There's a dead-ordinary linux command 'rename':
>> rename 1055 '' 1055*.osc
Saved my butt numerous times.
phx.
James Stroud wrote:
I don't know where this comes from, but its called rename-alot. Its a
perl script. I'm guessing "Larry" is Larry Wall, but who knows. chmod
a+x it and then put it
for me following works (just an example):
The objective was to remane all 336 images files to 760D6a0001(to 336).img
to 760D6a0_001(to _336).img
Just save the script below (like filename.com) and run as sh filename.com
***
for i in 760D
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Hello;
While using the CCP4 version 6.0.99 during the Bangalore workshop, I
realised that it is not any more possible to "freely" choose the
weight/sigma labels from a mtz input file. In particular when trying
to use phases coming from refmac
Just for the sake of completeness:
mmv is also a package available for some linux distributions (SuSE at
least), so you don't need the alias.
If you like doing so using shell features, you could, with bash, issue
for i in 1105\ A*; do mv "$i" "${i#1105\ }" ; done
This might work in m
Dear all,
What is the currently accepted view on the percentage of residues in
disallowed regions of the Ramachandran plot (for publication purposes) ?
This is because I have a structure where there are several stretches of
not so well defined density. As a consequence there are about 5% of t
University of Oxford
Weatherall Institute of Molecular Medicine
Department of Molecular Oncology
Cell Signalling Group
Postdoctoral Researcher Crystallography/Biochemistry
University Grade 7: £26,666 - £32,796 p.a
A highly motivated postdoctoral researcher is sought for our team
to
work on a proj
This is a re-post (the previous ad had an incorrect job requisition
number - my apologies for any confusion this might have caused):
Macromolecular Crystallography Laboratory Manager. The University of
Oklahoma Department of Chemistry and Biochemistry seeks an individual
with a doctorate in C
Beam time available @ X6A
http://protein.nsls.bnl.gov
The NIGMS beam line X6A at the National Synchrotron Light Source provides FAST
access to beam time through out the year. To apply submit a short proposal to
http://protein.nsls.bnl.gov at any time. Proposals are continuously reviewed
and
Beware that 'rename' on Fedora/Redhat and the like works differently
from 'rename' on Debian/Ubuntu etc. Both are in /usr/bin but the former
is an executable and the latter is a Perl script (it's apparently
installed with Perl), and is probably descended from your 'rename-alot'
(the syntax appears
A Postdoctoral Research position / Senior Research Engineer
is available from May, 1st 2008 in the Department of Structural Biology,
University Kiel, Germany.
The position is initially on a 3-year contract.
The position involves research in structural biology of medical relevant
proteins (www.
This is also easily done using midnight commander.
http://en.wikipedia.org/wiki/Midnight_Commander
http://linuxgazette.net/issue23/wkndmech_dec97/mc_article.html
Here are the details on changing names.
http://www.chm.tu-dresden.de/edv/mc/mc4.5/manual1.html#45
Dear CCP4bb,
I was looking through the REFMAC manual today and found the following
advice:
"Completing the data to include all possible hkls. Should do this
after data reduction, and certainly before using REFMAC. This is now
done with the uniqueify script. It is best done using CCP4i."
All these programs only refine against reflections that were actually
measured. REFMAC, but not SHELXL, provides the 'Sigma-A' weight
coefficients for Coot to use DFc instead of 2mFo-DFc for the reflections
for which Fo is not known (or is reserved for the free R) to calculate a
map. This will
Dear Serge --
While using the CCP4 version 6.0.99 during the Bangalore workshop,
I realised that it is not any more possible to "freely" choose the
weight/sigma labels from a mtz input file. In particular when
trying to use phases coming from refmac (after MR + rigid body)
with there FoM
Thanks for the reply,
Does this mean REFMAC/Coot does need the missing number flags (and
thus you will get improved maps ONLY if uniqueify is run) or does
REFMAC/Coot recognise when a reflection is missing and use DFc
regardless (in which case there is no point running uniqueify)?
Simon
Refmac (and dm and pirate and probably some other programs like phaser
too) will only restore missing reflections if there are entries (albeit
bblank ones) for those reflections in the MTZ file.
So it's not a matter of running uniquify before refmac, its a matter of
running uniquify before you
Dear Crystallographers,
does anybody know the extent to which the outer membranes of e. coli and/or
the cell walls of s. cerevisiae are permeable to various solutes? In
particular, I was thinking of small, hydrophilic molecules. References would
be great as well--I am not sure where to look...
Hello everybody,
I wonder if anybody has experience with heme (or to be more precise: heme b)
containing proteins which Xtals do not look red under the microscope. How might
the technique for crystallization (e.g. sitting drop, hanging drop) influence
the intensity of the color? Many thanks!
On Mar 12, 2008, at 12:48 PM, Jan Schoepe wrote:
Hello everybody,
I wonder if anybody has experience with heme (or to be more precise:
heme b) containing proteins which Xtals do not look red under the
microscope. How might the technique for crystallization (e.g.
sitting drop, hanging drop
Crystals are supposed to be red if you have oxidized iron in the heme
and deep pink/scarlet if the iron is reduced.
If you removed the iron (for example EDTA during purification) or
substituted with something during purification or crystallization, you
could loose the color.
It is trivial to check
Jan
Are you saying that the protein you are starting with is not colored (heme
is gone or damaged) or that the native protein is only weakly colored (low
extinction coefficient at the Soret wavelength)?
The former is more disturbing than the latter. For some heme proteins, like
peroxidases,
Hi,
I am looking over a number of models from the PDB but have been
unable to reproduce the R-factors for any model that was refined
with Refmac and contains TLS parameters. I usually can't get within
5% of the reported value. On the other hand, I usually do pretty
well for models w/o TLS.
Dale,
You raise a very important point. The electron density server will not
put out the data unless there is a reasonable agreement between the
Author reported R-factor and the calculated R-factor. I guess for the
same reasons (and more - Gerard?).
The question I have is - if we are going to
Clearly a few interesting entries .
2) in the context of PX, only the total "B factor" contribution to Fcalc needs
to be positive definite, the TLS component might not be (though it is
satisfying if it is)
3) how do you calculate the "TLS origin" ? The PDB entries should contain the
origi
Hi Martin,
2) in the context of PX, only the total "B factor" contribution to Fcalc needs
to be positive definite, the TLS component might not be (though it is satisfying if it is)
Please correct me if I'm wrong My understanding was that the T and L
matrices must be positive definite,
Hello,
I want to make a movie to show the process of ligand
switch. In the movie, the first ligand will gradually be replaced by the
second ligand(Include the conformation change such as the bond rotation
when the second is approaching). possible to make this movie? I will use
Pymol+eMovie to
The 5 Day eCheminfo Hands-on Drug Discovery Workshop Week will
take
place this year 21-25 July 2008 at the Medical Sciences Teaching Center,
Oxford University, Oxford, UK. Topics to be covered include Virtual
Screening & Docking; Structure-based Drug Design; Ligand Optimisation &
Library Design; St
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