-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Atul,
the "resolution" of your data set would affect the whole unit cell and
not just the region of 30-40 residues. The more likely reason is a
disordered N-terminus. There is nothing to do about this in silico.
It may be worth recloning your pr
Dear all
I have crytals which diffract up to 3.2 A at synchrotron, I am solving this
by molecular replacement. I have built 70% of the model successfully,but
the problem is it have a very poor density for some 30-40 residues at N
terminal. I can't build anything in this region,this could be becaus
Consurf will do this for you.
Bostjan
---
Bostjan Kobe
NHMRC Research Fellow
Professor of Structural Biology
School of Chemistry and Molecular Biosciences
and Institute for Molecular Bioscience (Division of Chemistry and
Structural Biology) and Centre for Infectious Disease Research
Cooper Roa
Usually you put a statistic like this in the tempFactor field (B) and then
color by "B-factor" in pymol or similar.
I'm certain there is a facility for filling this entry somewhere. If not, then
a fairly trivial server is waiting for someone to create it and claim the glory.
Google something li
I once saw a figure showing the protein as surface, but instead of having it
coloured by atom type
or potential, it was shown by percent conservation in the family. Something
like red highly conserved, all the way to white, not conserved at all...
Now, I assume the figure was done by uploading al
Works fine with MacPyMOL v. 1.5. You have to copy MacPyMOL.app to
MacPyMOLZalman.app and fire this off.
Cheers,
Scott
Scott T. R. Walsh, Ph.D.
Assistant Professor
University of Maryland College Park
Institute for Bioscience and Biotechnology Re
Yep - works fine on Coot and Chimera. Others may correct me, but I don't think
Schrodinger have re-instated support in PyMol?
I use it daily - the Zalman is the primary monitor on my desk. The great
advantage of this type of monitor (IMHO) is that it is hardware independent.
Applicants are invited to apply for a postdoctoral position in the area of
structural biology and signal transduction. We are seeking one
enthusiastic, well-trained and self-motivated scientist with excellent
organizational and communication skills to join Dr. Nicolas Nassar's team
at CCHMC. The re
On Wed, Dec 7, 2011 at 3:48 PM, Erik Martinez-Hackert wrote:
> Can anyone positively confirm that the new Zalman monitors M240W or M215W
> actually work on macs and pymol/coot? Specifically, I want to put this on a
> new macpro with an ATI Radeon HD 5770 card, but we also have older systems.
Ye
Can anyone positively confirm that the new Zalman monitors M240W or M215W
actually work on macs and pymol/coot? Specifically, I want to put this on a new
macpro with an ATI Radeon HD 5770 card, but we also have older systems.
Answers are very much appreciated, thanks in advance.
Erik
On 07/12/11 11:58, matthew vetting wrote:
I think you are probably asking the wrong question, and what you are
eventually going to want to know is how do I get a modified amino acid
recognized in PHENIX or REFMAC so that it makes proper peptide bonds.
The making and breaking of bonds in COOT
The Protein Crystallography Station is a high performance neutron beamline
located at the spallation neutron source at the Los Alamos Neutron Science
Center in Los Alamos, NM. We have limited beam time available for Fast
Access proposals for the Jan/Feb beam delivery cycle. We are also pleased
to a
Oops,
Meant to hit reply all...
Hi there,
You can generate a link via jligand which gives you a covalent linkage with
your enzyme / ligand.as well as a cif file
Try the tutorial ftp://ftp.ccp4.ac.uk/JLigand/tutorial_link.html
J
_
Joel Tyndall, PhD
Senior Lec
Then probably PFAM does what you want
http://pfam.sanger.ac.uk
Best
Jose
On 12/07/2011 11:43 AM, 商元 wrote:
-- Forwarded message --
From: *商元* mailto:shangyuan5...@gmail.com>>
Date: Wed, Dec 7, 2011 at 6:41 PM
Subject: Re: [ccp4bb] Did anyone here know how to config a local
Dear colleagues,
I would like to bring your attention to the following vacancy at Brown
University. Please feel free to forward to any NMR structural biology
colleagues that might be interested in this position:
*Assistant Professor in Structural Biology, NMR*
The Department of Molecular Pharmac
I think you are probably asking the wrong question, and what you are
eventually going to want to know is how do I get a modified amino acid
recognized in PHENIX or REFMAC so that it makes proper peptide bonds. The
making and breaking of bonds in COOT (or O for ligands) is not something
that gets
On 7 Dec 2011, at 10:08, Paul Emsley wrote:
> On 07/12/11 09:47, Tim Gruene wrote:
>>
>> if you want coot to refine the bond length, you have to rename the
>> residue to some name coot does not yet understand and create a cif-file
>> which includes the restraints of the residue, the ligand, and t
-- Forwarded message --
From: 商元
Date: Wed, Dec 7, 2011 at 6:41 PM
Subject: Re: [ccp4bb] Did anyone here know how to config a local protein
secondary structure prediction server?
To: Jose Duarte
Dear Jose,
Thanks for you kind replies and they are very helpful.
Both HSSP an
Research Associate at Imperial College London
We are seeking to recruit a Research Associate to work with Professor Xiaodong
Zhang’s research team in the Division of Molecular Biosciences, Centre for
Structural Biology, at the South Kensington Campus of Imperial College London
(www.imperial.ac.
On 07/12/11 09:47, Tim Gruene wrote:
if you want coot to refine the bond length, you have to rename the
residue to some name coot does not yet understand and create a cif-file
which includes the restraints of the residue, the ligand, and the bond
between the two.
JLigand is the way to do this.
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Hello Saugata,
if you want coot to refine the bond length, you have to rename the
residue to some name coot does not yet understand and create a cif-file
which includes the restraints of the residue, the ligand, and the bond
between the two.
Tim
On
>
--
AstraZeneca UK Limited is a company incorporated in England and Wales with
registered number: 03674842 and a registered office at 2 Kingdom Street,
London, W2 6BD.
Confidentiality Notice: This message is private and may
Anyone know how to minimize the domination of heavy atoms during RSR in coot.
The density from my zincs causes the coordinating His residues to collapse onto
the metal ion when I try RSR.
Cheers in advance
Dean
23 matches
Mail list logo
