Mitch,
For discernment of Sodium versus Potassium, you could also look at the bonding
distances and coordination of the metal present. Ran into this problem back in
the day. Check out Figure 6 C,D in the following pub:
https://pubs.acs.org/doi/10.1021/bi060653d
Scott
--
Scott Pegan
overkill.
Scott
--
Scott Pegan
Professor
Division of Biomedical Sciences
School of Medicine
University of California Riverside
205 SOM Research Building
900 University Avenue
Riverside, CA 92521-0001
(951) 827 7907
sco...@medsch.ucr.edu<mailto:sco...@medsch.ucr.
Been looking for Coot 0.9 or better package install files for OSX, anyone know
where to look? I seem to only find 0.8 or less through the web.
Scott
--
Scott Pegan
Professor
Division of Biomedical Sciences
School of Medicine
University of California Riverside
205 SOM Research Building
900
UES-0z62ageiNePBE9Gpp3dgqAPNRz3VZzIHMro=Iz8lWyIbP3vL-NGKrg5yVkzo7s8ezLFTDapmmb1Ohx8=52YlnmPwBgb3lt5fqknA14rv_L5tgPK4suCKlO1nSWU=>.
Come check us out!
Scott
--
Scott Pegan
Professor
Division of Biomedical Sciences
School of Medicine
University of California Riverside
205 SOM Research Building
900 Univ
Finally looking to replace my 2014 Mac Pro lap (duo core; 16 gb RAM. I
would welcome any input or being put in the direction of some related to
the following:
13" versus 16"
I know the 16" has a better and standalone GPU. Is there anyone using a
13" that finds that it works well? If so, what
Seeking Post-Doctoral candidates for my rapidly expanding laboratory
located in the University of Georgia's Department of Pharmaceutical
Biomedical Sciences.
In this recently available positions, the individual will assist in my
ongoing NIH funded infectious disease related projects that involve
Seeking Post-Doctoral candidates for a position in my laboratory located in
the University of Georgia's Department of Pharmaceutical Biomedical
Sciences. In this newly added position, the individual will assist in my
ongoing USDA funded infectious disease related projects that involve the
use of
Anita,
From your description, you most likely are looking for a prefilter6000.
http://www.gelifesciences.com/webapp/wcs/stores/servlet/productById/en/GELifeSciences/18458201
Scott
Scott D. Pegan, Ph.D.
Associate Professor
Pharmaceutical and Biomedical Sciences
College of Pharmacy
University
In the process of acquiring a crystallography robot for the laboratory. I
have narrowed along capability and budgetary constraints to either an
Formulatrix NT8, or a Art Robbins Gryphon. I know the Art Robbins
instrument characteristics pretty well, does anyone have any
experience/advice on the
Seeking Post-Doctoral candidates for a position in my laboratory located in
the University of Georgia's Department of Pharmaceutical Biomedical
Sciences. This individual will assist in my ongoing NIH funded infectious
disease related projects that involve the use of structural biology
Dear CCP4 Bulletin Board Members,
I am looking for Post-Doctoral candidates for a position in my laboratory
located in the University of Georgia's Department of Pharmaceutical
Biomedical Sciences. This position will assist in my ongoing NIH funded
infectious disease related projects that
Hey everyone,
Both Mark and Fred make some good points. I totally agree with Nat (beat
me to the send button). Although in an ideal world with all the
advancements in crowd sourcing and electronic media, one might think that
posting data on a bulletin board might be considered marking one's
CCP4,
I will be doing some MBP fusion purification in the near future and I was
wondering if anyone knew what the most cost effective MBP trapping resin to
use. So, far I have seen the following two products, are there any others
I should consider?
GE* Healthcare MBPTrap HP ColumnsNew England
Dear Jose,
Last year we acquired a TA instruments nanoITC after evaluating it and a
Microcal model. For the price, the TA instrument was a considerable steal,
was ~$50,000 cheaper the the Microcal Model. We didn't see or have since
seen any issues with quality of the instrument. Software
Hey all,
Does anyone know of a good article that deals with differentiating between
a lithium ion and sodium ion for density in a X-ray structures?
Scott
--
Scott D. Pegan, Ph.D.
Assistant Professor
Chemistry Biochemistry
University of Denver
Office: 303 871 2533
Fax: 303 871 2254
Yeah, maybe if he got down to 1.0 Angstrom he could get it in the front
door.
Scott
On Tue, Nov 1, 2011 at 8:39 AM, Jacob Keller j-kell...@fsm.northwestern.edu
wrote:
Maybe you could refine it using our new-fangled methods to improve the
model? (Couldn't resist such irony!)
Jacob
On Tue,
Here is also a very effective method:
1Gill, S. Hippel, P. v. Calculation of protein extinction coefficients
from amino acid sequence data. Analytical Biochemistry 182, 319-326,
(1989).
On Thu, Jun 16, 2011 at 5:56 PM, Filip Van Petegem
filip.vanpete...@gmail.com wrote:
A convenient
Trying to calculate a difference map from a dataset downloaded from the RCSB
and one I have. The following applies:
Object find the difference between two bound ligands of the same structure
in the same space group.
My following work path has been:
1) Convert mmCIF to mtz (RCSB data set)
2)
Rakesh,
Composite maps are used in publications some times however many folks also
publish the 2Fo-Fc or even better the 1Fo-Fc. These can be obtained by
selecting a button in refmac to export the maps and then visualize them in
pymol.
Scott
On Mon, Aug 9, 2010 at 8:37 AM, Rakesh Joshi
Kelly,
You can do it with swiss-model, just have to use the alignment mode. I will
ask for a pdb or RCSB code. Also, in the past I have found Jigsaw 3D model
server to be a comparable tool.
Scott
On Wed, May 12, 2010 at 10:10 AM, Kelly Daughtry kddau...@bu.edu wrote:
Hello all,
I would
Nat,
A few years ago I had K channel crystals that formed under similar
conditions. I found that using MPD as a cryo-protectant worked best. As
for the evaporation issue, I had a little extra time as I was performing the
mounting in a cold room.
Scott
Pegan S, Arrabit C, Zhou W, Kwiatkowski W
Nice
Scott
On Mon, Nov 23, 2009 at 1:07 PM, Ed Pozharski epozh...@umaryland.eduwrote:
Ian,
On Mon, 2009-11-23 at 17:34 +, Ian Tickle wrote:
Ed,
For instance, if angles are measured in degrees and x1
sin x ~ pi * x / 180
sin x ~ x
Your equations cannot simultaneously be
I am looking for a good review on SBDD that includes a few successful
attempts. Anyone know one?
Thanks,
Scott
--
Scott D. Pegan, Ph.D.
Assistant Professor
Chemistry Biochemistry
University of Denver
Starting a new lab and looking for an inexpensive stereo microscope to
support my crystallography. Any thoughts or recommendations? Would like
for it to have a way to take a photo of the crystals either through an
eyepiece or dedicated camera port. As any new lab, a cheap option won't be
bad.
Recently tried to install ccp4-6.1.1-i386 on a leopard 10.5.7 system
Installer worked
Then I corrected the ccp4.setup-sh file to reflect the location of bltwish
/usr/local/X11/bin
Ran ccp4i and it worked once. Every-time after that it opened and closed
immediately. Using X11 2.3.3.2. Anyone
Andy,
We do a lot of liganding fitting with CCP4. This is the general order of
steps we take (post initial solution of the protein itself):
1) Build the potential ligand in CCP4 Sketcher
a) Rename all the Hydrogens to H#, CCP4 Refmac has some issues with
Hydrogens marked OH1, NH1, etc. To
Warren,
If we are buying a system from scratch, can I get the GeForce 2 card and 3D
bundle and have it work for winCoot?
Scott
On Tue, Jan 27, 2009 at 2:58 PM, Warren DeLano war...@delsci.com wrote:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0901L=CCP4BBT=0F=S
Jacob,
You could also just use reindex app in CCP4 to change the original MTZ to a
P22121 MTZ.
Scott
On Sat, Nov 8, 2008 at 1:46 AM, Kay Diederichs
[EMAIL PROTECTED] wrote:
Jacob,
you could use, for refinement, the FP SIGFP columns from the .mtz-file that
PHASER writes out, together with
The best why that I have put inhibitors in is by using the sketcher program
in CCP4. Its a little unwieldy at first but if you get the hang of it, it
provides pdb's and library files that can be directly inputed into refmac
and Coot. The Coot ligand find function does a pretty good job of
Just to put my two cents in on this as I would fall into that new generation
so to speak:
I started out with the SGI and linux systems with stereo, O, and dials about
eight years ago. Never used the dials and rarely seen anyone else use
them. Over the past few years I have transition to coot,
I just recently purchased a Mac Pro Intel with Leopard. I was able to
install, Coot and ccp4. Both were not as straight forward as I would have
hoped but still possible.
For Coot:
Go to:
http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Coot-0.5-pre-1-968_for_Intel_10.5_only
Download :
Deena,
If you are going to run windows, have to use XP. I tried vista, and the
software wouldn't work.
Scott
On Wed, February 20, 2008 2:44 pm, Paul Paukstelis wrote:
Or don't buy an OS at all. There are a number of vendors out there that
sell OEM notebooks without OSs. I picked up a Compal
:[EMAIL PROTECTED] On Behalf Of
Scott
Pegan
Sent: Wednesday, February 20, 2008 22:04
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Vista
Deena,
If you are going to run windows, have to use XP. I tried vista, and the
software wouldn't work.
Scott
On Wed, February 20, 2008 2:44 pm
Don't know if anyone has mentioned this paper but its an exact example how
to make a K channel soluble.
Roosild TP, Choe S.
Redesigning an integral membrane K+ channel into a soluble protein.
Protein Eng Des Sel. 2005 Feb;18(2):79-84. Epub 2005 Mar 23.
PMID: 15788421 [PubMed - indexed for
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