Hi Daniele,
we had a possibly similar case and in collaboration with Andrey Lebedev
we demodulated the data using different methods including a novel
method, DIGS, (see Acta Cryst. (2014). D70, 1680–1694). We have a few
scripts to analyse the data and to use the described methods. Sadly we
Just for completeness the pythonic command line way:
coot --pdb input.pdb --auto input.mtz --python -c
'set_go_to_atom_molecule(0); set_go_to_atom_chain_residue_atom_name("B",
42, " CA ")'
Bernhard
On 17/11/2017 09:00, Martín Martínez Ripoll wrote:
We have used it in this way...
coot
Dear Ying,
Dear all,
I was trying to use wincoot (v0.8.7.1) on my PC (Windows 8.1). Starting Coot
from CCP4 or 'runwincoot.bat' gave me the following error message:
coot-bin.exe Entry Point Not Found
The procedure entry point deflateSetHeader could not be located in the dynamic
link library
On 10/04/2017 20:14, Xiao Lei wrote:
Thanks Paul,
I tried, it failed with a message as below:
Coot>> set-symmetry-shift-search-size 2
BL Warning:: Python syntax error!
(or you attempted to use an invalid guile command..)
Python error:
invalid, syntax (, line1)
coot>>
You are mixing python
py>
and replace the same file (maybe make a backup first) in
C:\yourwincootinstallationdrirectory\python27\lib\site-packages\coot\*
*4. Done. Works!*
*
*
Thanks Bernhard!
On Wed, Mar 29, 2017 at 11:58 AM, Xiao Lei <xiaolei...@gmail.com
<mailto:xiaolei...@gmail.com>> wrote:
Hello B.,
Hi ...,
Hi Ethan,
Thank you for the information. I have ccp4i installed on the same PC,
the error from Coot is "Couldn't find render in default path and PATH
Shall we search the whole disk?" If I click "Yes", then Coot freezes
forever and I need to force close it.
This can take a long time
...and there is a residue missing (159).
B
It seems your chain ID is different, so it would not connect two
different chain ID covalently. So please change your chain ID and try to
connect.
Good luck
On Sat, May 23, 2015 at 3:53 PM, Ishan Rathore ishanrathor...@gmail.com
Just for completeness, of course (!?) you can get something like this in
Coot. In terms of return value and accuracy (3 digits) I would use the
scripting function:
ncs_ghosts(imol) - pythonic
(ncs-ghosts imol) - schemey
imol - your protein with NCS
Bernhard
Alright, thanks!
Just recently, we updated Coot to use the Ramachandran plot according to
some newer distribution as defined by MolProbity (thanks to Kevin
Cowtan's clipper). This is available from Coot rev 5581.
However, please keep in mind as pointed out by Gert that there are
different version of the
As for python I would rather use:
molecule_chooser_gui(Choose molecule for PISA assembly analysis,
lambda imol: pisa_assemblies(imol))
or
molecule_chooser_gui(Choose molecule for PISA interface analysis,
lambda imol: pisa_interfaces(imol))
The latter has a bug which causes the scripting
Dear Laurent,
I run the same multiple desktops. The only convenient way I found to fix
this is to show WinCoot on all desktops. Its due to the new graphics
libraries which were updated and I didnt want to dive into this to fix
it properly (I thought I would be the only one running this -
A postdoctoral position is available immediately in the Molecular
Structural Biology group at the Karolinska Institutet in Stockholm.
The position is initially available until 31 Dec. 2015 (approx. 1+
years) with the possibility of extension.
Duties
We are seeking a motivated scientist to join
Hi Alisa,
almost the right syntax. The last one is a list, i.e. it should read:
copy_residue_range_from_ncs_master_to_chains(0, C, 377, 402,[B])
... and make sure you have the mast chain set to C.
... and there was a similar discussion earlier:
Hi,
off list we figured out that the occupancies (and B factors) were
missing in the pdb file (no occ- no atoms- no clashes).
I have fixed Coot as to permanently be able to add new b factor and occ
columns (available from revision 5077). Please use the functions
fill_occupancy_residue_range
... and there will be (shameless self-advertising):
Ponnusamy et al. 2014 Acta D accepted
You may also want to make pseudo-precession photographs using LABELIT.
This will give you a better indication on the characteristics and
directionality of the disorder.
Bernhard
Thanks to all who
15 matches
Mail list logo
