On Mar 12 2007, Andy Purkiss wrote:
Quoting Andrew Wong <[EMAIL PROTECTED]>:
I was using Phaser for some MR with a data set in P1 (may not actually
be P1, but..), and in every run I always got a list of "solutions" that
all have TFZ=100.0, with a very small LLG (around 0 or even in the
negat
The X6A workbench: Advanced structural biology tools
April 10-13, 2007
is a hands on course for those interested in experiencing synchrotron data
collection.
Participants will learn about synchrotron hardware, crystals, data collection
strategies and
how to obtain an electron density map.
When I've wanted to show an internal cavity I've found the best route is:
pdb file->voidoo->mapman->ccp4 map->pymol
(play with your probe size in voidoo to prevent thr probe from "rolling out" of
your cavity)
You can load the ccp4 formatted cavity maps into xfit/coot, you get your volume
meas
Hiya
In PYMOL, you could use the selection feature to select which residues you want
to draw surface over (there are some pretty powerful selection syntaxes in this
package so could could select your actve site residues in a number of ways -
see http://pymol.sourceforge.net/) - then create surf
Hi Juan,
This doesn't directly apply to Superpose -- but THESEUS (which does
both conventional least-squares and maximum likelihood
superpositions) puts RMSD values by default in the B-factor column of
the PDB of the mean structure for a superposition. It is
undocumented, but via the THE
Dear all
I have three questions that might have been answered before but I haven't
been able to find them.
1) I was wondering whether anyone could tell me what does (in the Superpose
output) "RMS B DISPLACEMENT" stand for?
2) If "B" is B-factor how meaningful is it if the haven't been n
Hello All,
I would like to make an illustration which has a semi-transparent surface
rendering for a large cavity. I just want the suface to cover the cavity not
the entire protein (which will most likely exist as a ribbon drawing). Is there
a way to set a boundary for a surface drawing? By tha
Deal all, thank you for all the wonderful helping tips. A quick test
of ATP-Mg at 2mM at 37C for 2 hours had proved ineffective in my case
so now I'm thinking of trying the other protocols that you had offered
as listed below. Many thanks and have a wonderful week! -yong
Original Question
RE: Rem
MRC PROTEIN PHOSPHORYLATION UNIT
COLLEGE OF LIFE SCIENCES
UNIVERSITYOF DUNDEE, SCOTLAND
PROGRAMME LEADER, CELL BIOLOGIST WITH X-RAY CRYSTALLOGRAPHIC EXPERTISE
The Unit is seeking to recruit a cell biologist with X-ray
crystallographic expertise who will develop a structurally-based
pro
Quoting Andrew Wong <[EMAIL PROTECTED]>:
> I was using Phaser for some MR with a data set in P1 (may not actually be
> P1, but..), and in every run I always got a list of "solutions" that all
> have TFZ=100.0, with a very small LLG (around 0 or even in the negative).
> The RFZ is like 4 or less
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