I got VOIDOO to work by editing the library file, mine was only reading
protein.
To make it read the bases, I added this lines to the file:
RESI 'THR' (example)
RESI ' DA'
RESI ' DT'
RESI ' DC'
RESI ' DG'
Thank you Eric for the web site.
vincent
Eric Pettersen wrote:
Hi,
I would like to mea
Hi,
I would like to measure the volume of a protein-DNA complex.
I'm using VOIDOO but it only gives me the volume of the protein.
Does anybody know of a software that allows calculation of DNA
volume too?
The StrucTools server (http://helixweb.nih.gov/structbio/basic.html)
can calculate the
Hi,
I would like to measure the volume of a protein-DNA complex.
I'm using VOIDOO but it only gives me the volume of the protein.
Does anybody know of a software that allows calculation of DNA volume too?
thanks a lot
vincent
--
Vincent Chaptal
Dept. of Physiology at UCLA
http://www.physiology
The Stroud Lab at UCSF (http://www.msg.ucsf.edu/stroud/index.htm) is looking to
fill a post-doctoral position in membrane protein crystallography.
Applicants should have background in biochemistry, molecular biology, and/or
crystallography.
The position in membrane proteins will be in close a
Another very nice script to run and collect statistics from XDS is
xdsme from Pierre Legrand
http://code.google.com/p/xdsme/
Daniel
Le 05/08/2010 16:55, Jovine Luca a écrit :
WRT the redundancy, I am afraid you have to recompute an approximate value
yourself using the number of observation
As part of the recent Midsummer Make-over of the Protein Data Bank in Europe
(PDBe) website, we acquired the domain name pdbe.org and have used it to
implement a number of shortcuts to many of our services etc.
- http://pdbe.org/ - the new PDBe website
- http://pdbe.org/1cbs - go directly to t
Apologies for the repetition, but only the first link:
http://cc.oulu.fi/~pkursula/xdsi.html
is for the xdspub program that produces the output I attached. The other one
has the same name, but does something else!
Luca
> WRT the redundancy, I am afraid you have to recompute an approximate value
> yourself using the number of observations and number of unique reflections
> (this is what I do all the time). I suppose one could always write a jiffy
> program to compute the correct values using both files INTEGRA
Postdoctoral Position in Membrane Protein Crystallography
A postdoctoral position in membrane protein crystallography is available at the
Center of Membrane Biology at the University of Virginia. The position is
available in the laboratory of Dr. Jochen Zimmer who studies the membrane
transloc
anna delprato wrote:
Hello All;
I've just started using XDS and have scaled three data sets from the
same crystal - unmerged. It was a SAD experiment
My question is concerning which R values to use as data processing
statistics. I don't find any Rsymm or even Redundancy values in the
LP fi
Dear Anna,
Something I find useful is to convert the output of XSCALE (unmerged) to MTZ
format using pointless (pointless -c xdsin SCALED.XDS hklout sorted.mtz)
then to merge the reflections with Scala:
scala hklin sorted.mtz hklout scaled.mtz << eof
run 1 all
scales constant
anomalous on # or of
Hello All;
I've just started using XDS and have scaled three data sets from the same
crystal - unmerged. It was a SAD experiment
My question is concerning which R values to use as data processing statistics.
I don't find any Rsymm or even Redundancy values in the LP files.
I came across an ex
Dear Changyi,
If refmac distorts the ring to fit INTO the density, the first question
I would ask myself is whether the sugar ring has been fitted correctly.
Sugars can be a pain in the neck with different puckers, chair/boat
conformations, different anomers etc. If the sugar is somewhat
disorder
Dear Changyi,
If refmac distorts the ring to fit INTO the density, the first question
I would ask myself is whether the sugar ring has been fitted correctly.
Sugars can be a pain in the neck with different puckers, chair/boat
conformations, different anomers etc. If the sugar is somewhat
disorder
Seema Nath wrote:
I've got a data at 3.7 angstrom resolution,P3 space group but smallest cell volume as predicted by
marIndex is very large in comparison to the 90 residue small protein & I'm supposed to solve it
using auto-MR and CNS, now when I'm using auto-MR to search CRF & TF peaks with lo
Apologies if this has been posted already but I couldn't see it yet!
Hi,
Sorry for the off topic question!
I'm looking at Dali search results and find the molecule names are not
always the same as the ones for the chain identifier from the pdb
entry (maybe the molecule names are always of chain
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