One of the features that Global Phasing's routine runs of deposited PDB
structures often pick up is very close contacts between the SG of cysteine
residues and the CAB and CAC atoms of the propenyl groups on HEM ligands, not
described by LINK cards in the header of the deposited structure.
Yes, thanks for asking. Having 6 active sites in my AU, showed that 4 of
them had a single beta-mercaptoethanol molecule, and the other two had the
density I posted here. It turned out to be a single BME in 2 different
conformations. thanks for the help and suggestions!
Hello all,
I am sorry for this off-topic question. I see it has been discussed many
times, but somehow I got stuck in the very beginning.
I want to assign ss to my pdb file in DSSP, but I could not find a
server to run it. Does anybody know a webserver where I could run this
kind of tasks?
Hello Jane,
if I remember correctly, rasmol uses the dssp algorithm for the secondary
structure assignment. You can also use pymol or molscript (molauto) for
the same task. In any case you should always check the boundaries of the
secondary structure elements manually because no program is
Jane,
you could use ksDSSP, which is an OpenSource implementation of DSSP.
Requires some compiling though and I am not sure if OSX is supported.
You also need to compile the PDB record I/O libraries.
http://www.cgl.ucsf.edu/Overview/software.html
Cheers,
Carsten
-Original
Hello Jane,
CMBI (http://swift.cmbi.kun.nl/gv/dssp/) offers the source code after
signing a licence agreement. I compiled it on my Mac using one of the
compile-scripts that came with the tar file. You have to install the Mac
developer package Xcode (free from developer.apple.com) for getting
Thomas Womack wrote:
. . .
There are a number of high-resolution structures deposited recently containing haems near
cysteines, and in most of them a re-refinement gives substantial positive difference
density about the CM atoms; there is even occasionally a sign of some kind of longer tail
Hi,
you can use the nice tool dssp2pdb by James Stroud
(http://structure.usc.edu/dssp2pdb) to assign the ss of the DSSP output
to your pdb file. See instructions there.
HTH
Guenter
I am sorry for this off-topic question. I see it has been discussed
many times, but somehow I got stuck in
On Thu, Jan 14, 2010 at 7:02 AM, Schubert, Carsten [PRDUS]
cschu...@its.jnj.com wrote:
you could use ksDSSP, which is an OpenSource implementation of DSSP.
Requires some compiling though and I am not sure if OSX is supported.
You also need to compile the PDB record I/O libraries.
It runs
Or know of any references besides Declercq and Evrard, 2001 ? I'd love
to hear from you. Please PM me.
Cheers
FR
-
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder
gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
8AE2 F2F4 90F7 9640
The Canadian Light Source (CLS) is pleased to introduce the fifth annual
Saskatoon Synchrotron Summer School (S4V) scheduled for June 13 - 18th, 2010 in
Saskatoon, Saskatchewan. This year's school is for students and researchers
interested in learning synchrotron techniques for life science
Hello All,
Has anyone else noticed a lack of availability of Zalman 3-D LCD
monitors? For at least a few weeks now, NewEgg and Dell are currently
out of stock, as is every retailer that lists their inventory.
I attempted to contact Zalman, but have not yet had a response.
If you know of a
On Thu, Jan 14, 2010 at 3:57 PM, Andrew Ring ar...@berkeley.edu wrote:
Hello All,
Has anyone else noticed a lack of availability of Zalman 3-D LCD
monitors? For at least a few weeks now, NewEgg and Dell are currently
out of stock, as is every retailer that lists their inventory.
I attempted
Hi Andrew,
Has anyone else noticed a lack of availability of Zalman 3-D LCD
monitors?
Yes, we noticed the same thing. Newegg went out of stock around
Thanksgiving, and various other retailers were either out of stock or had
coming soon sort of notices on the product pages over the last month
Hi,
http://www.provantage.com/zalman-tech-trimonzm-m220w~7ZALM03E.htm
As someone mentioned still showing 4 in stock. That's where we got ours from.
HTH,
Sabuj Pattanayek
Postdoc position at the University of Oregon, Institute of Molecular Biology
Eugene, OR
We are seeking a highly motivated postdoctoral researcher to join our lab
full time on a flexible start date. Our interest is in understanding the
molecular basis for the regulation of the cytoskeleton. We
Postdoc position in cryo-electron tomography
A postdoctoral fellow position is available beginning in April 2010
in Dr. Liu’s laboratory at UT Houston Medical School
(http://www.uth.tmc.edu/pathology/faculty/faculty-Liu-Jun.html). My
laboratory is studying 3-D structure/function of
Does anyone know how to get extra glasses?
Yes,
contact mark.gar...@asipartner.com and ask for it.
ASI – Fremont, California
48289 Fremont Blvd.
Fremont, California 94538
Jürgen
On Jan 14, 2010, at 10:07 PM, William G. Scott wrote:
Does anyone know how to get extra glasses?
-
Jürgen Bosch
Johns Hopkins Bloomberg School of Public
Hello,
By the way, does anyone got this LCD in Japan?
My team is interested to know the model's exact
reference as well as from where you ordered it.
Thanks a lot,
Francois.
Hi, Francois
We bought it 5 months ago from a supplier in Japan.
(and it has been put back in a box under a desk.)
Zalman has its own web site in Japan. Model name is the same.
http://www.zalman.com/jpn/product/monitors/ZM-M220W.asp
You can buy it from many shops through the web.
Check the
BTW, has anyone tried out the higher resolution 24 inch 3D model from Zalman
that appears to be available
from this reseller in Japan?:
http://mikimoto-japan.com/beans/products/product_dsp.htm
and this reseller in the UK:
http://www.cleverpc.co.uk/index.php?productID=5338
My guess it that it is
22 matches
Mail list logo
