I think it is still hard to beat lsq_imp as implemented in 'O'.
http://xray.bmc.uu.se/alwyn/A-Z_of_O/everything_e-l.html#anchor1342614
Cheers,
Martin
On Nov 15, 2010, at 2:32 AM, Clement Angkawidjaja wrote:
DALI server (http://ekhidna.biocenter.helsinki.fi/dali_server/). Choose the
Hi,
maybe you solved your problem,
if not, you can try this : You prepare your protein at high salt
concentration. After that you add your ssDNA directly and you proceed by
dialysis. You prepare your dialysis with a low salt concentration
buffer. You can use different buffer by step in order
Eric Karg harvard...@yahoo.com
Datum:
Sun, 14 Nov 2010 21:37:10 +
Dear all,
Thanks for your suggestions. From what I learned new GPUs from NVIDIA are
using the Optimus technology which does not support Linux, meaning that only
the dedicated graphics on the system will be used in
I would first calculate least square superposition of the first monomer between
2 structures (one to be fixed and one to be moved) using a program such as
lsqkap or any other programs suggested by others. You may need to define a
relevant region for the superimposition.
Then take the output
Raj,
There are many programs that will give you an RMSD per residue difference
between your bound and un-bound protein. Some will even write the RMSDs to
the B-factor column of your PDB. You can then visualize regions in your
protein that have structural changes/movement in the bound vs.
Hi
I'm refining my first structure with a significant amount
of ncs and am not looking forward to my usual, manual, editing
of the water model. Could someone point me in the direction of
a program that will encourage my water to obey the ncs?
What I have in mind is to, first, find each
Dear Dale,
concerning the first part of your request you can use BUSTER and
include your water molecules in ncs restraints.
Here is the link for the wiki explaining that
http://www.globalphasing.com/buster/wiki/index.cgi?AutoBusterExample4chawaterNCS
HTH
All the best
David
Le 15 nov. 10 à
Dear colleagues,
I would like to draw your attention to an upcoming webinar to be presented
by Janet Newman, Ph.D. titled When you need a challenge, try protein
crystallisation: Tips and suggestions for helping you over the hurdles.
Janet currently runs theBio21 Collaborative Crystallisation
Here's an ignorant question: When people express an exogenous tRNA in E coli
(to overcome rare codon issues, for example, or to supply a cognate tRNA for an
orthogonal synthetase), what sorts of promoters are used?
My (ignorant) guess is that something as potent as the T7 promoter might be a
