Hi,
Our lab is planning to buy an X-ray machine for protein crystallography.
Which system would be best for home source, Oxford diffraction system
Xcalibur Nova or a MSC/Rigaku MicroMax-002.
sincerely,
sankar
--
Sankar naraya
I failed to mention that this particular group is a small set of
terminal residues (48 atoms I think) that are part of a poorly-
resolved HIS tag, so it turns out not to be a meaningful part of the
model anyway. I was just surprised to see negative values reported.
The other body (different
Molprobity has a great tool for this under the section Visualize
interface contacts. One caveat though, if the small molecule isn't
already in ligand depot you have to provide your own PDB format
description.
On 2/27/07, mathias <[EMAIL PROTECTED]> wrote:
Dear all,
Can anyone of you guys reco
Dear Mathias,
In the old days, I used a program called "ligplot", which gives you
a .ps output file with the interactions involved, and the distances.
I'm using PyMol as well, but things might not be exactly what you
want. Here, I'm just looking at residues 4.2 angstrom away in the
intera
Hi Friends,
Here is a summary for my question regarding "Glove boxes for crystallization".
They are given approximately in the order they received. I have also kept the
name and e-mail address for any additional information.
Hope some you will find this information helpful for your research. T
I have a perl script to do this job.
The pdb file should contain your ligand.
Simplest way to run it is "lig_contact file.pdb"
If the script does not find the ligand, you can switch to command line options.
The script prepares a pymol input file and fires it up to display the
interactions.
Afte
Dear all,
Can anyone of you guys recommend free software, or any open access
internet server, to calculate VDW interactions of small molecules
binding to protein. The only information I need is an output file
which lists all amino acids of the target protein which make VDW
interactions wi
Dear all,
I am trying to solve the structure of a protein complex, via MR, and when the
phasing is complete there is 1/3 of the unit cell that is missing electron
density. The density present looks very good and shows helices in regions that
were disordered in my NMR model, suggesting that it
Hi all,
joining this discussion late, however, it might worth mentioning that
Amersham/GE has phased out the good old FPLC and is no longer providing
neither service nor spare parts. Best to my knowledge the same will
happen to the Äkta-FPLC system soon leaving the Explorer and Purifier
their
I wouldn't call it numerical error, as such. Refmac doesn't
restrain/constrain the T, L or S values at all. In particular, the L
value can refine stably and accurately to a negative value.
Refmac is refining a set of ADPs constrained to fit a certain functional
form with parameters T, L and S. Th
Dear everyone:
An off topic question. I first build up a model using ARP/wARP,delete the
"DUMP" atoms, add the lost parts directly from the existing model(because of
the sequence identity) and then refine it with simulated annealing
program(anneal.inp) in CNS.The error is:
Run cad to merge the mtz files ( Reflection utilities)
(And make sure the labels are different..)
Then there is a Clipper utility which compares phases and makes all the
appropriate origin shifts etc..)
Eleanor
#
yang li wrote:
Hi All:
Now I have two sets of data from the same crystal,
Hi,
The hklview panel has a 'ps' button which is for writing a ps file out, as far
as I can tell from the prompts I get after pressing it. However, I keep getting
an empty file. Is this option working or am I missing something ?
Thanks for your help.
Boaz
Hi All:
Now I have two sets of data from the same crystal, and I want
to calculate the
phase difference of them. Anyone knows if there are programs that can calculate
it from two .mtz files?
Thanks
Li Yang
In Coot, you can "beam in an xxx" where xxx in this case is an
"acetate" using
File -> Search Monomer Library
Text: "acetate"
Click Search
Click "ACT: Acetate ion"
You can then Use Copy Molecule on this monomer and "Move molecule" to
move the copies to where you want them and use "Merge Molecu
Why not start your script with
pdbset xyzin ...
OCC UP ALWAYS OCC_RESET 1.0
BFAC ALWAYS B_reset 20
end
acob Corn wrote:
Dear everyone,
I'm attempting to do a large scripted pairwise alignment of
theoretical models to calculate rmsd over a pre-determined residue
range, but the PDBs that I'm u
Dear Deliang
The SURFACE program is still included in the current version of the
suite, so you should be able to run it from the command line or from a a
script. However there is no CCP4i interface to SURFACE, so you cannot
run it that way.
There is an interface to the AREAIMOL program which give
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