Dear all,
I am sorry to trouble you again because I am facing a very weird
situation:
Three copies from Phaser are the right solutions based upon:
1, Rfree 42% R 39%
2, No packing clash
3, The packing within the 3 makes good sense
4, Density evenly distributed among the 3 copies even without
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Dear ccp4bbers,
I agree with Dirk. I have also noticed that much due to the way X-ray
crystallography is evolving, a lot of students/early-postdocs find
themselves doing crystallography in labs without a tradition in
crystallography, even without
hi ...
there is very likely a correlation between quality of the vacuum and
filament lifetime.
it had been recommended to us to monitor the vacuum continuously on the
rigaku ru300 (?) generators we had at the time. this was fairly easy by
just plugging a left over plotter from an old
gruzi dirk,
come on - lighten up a little! your reply wasn't funny or helpful either -
just moralising. (by the way - 't is a strange fact that whenever i get any
negative reactions to my own postings they stem *exclusively* from any or all
of these three countries: the us, germany and
Such a twinning operator can also indicate that you spacegroup has an
extra symmetry operator (h,-h-k,-l)
That is in fact one of the symmetry operators for P3i21 H32 P6i22
Have you solved the structure in the lower symmetry and is that missing
density properly generated by this operator?
mathias wrote:
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
I have found in my usenet adventures that usenet mavens often point
to this link before trying to sort out among themselves exactly what
level of humor to take with dubious posts:
http://www.catb.org/~esr/faqs/smart-questions.html
Of course usenet mavens also complain a little too
Dear Shivesh
Below I've tried to give you some broad ideas about where to look / read and
some packages / approaches to try.
For a start there is a very comprehensive tutorial on the ccp4 site together
with the experiemental phasing roadmaps.
Goede dag Gerard,
interesting that you think my last e-mail was addressed to you ;-)!
Yes, this was my first moralizing posting on this board after some 16
years. A bit sense of humor is fine, but the last posting was simply too
much. We shouldn't attack people personally or discriminate
Risking a potentially trivial question:
Is there a program that will calculate the RMS of distances
between specified (listed) atoms in two different structures?
As far as I could see, LSQMAN will only compute same with same?
Calculate RMSD of M1 A20 A30 A40 A50
And M2 A20 A30
HI - try the program contact from the ccp4 suite.
http://www.ccp4.ac.uk/html/contact.html
J
Eleanor Dodson [EMAIL PROTECTED] wrote:
mathias wrote:
Dear all,
Can anyone of you guys recommend free software, or any open access
internet server, to calculate VDW interactions of small molecules
Dear Jan,
I think GROMACS can do that (www.gromacs.org):
g_confrms computes the root mean square deviation (RMSD) of two
structures after LSQ fitting the second structure on the first one.
The two structures do NOT need to have
Hi,
Yes refmac, use weighting term 0.05
Thanks
On Thu, 1 Mar 2007, Tim Gruene wrote:
How did you do the refinement? Did you use refmac? Did you let the matrix value
at 0.5? That's too high. lower it to, say, 0.1 to start with.
Original-Nachricht
Datum: Thu, 1 Mar 2007
shivesh kumar wrote:
Dear all,
I have a data set at 2.2A, of the selenomethionene labelled
protein.How should I process the data.Thanx for the help.
Shivesh
I think you should ask your local crystallographer for help. There are
several programs ( MOSFLM in CCP4, DENZO, XDS, D*TREK ) but
Attached is an advertisement for a 5 year scientist post in Small Angle
Neutron Scattering at the ILL. It is also posted on the ILL site at
www.ill.fr (Jobs and Careers)
Peter Timmins
VACANCY RESEARCH SCIENTIST (Neutron Small Angle Scattering) (m/f)
The Institut Laue-Langevin (ILL), situated
John Bruning wrote:
When using Refmac how does one find/calculate R-free error in the
highest resolution bin?
Look at your loggraph for the final R Rfee - that gives the numbers in
resolution shells.
Eleanor
Hmm - I think this is a bug..
Garib - what do you think?
Eleanor
Jianghai Zhu wrote:
Dear all,
I have some N-acetyl-glucosamine (NAG) in my structure. When I
searched the monomer library in CCP4 6.0.1, I found out that NAG is
actually N-acetyl-glucose, which is much less common, I believe.
Dear colleagues,
I have a dataset form a protein-ligand complex. I want to use the same
Rfree test set for refinement as used for the protein alone. How can I
extract the test set from the CNS reflection file of the protein-alone
dataset (created with make_cv) to use it with the
I use a multimeter from Radioshack (catalog number 22-812) that can
record this data on a PC via a serial connection. Presumably by now
there is a similar device with a USB connection. Publishing the
resulting text file on the web would be effortless on a *nix
machine, but I'm not sure how to do
Where can I generate the following numbers in CCP4 coming with pdb and mtz from
Refmac?
Luzzati SigmaA (obs)
Luzzati ESD (R-free set)
Luzzati SigmaA (R-free set).
If the answer is sfcheck, where exactly are the numbers located, all I can find
is Luzzati ESD overall?
On Thursday 01 March 2007 10:32, John Bruning wrote:
Where can I generate the following numbers in CCP4 coming with pdb and mtz
from Refmac?
Luzzati SigmaA (obs)
Luzzati ESD (R-free set)
Luzzati SigmaA (R-free set).
The answer is that you should not be using Luzatti plots to estimate
Actually, the merge script will create the superset of both reflection
data sets, so it won't delete reflections from one data set that are
not present in the other data set.
Once you have done the merge.inp script, you can use the make_cv
script to extend your test set while keeping your
On Thursday 01 March 2007 10:17, Ian Tickle wrote:
All, I thought this would be a simple task, but for the life of me I
can't see how to do it! All I want to do is convert an MTZ file to
Shel-X format for refinement. I thought it would take me 2 secs, but
it's taken me at least 5 attempts,
Yes I have always been annoyed by that. I tend to use sftools to trim
and then rename the columns I want followed by mtz2various with
something along the lines of labin FP=F SIGFP=SIGF FREE=FreeR and then
finally edit the resulting text file to remove the header and all the
FREE's as you did. It's
Risking a potentially trivial question:
Is there a program that will calculate the RMS of distances
between specified (listed) atoms in two different structures?
As far as I could see, LSQMAN will only compute same with same?
lsqman does in fact calculate rmsd valus between arbitrary sets of
A few years ago I did this by first using the solved structure to
generate a hypothetical (FCALC) data set to some rather optimistic
resolution limit (2A when I was stuck at 2.7), carrying out a random
Rfree selection on this FCALC set, and then dumping the FCALCs while
retaining the Rfree
Greetings (or in correct Swiss German Grüezi
wohl, with Umlaut=vowel mutation) to all CCP4BB
subscribers,
being a CCP4BB reader (and sometimes writer)
since something like 15 years, I realized today
that the comment of Gerard was the first one I
read since then containing a side-swipe
Emmanuel Skordalakes, Ph.D.
Assistant Professor
Gene Expression and Regulation Program
The Wistar Institute
3601 Spruce St
Philadelphia, PA 19104
215-495-6884 Office
215-898-2202 Lab
[EMAIL PROTECTED]
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