that I am
looking for help in overcoming.
1. There are no structur
Dear All,
I'd like to find a way to calculate the volume of an arbitrary
selection of atoms in a protein structure. Could anyone suggest a
program that could perform this task, ideally, one that could be
called from inside pymol and calculate the volume of a pymol selection?
Thanks! and a
Dear All,
Does anyone have a python routine that can be used to calculate the
moment of inertia matrix and principal axes of a selection of atoms?
Thanks! and all the best,
--Buz
Dear All,
I'm having trouble installing coot on MacOSX 10.5.2 on my MacBook Pro
(Core Duo model).
I would like to install coot using fink, but am getting stuck when it
comes to installing ruby. Has anyone else experienced this problem?
Also, are there any alternative solutions to installi
Scott
Contact info:
http://chemistry.ucsc.edu/~wgscott/
On Apr 17, 2008, at 11:51 AM, Chris Richardson wrote:
On 17 Apr 2008, at 6:07 PM, Buz Barstow wrote:
I'm having trouble installing coot on MacOSX 10.5.2 on my MacBook
Pro (Core Duo model).
I would like to install coot using fink,
lot of bugs, so the pain you are being subjected to now
will be worth it.
Bill
William G. Scott
Contact info:
http://chemistry.ucsc.edu/~wgscott/
On Apr 17, 2008, at 1:48 PM, Buz Barstow wrote:
Hi Bill,
Thanks for your advice! Ruby now installs on my machine, as does
Coot (which is what
:34 PM, Buz Barstow wrote:
Hi Bill,
Thanks a lot for your advice. Coot now installs and runs, however,
I do get some warnings;
** (coot:20738): WARNING **: Error loading pixmap file: /sw/share/
coot/pixmaps/connect-to-ccp4.svg
** (coot:20738): WARNING **: Error loading pixmap file: /sw/share
Hi Subbu,
Here's my two cents.
Your project sounds really interesting.
You mentioned in your email that the active site and associated waters
in the active site of the wild type and mutant enzymes are
"identical". It's worth noting that even very small (on the 1/10th of
an angstrom level)
|--|
Buz Barstow
Biophysics Group
Physics Department
192 Clark Hall
Cornell University
Ithaca, NY 14853
USA
Telephone: +1 607 255 8678
Fax: +1 607 255 8751
Email: [EMAIL PROTECTED]
|--|
Dear All,
Does anyone know of a program that is capable of drawing the secondary
structure of a protein molecule?
I'd really like to be able to take a protein molecule, and draw the
secondary structure out along a line, indicating the positions of
secondary structural elements like sheets
Dear All,
Thanks for your suggestions about software to map out the secondary
structure of a protein onto a line.
I've compiled all of the suggestions into one list:
http://tardis.nibio.go.jp/joy/
http://www.biochem.ucl.ac.uk/~roman/procheck/manual/examples/plot_06.html
http://webclu.bio.wzw
Dear All,
I'd like to add substitute a natural base (adenine) for a non-natural
base (2-aminopurine), in a molecular model of an RNA molecule.
I'd like to do this with CCP4 and Coot. Could I ask for some help
please?
Thanks! and all the best,
--Buz
On Mar 28, 2009, at 8:37 AM, Paul Emsley wrote:
Buz Barstow wrote:
Dear All,
I'd like to add substitute a natural base (adenine) for a non-
natural base (2-aminopurine), in a molecular model of an RNA
molecule.
I'd like to do this with CCP4 and Coot. Could I ask for some help
plea
Hi Bill,
Sorry if my first message was confusing. I do want to convert from A
to 2AP.
I'm working on following Paul Emsley's suggestions.
Thanks! and all the best,
--Buz
On Mar 28, 2009, at 11:48 AM, William Scott wrote:
On Sat, March 28, 2009 5:37 am, Paul Emsley wrote:
B
Dear all,
I'm sorry for the somewhat non-ccp4 related questions, but here goes;
1. Could anyone recommend a good mailing list for bioinformatics
related problems, where I might be able to re-ask question 2.
2. Does anyone know of some good software for visualization of the
domain analysis
Hi All,
Does anyone know of a program that can extract the amino sequence of a
protein from a PDB file and output it as a FASTA file?
Thanks! and all the best,
--Buz
Thanks Mark!
--buz
On Aug 13, 2009, at 5:45 PM, Dr. Mark Mayer wrote:
try PDBSET (ccp4)
Hi All,
Does anyone know of a program that can extract the amino sequence
of a protein from a PDB file and output it as a FASTA file?
Thanks! and all the best,
--Buz
--
+++
Dear All,
Thanks to everyone who replied to my query about extracting an amino
acid sequence from a PDB file!
Here is a summary of responses of my query;
1. Use SwissPDBViewer
2. Use Pymol 1.2
load $TUT/1hpv.pdb
save 1hpv.fasta
# or by selection
save 1hpv_A.fasta, chain A
3. With Phen
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