Yuan SHANG
1) DIY
The way that has been used is to calculate the inertia tensor matrix for
helix (or
any other secondary structure element). You can chose backbone atoms or
just
the CA atoms. Then calculate the eigen vectors and values from this and
the largest
eigen vector will be the best
I've put a couple of example programs that do this sort of thing (using the
clipper libraries) in
ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/helixanglethings.tar.gz
Phil
1) helixangle.cpp
Calculate angle beween two helices
Superimpose standard helix on two specified chains ranges,
then
Hello,
Is there some C or C++ code out there doing what you described in 1).
If not, is there a very detailed explanation of this procedure
somewhere, detailed enough in order to implement it (just getting
the best fit vector and its length, no other parameters)?
Thanks a lot,
Francois.
Tom
The problem with the inertial matrix approach is that it is very sensitive to
end effects on the helix, ie a helix is not a perfect cylinder. So
superimposing an ideal helix is more reliable
Phil
On 17 Aug 2010, at 10:17, Francois Berenger wrote:
Hello,
Is there some C or C++ code out
Dear,
I've just installed the latest iMosflm 1.0.4, as well as the CCP4
6.1.13 suite (under Mac OS 10.5.8).
However, where does iMosflm get its font sizes..?
(these are quite big actually, and I'd like to reduce them)
Thank you very much
Sincerely
Kristof Van Hecke
I really dont think this is a very good idea - B values are correlated
to the optimum position of the atom - if thast is a fraction of an A out
the B factor will be much higher than it should be..
Eleanor
Hailiang Zhang wrote:
Dear Pavel:
Thanks a lot! I will try phenix.refine!
Best
When I started doing various analyses of conformational changes in AP2 (bending
of helical solenoids, see supp data fig S2 for Jackson et al, Cell 141,
1220-1229 (2010)) I was first going to do lots of scripting around this sort of
thing, but Kevin Cowtan persuaded me that it was easier to
Hi Kristof
If you use the ActiveTcl wish for your MOSFLM_WISH environment
variable rather than the X11 wish that the ccp4 install uses, you get
nice Mac fonts which have had their sizes chosen so they look good.
You would need to
(1) Install the ActiveTcl distro (unnecessary if you're
Dear ccp4BBs,
I would like to inform you that the 3rd edition of the *Master and PhD in
Crystallography and Crystallization* is open.
The MCC offers an unique opportunity for the training of young researchers
that is normally absent or under-represented at graduate level despite its
Hold on--did you add free NADPH into the top of the concentrator, and spec the
sample pre-spinning? You need to be sure that you can see the NADPH in the
sample before you spin it, because you are looking for a *loss* of NADPH
absorbance in the flow-through.
A similar method uses a very low
In Refmac: Does anyone know if lactose should be designated as one component
(Lat) or two components (Gal and Glc)?
Rex Palmer
Birkbeck College
On 17/08/10 22:58, Rex Palmer wrote:
In Refmac: Does anyone know if lactose should be designated as one
component (Lat) or two components (Gal and Glc)?
With Refmac, you can do it both ways.
Dear All:
I am currently using autoBuster to refine my structure. I notice that
autobuster generates a new column in the MTZ data file with the label of
FreeR_flag.
Because my MTZ file has already had the FreeRflag, I am wondering whether
autoBuster generated a new set of Rfreeflags
There are many ways to test if the two test sets are identical. For
example (using CCP4i):
Go to Reflection Data Utilities - SF file analysis
and then perform data correlation between your two FreeFlag columns. If
they are identical, the resulting R-factor should be 0 and correlation
Dear Rex,
Beta-lactose is in Ligand-Expo as 'LAT' so I'd stick with that.
Regards,
Robbie
Date: Tue, 17 Aug 2010 22:58:27 +0100
From: rex.pal...@btinternet.com
Subject: [ccp4bb] Lactose again
To: CCP4BB@JISCMAIL.AC.UK
In Refmac: Does anyone know if lactose should be
designated as one
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