I see some solutions to your problem and one works well for me on a small
protein domain.
I had exactly the same problem of crystallization during concentration and
in my case I solve the problem by heating the crystal suspension. The
validation of the protocol was made with support of 1D NMR to
Dear BBers
I would like to draw your attention to a scientific instrumentation
support post (http://www.diamond.ac.uk/Home/Jobs/Current/DIA0547.html)
available at Diamond Light Source. Whilst this position is principally
working for the tuneable MX beamline I04
Hi
In addition to what Fred and others have said, it is important to remember
there are several native, stress-responsive proteins of E. coli that show
good affinity for metal ions. Hence, they can be easily co-purified by
immobilised metal affinity chromatography (IMAC). This seems particularly
Ethan Merritt wrote:
On Thursday 18 February 2010 14:48:57 Paul Emsley wrote:
Ursula Schulze-Gahmen wrote:
I am a new user of Coot and I haven't found an easy way of displaying the
phi/psi angle of a specific residue while I am rebuilding. I found of course
the Ramachandran plot, but i
Hello,
sorry for my off topic question.
I found a PEG molecule bound to the active site of my enzyme structure. And I
did not expected it there, though I used PEG as precipitant in the
crystallization condition. Now I'm wondering how could bind PEG with its
hydrophobic nature at all in the
Dear all,
This is a remark I have wanted to make for a long time but managed so
far to repress. However, this case is absolutely clear: Ivan was not asking
for general advice on how to carry out a general task, but how to perform a
specific task with the CCP4 software.
In response we
The X6A workbench: Advanced Structural Biology Tools
(http://protein.nsls.bnl.gov)
We would like to invite you to participate in this four day hands-on course at
the NIGMS Research Facility at the National Synchrotron Light Source. This
course is intended for beginners who would like to obtain
Dear Gerard,
I can only agree with you - I've also noticed a growing and sometimes
irritating cross-advertisement of non-CCP4 programs on the CCP4BB over
the last months (mainly Phenix). Unless, the specific task that was
asked for, can only be (reasonably) solved with non-CCP4 programs, such
Hi Dirk,
When it happens that I reply to a ccp4bb message and that the answer, or
solution I may have (which I think is better or more appropriate)
involves using non-ccp4 programs, I do it off-list. By replying
privately to the person who asked the question.
Fred.
Dirk Kostrewa wrote:
I am inclined to agree with Gerard. Of course if there is a specific
question to CCP4bb about SHELX, I try to answer it. Since I am too
lazy to maintain my own bb, this is very convenient. However I have
stopped 'poaching', for example for the thread in question I resisted
the temptation to
Dear Armando,
Two similar, but not identical experiences:
- we expressed a protein and got some ugly small crystals. Then the
Edman degradation results on the purified protein came in and turned
out to correspond to chloramphenicol transferase (same size as our
protein).
- expressed a
Dear all,
I am trying to calculate the domain-domain contact surface from one
chain. I see AREAIMOL to only tell you the accessible surface
area/residue. Could any other software/webserve could specify residues
in the contact surface and calculate the total contact area?
Thanks
J.
The guidelines for the CCP4BB are extremely broad and certainly include
discussion of other software packages. Since the original poster's question
had to do with a specific problem with CCP4, it would have been appropriate
for Pavel to prefix his reply with something like I hope you receive an
You would have to cheat a little bit, and relabel the second domain chain id
to something different. Or you can split the pdb file into two. That would
still be necessary for using the EBI PISA server at
http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html
as I have just been doing. In my case I
Is this the active enzyme or an inactive mutant? does your substrate have
any similarity with PEG (size, conformation, bulk etc?) would you assume
that if there was a substrate bound to the active site and say a few waters,
and/or metal ions it would probably fill the space which in this case PEG
Dear Jane,
try to split your protein into two chains (e.g. domain 1 -- chain A / domain 2
-- chain B in a PDB file) and use the PISA server for processing. Besides
several interfaces with symmetry mates, one should represent your domain/domain
interface based on chain A/B you've chosen.
On Fri, 2010-02-19 at 10:37 -0500, Edward A. Berry wrote:
The problem is not that the phenix team was so quick
to promote their software, but rather that now 14 hours after the
original
post, no one has answered the CCP4 question.
The original poster returned to indicate that he had received
Hi Everyone,
my apologies for those who got irritated. I guess when someone got stuck
with something and asks for help, he/she deserves a solution for the
problem. Providing with a solution is what I have in mind replying to
the questions. The only reason why I reply to the whole list and not
I guess Phenix people are just trying to help. After all they are not selling us
Zinger sewing machines (zin...@sewing CO, my apology) nor they are trying
to push us Kirby (http://www.consumeraffairs.com/in_home/kirby.htm, no apology)
vacuum cleaners using naive chastity of CCP4BB site.
They are
Any chance that it is myristate or some other fatty acid?
Good luck-
Steve
On Fri, Feb 19, 2010 at 3:42 AM, Marek Frischerkase
frischerkasema...@yahoo.de wrote:
Hello,
sorry for my off topic question.
I found a PEG molecule bound to the active site of my enzyme structure. And I
did not
ok I think I should say something here.For some reason I was unable to find
REPLY-ALL button and my reply did not go to everyone first so I had to write
another message.I got the answer to my original query and I used CCP4 (CAD)
and coot as suggested by Jan.
Having said that I did not know that
I guess it is a BB hosted by CCP4, but I think it serves a much wider
community of structural biologists, and it is valuable for that
community that there are suggestions about how to solve problems using
SHELX, or BUSTER or PHENIX software.. Certainly I learn new tricks.
So speaking as a
Ed Pozharski wrote:
http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html
Try PISA server - it will identify contacts and report total buried
surface area per contact.
On Fri, 2010-02-19 at 16:42 +0100, Jane Bailey wrote:
Dear all,
I am trying to calculate the domain-domain contact surface
Dear Daniel,
You can also try adding 100-200 mM ammonium hydroxide. The jump in pH
will dissolve your crystals. If you then set up your protein drop
above the buffer of your liking, vapor diffusion will bring the pH
back down to the original value, and in the process hopefully lead to
Hello Again,
The buried surface area is twice the interface area, because the interface is
counted twice when working out the solvent accessible area which disappeared
upon interfacing, once on molecule 1 and once on molecule 2. This is a matter
of definition. While I prefer to quote the
Dear Ivan,
It is great to have confirmation that you got answers to your initial
question that enabled you to solve your problem. The idea of the BB is that,
in exchange for the gift of other people's contribution to solving your
problem, you are expected to share the solution with the other
Dear all,
Problem is coming one after another. I got another question about how to
calculate the domain/domain orientations (tilt and twist angles). Sorry
I probably disturb a bit often
I searched a lot, but no publication says how it was calculated. Does
anybody know anything about
Begin forwarded message:
From: Charles W. Carter, Jr car...@med.unc.edu
Date: February 19, 2010 10:28:55 AM EST
To: George M. Sheldrick gshe...@shelx.uni-ac.gwdg.de
Subject: Re: [ccp4bb] anomalous difference fourier maps
I'm also inclined to join this discussion. I agree with both Gérard
American Crystallographic Association, Inc
2010 Annual Meeting
Chicago, IL July 24-29, 2010
http://www.amercrystalassn.org/content/pages/2010-meeting
CALL FOR PAPERS Abstract Submission Deadline - March 31, 2010
Session Name: 01.05 Structural Enzymology: Mechanistic (BioMac)
Day:
I have another basic question about the definition of the connectivity in
residues. The side chains of my Se-methionines show up as disconnected
atoms. There is no bond between the Se and the neighboring C atoms. Which
library or data files contain the information about bond distances etc? Or
how
The current remit of CCP4BB is protein crystallography. As such,
contributions from Phenix developers are welcome. Having said that, if
the question is about how to perform some operation(s) with CCP4 then
they perhaps ought to be somewhat circumspect in their response. If
after a week or so
Hi Everyone,
I hope everyone gets this email.
Below are the two answers I got on how to solve my problem using ccp4.I
actually emailed another person who wanted to know how I did it. So I got
to transfer what I learned immediately. But his email was offline not
through the forum.
The
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