On Thu, Jan 22, 2015 at 10:53 AM, Kenneth A. Satyshur satys...@wisc.edu
wrote:
moving thru a space. In a graphics run program, like Sybyl from Tripos,
all work is done by the
graphics engines. Rotations and translations are equally fast. In a
non-graphics engine program like
pymol, the
On Tue, Dec 9, 2014 at 6:55 AM, Paul Emsley pems...@mrc-lmb.cam.ac.uk
wrote:
I think that you probably want the one from Phenix - I believe that that
plot is created from a larger and more modern dataset.
Correct, although I think the most significant difference is the use of
2-degree grids
On Wed, Jun 18, 2014 at 11:09 AM, Thomas, Leonard M. lmtho...@ou.edu
wrote:
OK this has me puzzled. Coot was working fine until I had to update
something in order to install the latest version of Phenix. I don't
remember exactly what the module was but Phenix needed it.
Probably the
On Thu, May 29, 2014 at 3:17 PM, George Devaniranjan devaniran...@gmail.com
wrote:
Thank you for your reply, Dale.
Let me rephrase the question:
Essentially I want to use COOT's Calculate--map sharpening
but only use the backbone atoms in the process.
Perhaps you want an omit map? In that
Since you mentioned phenix.cif_as_mtz, here is an even easier method that
will work for most structures:
phenix.fetch_pdb --maps PDBID
phenix.mtz2map PDBID.pdb PDBID_maps.mtz
Caveat: this makes some assumptions about the contents of the deposition
which are not always justified, also a
the
main coot window).
I think I stumbled on the solution though, if I go to the molprobity
tab in Phenix, I can toggle the dots on or off in coot!
Nat
I guess I will have to just close out the Phenix-initiated coot window
and start a fresh one.
On Tue, Jan 29, 2013 at 3:19 PM, Nat Echols
This is an issue with system memory limits, but I would first check whether
it's a 64-bit build of Coot - if not, upgrading the memory may not help. I
think you can do something like this:
file /Applications/ccp4-6.4.0/bin/../coot.app/Contents/coot/bin/coot-real
On Thu, Dec 5, 2013 at 10:16
Just to add to Hari's question: I tried to show a user how to do the same
thing last week, and found it much too complicated. I'd love to see a
function that lets me swap chains with their symmetry mates - this
situation comes up all the time and I've also had to resort to PyMOL in the
past.
Is it just me or is this feature broken? I tried to rest the occupancy for
all atoms in a ligand that Phaser zeroed out, using Apply occupancy to all
atoms in residue, and nothing happened. r4549, Mac, from Bill Scott's
page.
thanks,
Nat
, 2013 at 12:05 PM, Nat Echols nathaniel.ech...@gmail.comwrote:
On Mon, May 6, 2013 at 11:44 AM, Joe Batchelor joe.batche...@gmail.comwrote:
Coot is working wonderfully for us. I was hoping to get guidance on how
to modify initial settings using the .coot file. Apologies if this already
has been
On Sat, Apr 20, 2013 at 11:17 PM, Ethan Merritt merr...@u.washington.eduwrote:
This is far from the first time I've ranted on the subject.
What is really needed is a TLS group field in the ATOM record so that
each atom is unambiguously associated with a TLS group that
describes its
On Fri, Mar 29, 2013 at 8:16 AM, Paul Swartz paul_swa...@ncsu.edu wrote:
My processor is Intel Core i7-3630QM which appears from the web to be an IVY
bridge. I have no problems with coot in windows with this processor and now
have to boot to Win7 to model build with COOT and then back to
On Fri, Feb 15, 2013 at 5:24 AM, Paul Emsley pems...@mrc-lmb.cam.ac.uk wrote:
Anyway, I realized that there is a new version of coot (v0.7.0) and hoping
this version has fixed this ghost bug, I downloaded it and installed from
ccp4 coot-0.7.0-i386.dmg. Now, after File=smile, nothing happens ...
On Tue, Jan 29, 2013 at 12:33 PM, Nathaniel Clark
nathanielcl...@gmail.com wrote:
When I use a coot window that was started by Phenix, it shows those
'molprobity' dots which represent the Van Der Waals surface. Can
anyone tell me how to turn those off?
In theory, Draw menu -- Generic Display
On Mon, Jan 21, 2013 at 6:21 AM, Clemens Vonrhein
vonrh...@globalphasing.com wrote:
Just for the record: the map-coefficients written by BUSTER
(amplitudes 2FOFCWT and FOFCWT in the final 'refine.mtz' file) are on
the same scale as the model (amplitude FC) ie. on approximate absolute
scale.
Is there a Python function to specify the map used for real-space
refinement? I have searched the documentation and tried typing in
various words in the scripting console and letting the auto-complete
suggest functions, but nothing yet.
thanks,
Nat
I think I was looking at the wrong manual - I blame Google. Thanks!
-Nat
On Mon, Jul 30, 2012 at 1:25 PM, Edwin Pozharski epozh...@umaryland.edu wrote:
set-imol-refinement-map?
http://www.biop.ox.ac.uk/coot/doc/coot/set_002dimol_002drefinement_002dmap.html
Is there a Python function to
On Wed, May 9, 2012 at 8:07 AM, Michele Vigolo
michele.vig...@studenti.unipd.it wrote:
I installed Coot 0.6.2 from coot-Linux-x86_64-ubuntu-10.04.2-gtk2-python
but when I launch it from the terminal I get this warning:
What is the exact command you are using to start Coot?
-Nat
It's not just you. You should update Xquartz to 2.7.1, but if my
experience is any indicator, this won't entirely fix the Coot problem.
(Although I don't need to restart X11, just Coot.)
-Nat
On Thu, Apr 5, 2012 at 8:23 AM, Francis E Reyes
francis.re...@colorado.edu wrote:
Hi all
This one
On Mon, Mar 5, 2012 at 7:51 AM, Paul Emsley paul.ems...@bioch.ox.ac.uk wrote:
Full disclosure: I have spend a few minutes trying to get this to work with
a python socket server and it's not working as I hoped it would. Hmm... -
maybe this is the problem into which the Phenix people ran some
On Sat, Feb 11, 2012 at 10:55 AM, hari jayaram hari...@gmail.com wrote:
There has been a lot of opinions within the Ubuntu community about
Unity..just wondering what coot-ers are using with the new Ubuntu(s).
I think it's awful - after about 10 minutes I switched back to the old
gnome UI. I
On Tue, Jan 24, 2012 at 11:59 AM, Miguel Ortiz Lombardia
miguel.ortiz-lombar...@afmb.univ-mrs.fr wrote:
And really, is it so hard to give a unique identifier to each ligand?
I'm pretty sure it really is difficult (or at least inconvenient) for
the people at drug companies, because I've heard a
On Wed, Jan 18, 2012 at 7:13 AM, Ed Pozharski epozh...@umaryland.edu wrote:
The first time you call any command that need a target map to be defined
(e.g. real space refinement), the map chooser gui comes up. But then
the command that initiated it does not really get executed, and you have
to
On Mon, Dec 5, 2011 at 3:17 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote:
could you first explain why you display hydrogens in coot? Usually
hydrogens are used in refinement in riding (calculated) positions and
not saved to the PDB file, so there should not be any for coot to display.
This
On Wed, Oct 26, 2011 at 1:48 PM, Jerome Nwachukwu jnwac...@scripps.eduwrote:
I am trying to write a short script to open multiple .pdb and .mtz files
that have the same filename but are located in different paths, and adjust
their map and bond settings. I noticed that the multi-read-pdb
On Thu, Sep 22, 2011 at 6:29 AM, Swastik Phulera
swastik.phul...@gmail.comwrote:
I want to have a model of a chimeric protein having domains from two
different proteins(of known structure) . I now have structures of the
individual domains with me. How do I use coot to join these two domian
On Thu, Sep 15, 2011 at 10:37 AM, Engin Özkan eoz...@stanford.edu wrote:
I assumed Phenix, which runs molprobity tools, and definitely Molprobity,
which mentions checking nomenclature (but I guess just for pdb versions 2.3
vs 3), would check nomenclature. And after fixing them in coot and a
On Thu, Aug 18, 2011 at 5:41 AM, Huw Jenkins h.t.jenk...@leeds.ac.ukwrote:
Having spent a while on the CCP4bb trying to fix what I thought was a Coot
library problem but turned out to be an issue with the input pdb file, and
as was suggested by the original poster on the bb, it would be useful
On Mon, Aug 15, 2011 at 10:38 AM, Francis E Reyes
francis.re...@colorado.edu wrote:
I've made a mess and I've got lots of labels on my coot view (via shift
left click on atom). I shift left click on the same atom to remove the
label, but how do I remove all the labels at once?
Is there a way to view the console output from within Coot itself, if Coot
wasn't actually launched from a terminal window? It is sometimes difficult
to tell what is breaking when a map fails to load.
thanks,
Nat
On Mon, Mar 28, 2011 at 8:59 AM, Gregor Hageluken g...@st-andrews.ac.ukwrote:
is there any way to switch off the probe clashes in coot? When I do
rotate/translate with a molecule, the whole screen is full of little
probe-clash dots afterwards and that is a bit confusing...
I know that I can
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