Dear all,
post-doctoral position is available in Pavel Plevka's group at Ceitec in the
Czech Republic:
http://www.ceitec.eu/programs/structural-biology/x-ray-crystallography-ii/
The projects involve x-ray crystallography and cryo-electron microscopy of
human viruses.
If you are interested, det
Dear CCP4 Users
A CCP4 update has just been released, consisting of the following changes.
* Qtrview: Now uses runwincoot.bat script to start Wincoot on Windows
* MrBUMP: Assumes intensities rather than structure factor amplitudes when
calling SHELXE
* Pdb_merge: Execution permissions adde
On Mon, Jan 28, 2013 at 8:39 AM, Robbie Joosten
wrote:
> DSSP recently went open source with a very liberal license. So you can
> consider using the real DSSP now. This may also be the moment to integrate
> DSSP in CCP4.
Based on the info here:
http://swift.cmbi.ru.nl/gv/dssp/
the license isn't
Hi Nat,
DSSP recently went open source with a very liberal license. So you can consider
using the real DSSP now. This may also be the moment to integrate DSSP in CCP4.
Cheers,
Robbie
Sent from my Windows Phone
From: Nat Echols
Sent: 2013-01-28 17:32
To: CCP4BB@J
On Mon, Jan 28, 2013 at 8:04 AM, Antony Oliver
wrote:
> If you don't mind using the ksDSSP implementation, it is already installed
> with the phenix suite if you have it.
Correct, but although the method is supposed to be the same, the
output is not, and there are bugs in how it presents helix
a
Sorry to cross-pollute…
If you don't mind using the ksDSSP implementation, it is already installed with
the phenix suite if you have it.
phenix.ksdssp from the command line.
With regards,
Tony.
---
Dr Antony W Oliver
Senior Research Fellow
CR-UK DNA Repair Enzymes Group
Genome Damage and Sta
Dear Rashmi,
you may want to try this web server instead of compiling & installing it:
http://www.cmbi.ru.nl/hsspsoap/
Otherwise, you'd better follow Tim's advice and give us more clues!
Jon
2013/1/28 Tim Gruene
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> Dear --
> rashmi,
>
> if yo
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Dear --
rashmi,
if you would kindly let us know what exactly you are thanking for, you
may actually have a reason for doing so - a good start is a
cut-and-paste copy of the error message(s) from the terminal where you
typed 'make' and 'make install'.
Correct, shelxe does not use the free -R flags, and works just
as well with the original unmerged unctruncated intensities.
George
Hi Ronan,
On 28 Jan 2013, at 12:18, ronan.kee...@stfc.ac.uk wrote:
Well spotted! We originally gave structure factors to SHELXE in our testing as for most
of ou
Hi Ronan,
On 28 Jan 2013, at 12:18, ronan.kee...@stfc.ac.uk wrote:
> Well spotted! We originally gave structure factors to SHELXE in our testing
> as for most of our test cases we only had F/SIGF available. We were advised
> to change to intensities but somehow in the released version the "-f"
Hi Huw,
Well spotted! We originally gave structure factors to SHELXE in our testing as
for most of our test cases we only had F/SIGF available. We were advised to
change to intensities but somehow in the released version the "-f" flag
remained. I'll make the change and put it in a CCP4 update.
Dear Huw,
It looks as though you have correctly diagnosed a problem with AMPLE.
For expansion from borderline partial structures, I recommend the latest
SHELXE (on my beta-test server since Jan. 20th) and experimenting with
the -O and -F switches, e.g.
-F0.9 -O100 -a30
However SHELXE is still
Hi,
I've been running Ample and I'm a bit confused about the input for the
shelxe-beta auto-tracing. The input mtz for Ample has F, SIGF and FreeR and it
appears that Ample converts the structure factor amplitudes to intensities
using mtz2various with the FSQUARED keyword as the log file contai
Best place to start:
http://scottlab.ucsc.edu/~wgscott/xtal/wiki/index.php/Crystallography_on_OS_X
--
A. Radu Aricescu, PhD
University Research Lecturer
University of Oxford
Wellcome Trust Centre for Human Genetics
Division of Structural Biology
Roosevelt
Hi all,
I am trying to install ccp4, phenix, coot and other crystallography
software on my mac. I am not familiar with mac, neither Linux system.
Please give me some protocols to install these software and how to update
them. I appreciate it.
Lisa
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