Dear Wenhe,
You don't need any skills to use Ligplot. Only thing you have to give is
the residue number of the ligand or the small molecule you are interested
in the command line.
There are other commercial software but i don't know whether they are of
any interest to you ! MOE or MAESTRO
PhD and Postdoc opportunities in Singapore in Structural Biology.
The Bob Robinson laboratory is looking for candidates to apply for a range of
scholarships and fellowships in conjunction with the laboratory. Joining the
laboratory will be conditional on securing the award.
The laboratory, in
Wenhe
There is a ligand environment viewer at the URL below that plots
environments of ligands
in various view types. At the moment is only works on existing
structures since the ligands
have to be correctly typed with correct dictionaries.
This has a number of export formats.
Hi Anita,
I have recently performed it following this protocol I found in the Internet:
http://wolfson.huji.ac.il/purification/Protocols/PAGE_Acidic.html
I hope this helps! Good luck,
Federica
--
Federica Basilico
Ph.D. student
Department of Experimental Oncology
European
Regarding our IMPRS:
Talented junior scientists are offered the opportunity to earn a doctorate
under excellent research conditions in Tübingen, Germany. Doctoral
students benefit from regular workshops and supervising tutors at the Max
Planck Institute for Developmental Biology, the Friedrich
For those of you interested, the reply to Tassos' question can be found
here:
http://www.iucr.org/resources/commissions/crystallographic-computing/schools/school96/ccp4-program-system
(on-line)
as well as here, http://www.*ccp4*.ac.uk/manual.ps (a ps file).
McLaughlin, Terry and Zelinka.
Let's have some more info here.
What resolution we talking about? What are the space groups?
What is the nature of the Co (is it a heavy atom soak?, a bound Co?)
Have you tried to find heavy atom sites? (anomalous Patterson, or some other
automated method)
Are they believable?
You say the
Hi all,
There is a good news and it is that we have got crystals this morning which
have diffracted upto 2.5 ang at home source and data collection is going
on. I hope this solves the problem though the not so good anomalous signal
at home source will probably make SAD phasing difficult. However
New Fourier transform algorithm supposedly improves the speed of Fourier
transforms get up to a tenfold increase in speed depending upon
circumstances. Hopefully this will get incorporated into our refinement
programs.
http://web.mit.edu/newsoffice/2012/faster-fourier-transforms-0118.html
--
On Fri, Jan 20, 2012 at 9:37 AM, Jim Fairman fairman@gmail.com wrote:
New Fourier transform algorithm supposedly improves the speed of Fourier
transforms get up to a tenfold increase in speed depending upon
circumstances. Hopefully this will get incorporated into our refinement
programs.
On Friday, 20 January 2012, Jim Fairman wrote:
New Fourier transform algorithm supposedly improves the speed of Fourier
transforms get up to a tenfold increase in speed depending upon
circumstances. Hopefully this will get incorporated into our refinement
programs.
The problem is however, that the coffee break is lost in the noise of this FFT.
Jürgen
On Jan 20, 2012, at 12:57 PM, Ethan Merritt wrote:
On Friday, 20 January 2012, Jim Fairman wrote:
New Fourier transform algorithm supposedly improves the speed of Fourier
transforms get up to a tenfold
Hello Everyone,
Does anyone know of a quick (yet somewhat reliable) sort of cheat-sheet/quick
reference sheet with the more common folds with an illustrative example?
Hi Yuri,
I don't know of a cheat-sheet, but I find the Introduction to Protein
Structure book by Branden and Tooze to useful for illustrations of
common folds.
Jeff
On Fri, Jan 20, 2012 at 10:13 AM, Yuri Pompeu yuri.pom...@ufl.edu wrote:
Hello Everyone,
Does anyone know of a quick (yet
A very similar question: how about smaller motifs, such as various
turn types, etc.?
JPK
On Fri, Jan 20, 2012 at 12:37 PM, Jeff Headd jjhe...@lbl.gov wrote:
Hi Yuri,
I don't know of a cheat-sheet, but I find the Introduction to Protein
Structure book by Branden and Tooze to useful for
From the rather non-technical inofrmation available so far, it seems to
me that it is like leaving out all but the strongest reflections (or
perhaps the strongest normalized structure factors). This is unlikely to
improve the quality of structure refinement, the importance of using as
much
In addition to the book recommended by Jeff, another good one is Protein
Structure and Function by Petsko and Ringe. A bit less cumbersome than Branden
and Tooze, but not as complete (it's a relatively thin paperback, rather than a
full-blown textbook). If you just want a nice protein domain
George Sheldrick gshe...@shelx.uni-ac.gwdg.de a écrit :
For all those interested in the technical details about this new
Fourier stuff, I saw that the whole paper is available from the web
site, not only the simplified account (look at right of this awfully
wrong 3-term Fourier synthesis
Thanks guys
After quick look at the manuscript: It is applicable to sparse signals (i.e.
number of non-zero elements is not whole space). It would be applicable to
inverse FFT after density modification and gain would not be that much.
k-sparse approximation would loose signal (strictly speaking it does
Hi-
I am trying to help my former chemistry teacher set up a demonstration of
protein structure for her class. I'd like to include electron density maps,
and maybe show an enzyme active site. Are there suggestions from the BB on
the easiest way to do this? Would pymol be the program of choice, or
Hi,
I think that spdbv (deepview) and the tutorial has some of what you need. The program is very simple to implement on any Mac or PC, although it's not the nicest program to use in the long run. It'll take you 5 minutes to install and test the features you'd
like from the tutorial.
Hi,
I've given a couple talks/demos to HS students. As much as I love enzymes, I
found it more effective to show structures of proteins binding to other
biological molecules (not just other proteins). I typically show
phosphatidylinositol binding protein (PITP) bound to phosphatidylcholine,
Thanks everyone for the helpful responses! For the curious, here is a list
of the postings:
*
I have two to recommend. I don't know how many outside samples they
process but Oak Ridge National lab has a spectacular mass spec facility
that we used extensively while i was at the University of
Does trimethyl lead tend to lose the Me in aqueous buffers?
A colleague is preparing to deposit a 2.9A structure that
was refined against the TML derivative (higher resolution than native).
Since the Pb was added as trimethyllead, the first inclination is
to report the heavy atoms as TML, ligand
James,
I would like to recommend the free ICM-Browser
http://www.molsoft.com/icm_browser.html . It is widely used for teaching
structural biology and it is easy to make fun and interesting fully
interactive 3D slides and animations of protein structures.
The students can view the fully
foldit doesn't do electron densities and I don't recall if there are
any puzzles in it that mention active sites/docking (it's been more
than a year since I played it), but it's worth a mention.
Hi-
I am trying to help my former chemistry teacher set up a demonstration of
protein structure
27 matches
Mail list logo
