Thanks for the 38 replies, both on and off the bboard. I have tested some of
them and my favorites so far are ApE and Gentle which are free and quite
good. But there may be others that are also good and I missed.
Darren
Summary:
*Firstly*, good advice from Warren DeLano:
1. Be wary of relying
Dear CCP4BB List Members,
first of all I am not a crystallographer, but I would like to get some
things clear, things I did not find in Crystallography Made Crystal Clear
and on the internet for now.
I am trying to read electron density maps in the EZD format. These maps
contain scaled values
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Scientific Programmer
EMBL Hamburg
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A position for a scientific programmer is immediately available in the
group of Thomas Schneider at EMBL Hamburg.
The EMBL Outstation in Hamburg (htpp://www.embl-hamburg.de) has a wide
research program in
Hello,
does anyone know of a tutorial which lays out some sort of pipeline,
hopefully using CCP4 packages, to fit and refine a small molecule
ligand please?
cheers
andy
Andy,
We do a lot of liganding fitting with CCP4. This is the general order of
steps we take (post initial solution of the protein itself):
1) Build the potential ligand in CCP4 Sketcher
a) Rename all the Hydrogens to H#, CCP4 Refmac has some issues with
Hydrogens marked OH1, NH1, etc. To
It seems like this space group will be the death of me.
I'm working on a structure in SG P41212 one molecule per asu that was
solved with experimental SAD phases. The resolution is to 2.5 and the
refinement is stuck at an R/Rfree of 30 and 33 with bonds rmsd of
0.011 and angles of 1.597 .
Hi Francis,
I would consider the possibility of a orthorhombic sg (a~b with
twinning). If unlucky maybe even monoclinic.
Cheers
Roberto
On 5 Feb 2009, at 18:10, Francis E Reyes francis.re...@colorado.edu
wrote:
It seems like this space group will be the death of me.
I'm working on
/lurk_mode_off
/dumb_question_on
Dear All,
I was recently trying to find references on how age may degrade a
crystal, i.e. grow them and use them or preserve them as fresh as
possible. I seem to remember seeing a couple of papers on this but my
memory is fading and I have been unable to locate
Some things improve with age. Here is one of my favorite stories:
http://tinyurl.com/oldtrna
The crystal structure of yeast phenylalanine tRNA at 2.0 Å resolution:
cleavage by Mg2+ in 15-year old crystals
Luca Jovine, Snezana Djordjevica and Daniela Rhodes
We have re-determined the
Here's another very similar case:
http://www.ncbi.nlm.nih.gov/pubmed/12270703
On Thu, Feb 5, 2009 at 11:48 AM, William G. Scott
wgsc...@chemistry.ucsc.edu wrote:
Some things improve with age. Here is one of my favorite stories:
http://tinyurl.com/oldtrna
The crystal structure of yeast
I had a structure that was done with crystals that were about a year
old. Initial crystals appeared in a less then a day and diffracted
very poorly. In trying to make room for more trays I reexamined the
old trays before throwing them out and low and behold nice well
diffracting
Here's the summary and some own experimental data.
First off all thank you all for your replies.
trick 1: put a glass bottle filled with water between fiberoptics and
the mirrors of your base (Isolde Le Trong)
trick 2: suspend plates to allow air circulation, with bulb under
plate scopes
A map file stores a density value for each point on a grid. The
units and nature of that item is not defined in the format of the map.
A map can store any number of things. The actual values are defined
by the process that created the map file.
For electron density maps you will find that
We are seeking talented and highly motivated Postdoctoral Fellows to
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protein expression,
This sounds like a case I had last year.
It looked like P41212 (in fact I solved it by MR in P43212 and refined
the data in shelxl reasonably well. Two superimposed molecules at 50%
occupancy began to emerge from the density - this was at very high
resolution).
It took me a while to get
Dear all,
I am using the density modification tool in ccp4 to generate improved phases
for/from my model. I find that the electron density map I generate using Fobs,
and density modified phases (PHIDM) are not the same as that generated using
Fobs, phicalc (original calculated phases) and
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