Dear David,
I dare claim that rather you do not know how to use the listed programs
in the case for small molecule data rather than none of them were
optimised. E.g. 10degree frames loose all the possible accuracy in the
phi-direction so I am not surprised you had trouble indexing. There is
no
Dear Tim,
I am sure your statement is too general and is not very precise.
10 deg oscillation range is as precise as 0.1 deg. Positions of diffraction
spots on the area detector have
defined position on rotation axis within the precision/accuracy of the stepping
motor and the spacial
The Worldwide Protein Data Bank (wwPDB) partners are pleased to announce
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The new validation reports are set to become an indispensable resource
for both crystallographers and the consumers
Dear Felix,
as far as I understand we are talking about the frame width, not the
total data range for indexing (10 degree rotations to get enough spots
per frame). I have used 180degrees of data for indexing. At least XDS
places the reflection at the centre of the frame so that with a 10deg
frame
Dear Tim,
My most experience is with HKL2000 which during the index doing something quite
mysterious and not very well described
such as a brute search for the correct reciprocal lattice. I do not know where
initially the reflections are placed by HKL2000,
but finally it converges. In the moment
Indexing involves storing all the reflection positions in orthogonal
reciprocal space and then finding a reciprocal lattice that fits most of
them.
For a 10 degree frame all we know is that a reflection lies somewhere on
a sort of 10 degree arc; only two of the three coordinates are
precisely
Applications for a PhD position are invited for the protein X-ray
crystallography group at Trinity College Dublin, Ireland. The project involves
a structural investigation of a viral protein in complex with a newly
characterized sensor of the innate immune system. More information and a
Good morning, Everyone,
We are trying to dock two small molecule ligands into a big active site
of the enzyme. We tried to dock two simultaneously using Autodock Vina,
but one always got kicked out. Is there a way we can dock both ligands?
Thanks for your suggestions.
Best,
Haiying
Dear all
We are pleased to announce an update to iMosflm available at
http://www.mrc-lmb.cam.ac.uk/harry/imosflm
which addresses two main issues -
(1) The QuickSymm and QuickScale options did not work correctly under some
circumstances, e.g. on MS-Windows and also when running the
There are detectors that are small and have fast readout time and others
that have much larger size and slower readout time. Large detector size
reduces background level very effectively by allowing data collection with
larger crystal-to-detector distance. For well ordered crystals, level of
As I recall autodock vina is not set up to dock two ligands at once. That
might be a better question to ask the autodock listserve.
Regardless, I would recommend docking one compound at a time to generate a
reasonable amount of docking poses.
From the first round of docking you could then treat
Second announcement
Fifth Workshop on Neutron Scattering Applications in Structural Biology
Oak Ridge, TN. June 16 - June 20, 2014
Application deadline: April 18, 2014
The workshop on Neutron Scattering Applications in Structural Biology aims at
enabling structural biologists to fully
Thanks again for all the responses to my question about small-molecule
crystallography. I almost regret having sent the student to the
chemist. Trying this at home sounds like a fun afternoon.
On the ccp4 wiki, there was already a section describing how to solve a
small-molecule structure.
Does anyone here have experience running sf_convert? I know it's not part
of CCP4, but it does rely on CCP4 for converting structure factors to MTZ
format.
When I try to run it, I get errors that suggest that my shell isn't bash,
but it really is. The program output is as follows.
sf_convert -o
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