Hi All,
I have used MRBS
http://mrbs.sourceforge.net/
to manage booking of a large number of instruments for a few years.
Free, open source, simple, local installation, works very well.
regards, Dmitry
--
Dr. Dmitry Veprintsev
Biomolecular Research Laboratory, OFLC/103 Paul Scherrer Institut
Dear Hua,
adding water as suggested by Jan Kern could also be accomplished in a more
sophisticated way by using dialysis buttons. They require large volumes, though,
5mul is the minimum as far as I know.
At the fancy end of this you could try the TOPAZ system by fluidigm.
At the ECM in
Hello everybody,
Currently I am refining my 6 x 220 amino acid structure and
I was wondering if COOT is automatically writing a kind of protocol
what I am changing in my pdb file when I am fitting-in new residues or mutate
amino acids. If so where can I find it?
Thanks a lot,
Stefanie
Dr.
Hi,
I'm on Garib's side here. The way the maximum likelihood targets work, the
variances are defined relative to the average intensity in a resolution shell,
so if you change the falloff the variances will change in the same way. In
fact, one way to implement maximum likelihood refinement is
Hi, Stefanie
Are those 6 molecules related by NCS? If so, you can model one first,
and use transform_coords_molecule (imol, rtop) to generate others.
I used to do this five times for a pentamer:
output_pdb='template'
for i in range (2,6):
transform_coords_molecule (1, [[x1, y1, z1, x2,
Dear Randy,
thanks for your comment - a good point with the likelihood target
estimated from E-values! So, in principle, there shouldn't be any
difference in maximum-likelihood refinement using sharpened data or not.
However, for curiosity, in one case at 4.3 A resolution and a sharpening
Dear all,
I have a 3 yr postdoc position available in my lab (Biochemistry,
Bristol), starting early/mid April. Please see below for further particulars.
Informal enquires welcome, though full applications MUST be made via the
University of Bristol website
Hi Zheng
I think, it's much easier to go this way:
Coot - Extensions - NCS - Copy NCS Chain or Copy NCS Residue Range
Cheers
Stefan
-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Zheng
Zhou
Gesendet: Montag, 28. Februar 2011 12:13
An:
I have brought my collection of teaching powerpoints etc. up to date. They
are available free for educational purposes. Please send me an email if
you wish to receive the password for accessing them. If you previously
obtained this password from me it should still be valid.
George
Prof. George
In a sentence, primarily due to cost and power constraints mobile
devices don't (currently) have the horsepower to do any serious
*generic* number crunching, as would be required for anything of
interest to this community.
On the topic of using otherwise-idle compute time, our group has a
On 2/25/11 5:41 PM, Nat Echols wrote:
On Fri, Feb 25, 2011 at 2:10 PM, Sean Seaver s...@p212121.com
wrote:
I've been curious if there has been discussion about moving
data processing and refinement to a software as a service
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)
I just looked at a previous thread by Dale Tronrud that explains this.
here it is:
Re: [ccp4bb] Fo-Fo Difference Map
Dale Tronrud
Mon, 03 May 2010 16:19:46 -0700
I've struggled with getting CCP4 to calculate Fo-Fo maps, since I
usually use other software. The tricks are that the data sets
Have you tried adding water to your reservoir and allowing it to vapor diffuse
into the drop?
Kris
Kris F. Tesh, Ph. D.
Department of Biology and Biochemistry
University of Houston
- Original Message
From: Tim Gruene t...@shelx.uni-ac.gwdg.de
To: CCP4BB@JISCMAIL.AC.UK
Sent: Mon,
Replacing the Coot step by FFT works too.
An additional benefit of the Coot approach is that you can use
LSQ-matched maps and maps on different grids and space groups. (I was
under the impression that that was not quite so easy with FFT.)
Also worth noting, Coot does not (yet) do
Yes - you are.
-
There are some extra steps.
Download pdbs and mtz files
csymmmatch -pdbin-ref 1.pdb -pdbin 2.pdb -origin-hand -pdbout 2-to-1.pdb
That checks they are on same origin and symmetry equivalent.
refmac for 1.pdb
refmac for 2-to-1.pdb
cad to merge two refmac outputs.
You will
2) Scale F-holo and F-apo. Use Experimental Phasing, Data
Preparation, Scale and Analyse Data Sets, Scale refinement using
Scaleit. Don't include anomalous differences unless your interest is in
changing anomalous scatterers. My notes indicate that Fhscal works
better but does
Hello,
I could not open the COOT GUI after installing either from
'coot-0.6.1-binary-Linux-x86_64-centos-5-gtk2.tar.gz' or from
'coot-0.6.2-pre-1-revision-3205-binary-Linux-x86_64-centos-5-gtk2.tar.gz'
I used the following commands:
1. from /usr/loca/src
sudo tar xvzf *.gz as suggested in
Hello Hena,
maybe the libpng12.so.0 libraries on your system happen to be all 32-bit
versions. You installed the 64-bit version (because of the x86_64 in the name
of the tar-archive), therefore you also require a 64-bit version of the
libpng12.so.0. Do you have such a file in /usr/lib, and if so,
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