Alan,
I guess as industrial crystallographers we are in the same boat. I highly
encourage my group to use Hydrogens throughout refinement, not a problem for
proteins as phenix.reduce is very good at adding Hydrogens and de novo
ligands/inhibitors can be easily defined with Hydrogens as well. I
nyone have any ideas?
Oli.
On Wed, 28 Oct 2015 14:11:40 +0000, Schubert, Carsten [JRDUS]
wrote:
>May be worthwhile to check if these settings are in effect (snipped
>from my coot.py) set_find_hydrogen_torsion (1)
>set_do_probe_dots_on_rotamers_and_chis (1)
>set_do_probe_dots_post_
the
application. As you said: A matter if choice or preference
Cheers,
Carsten
-Original Message-
From: Tim Gruene [mailto:t...@shelx.uni-ac.gwdg.de]
Sent: Wednesday, May 27, 2015 6:05 PM
To: Schubert, Carsten [JRDUS]
Cc: COOT@JISCMAIL.AC.UK
Subject: Re: Dragged refinement
Hi Tim,
that does not work for phenix, not sure about Buster/TNT; refmac behavior is
different. In phenix, which uses a riding model as well, but defines explicit
hydrogens, one has to be very conscientious to add hydrogens back after
mutating or adding residues. In part this is a phenix issue
Not sure what you guys are trying to accomplish, but I used the "hollow"
package which generates probe atoms in PDB format suitable for loading into
PyMol or coot. (Have not worked with this for a while hopefully I don't have to
eat my words (-: )
http://hollow.sourceforge.net/
HTH
Carsten
-
o run probe and reduce in coot under Linux
On 07/03/14 14:05, Schubert, Carsten [JRDUS] wrote:
> Thanks Paul,
>
> I'll give that a try. Is there any similar mechanism to load a global
> initialization file(s) under scheme as there is for Python, e.g. can I define
&g
users of COOT Crystallographic Software
[mailto:COOT@JISCMAIL.AC.UK] On Behalf Of Paul Emsley
Sent: Thursday, March 06, 2014 6:51 PM
To: COOT@JISCMAIL.AC.UK
Subject: Re: [COOT] Unable to run probe and reduce in coot under Linux
On 06/03/14 23:11, Schubert, Carsten [JRDUS] wrote:
> Hi,
Hi Carst
Hi,
I am bit stumped on how to get probe or reduce to work with coot under Linux. I
followed the instructions and defined the path to reduce/probe in various
startup and system files in which I could find a reference to probe/reduce:
* ~/.coot.py
* coot.py (path defined by COOT_PYTHON_EXTRAS
in 0.72: Extensions->Modeling->Atoms with Zero Occupancies
That should do the trick, or not?
Cheers,
-C.
-Original Message-
From: Mailing list for users of COOT Crystallographic Software
[mailto:COOT@JISCMAIL.AC.UK] On Behalf Of Eleanor Dodson
Sent: Tuesday, January 14, 2014 10:13
-
From: Bernhard Lohkamp [mailto:bernhard.lohk...@ki.se]
Sent: Thursday, September 12, 2013 3:18 AM
To: Schubert, Carsten [JRDUS]
Cc: COOT@JISCMAIL.AC.UK
Subject: Re: Problems with COOT_PYTHON_EXTRAS_DIR on WinCoot 0.7 rev 4459 on
Windows 7
Ok. I tracked down what's going wrong and fixed it (r
Hi,
This is probably more a question for Bernhard:
After upgrading to Windows 7 I am no longer able to read in a custom coot.py
located in a startup directory outside of the WinCOOT directory.
The error message is as follows
Coot Python Scripting GUI code found and loaded.
WARNING:: no directo
Kendall,
not sure if COOT is the right tool for this purpose. The main focus of the
program is for easy and excellent model building one structure at a time, which
it does very well. What you are describing is really more in the realm of
'density aware' professional modeling tools, like MOE or
For us it is only a real issue when dealing with FBDD structures, where
multiple ligands can be found in a single crystal structure. I wrote a
thin python wrapper around elbow (phenix's restraints generator) to give
each ligand a unique name, which takes care of that problem. This way I
can place a
Chris,
check the /var/log/messages logs. We battled the same problems and
finally discovered that the binary coot executables contained rpath
entries to Paul's home directory (/home/emsley/...). Our automounter
tried to find that non-existing mount-point several times during a load
and needed to t
14 matches
Mail list logo
