On 06/09/2017 16:03, Emilia C. Arturo (Emily) wrote:
Hello.
I wonder whether there is a way to turn off recentring when moving along from residue to residue within a
single molecule? I'd like for Coot to not recentre (or ... recenter :-)) automatically so that I can see
where the breaks in
On 06/09/2017 18:14, Seth Harris wrote:
Hello Paul, Coot users!
In the wonderful pantheon of Coot tools, is there a way to leap between equivalent points in symmetry mates
with a nice single key shortcut, for instance? Or could there be? I seem to be getting several cases with 8
copies/asu
On 17/10/2017 21:04, Xiao Lei wrote:
Dear All,
I got an error when I do real space refine with DNA base in Coot, Refmac5 did not give me any error, however
Coot give the error as attach. I do not know how to fix this.
I wonder where this model came from. Ad, Gd etc is how Coot used name
On 23/10/2017 06:45, Karsten Dreifus wrote:
Hi Paul,
I am using the dev version coot 0.8.9-pre (revision 6956). Trying to
use the Ramachandran plot atom-selection function. I used
"/1/A/10-20"
But does not filter.
Hi Karsten,
Yes, that dialog needs some work, doesn't it? Sorry. It's on the
On 17/11/2017 19:23, Edward A. Berry wrote:
Is there a way to open the "geometry" window (the box you open by "measures":"distances and angles") in the
initialization script, and perhaps set its position on screen as well?
No, I will add it. It will be in 0.8.9.
Is there a way
Sorry for the delay, it's hard for me to do non-trivial mails while I'm
travelling.
On 23/11/2017 15:52, Toon Van Thillo wrote:
For my master thesis I am busy with neutron crystallography. For refinement, the software used is
/phenix.refine /and COOT for manual corrections.
However, it
On 07/12/2017 16:19, Thomas Laughlin wrote:
I've been trying to build into an EM-density map using WinCoot and the program keeps crashing when
manipulating the model or density.
Using a .mrc seems to work fine, it is only when I use a .mtz that the program crashes upon manipulating
On 20/10/2017 14:31, Shintaro Aibara wrote:
Dear Coot BB,
I recently realized that on my Ubuntu 16.04 at home, certain panels such as dynarama and probe clashes were
not visible. I was using precompiled binaries revision 6998 for ubuntu 14.04, but this seemed to be a
version independent
On 08/05/18 18:21, Noor Agip wrote:
>
> I am trying to use the 'align and mutate’ feature in coot, in order to
> place the sequence of a subunit in a solved structure (the homologous
> subunit), and initially it looks like its working, but the numbering
> of the sequence seems off. Now the protein
On 11/06/2018 04:15, liyaowang2...@163.com wrote:
this is my first thread here, and I am not sure this topic was discussed or
not, please tell me if it was.
It was not! Not to my memory at least.
Coot I thought is originally for density map of crystal, it can work on the cryo-em map too.
On 07/06/2018 15:45, Murpholino Peligro wrote:
Dear all.
Putting this line
(set-use-stroke-characters 1)
into
~/.coot-preferences/coot.scm
fixes the slowness.
OK, interesting.
I wonder where's the coot.scm file for ccp4's coot?
I am not sure what this question means, please ask it
On 07/06/18 16:16, Jose Artur Brito wrote:
> Dear All,
>
> greetings from sunny Portugal!
Greetings.
>
> I had problems in the past with duplicate sequence numbers, namely
> when I had very high resolution and three different conformations for
> the same residue. However, I am refining a
On 07/06/18 20:15, Murpholino Peligro wrote:
> I was thinking that normal coot (i.e. the one installed from your
> site) reads from the preferences from ~/.coot-preferences/coot.scm.
> What about ccp4's coot where is located the respective coot.scm file?
> Or both coots read this single file?
>
I
On 11/06/2018 14:22, liyaowang2...@163.com wrote:
if I understood correctly, just forget about the rotation and translation.
I think I'd rather say "be not burdened by them" rather than forgetting about
them :-)
First I have to make copies myself, just what I did before. (edit the pdb
On 06/06/18 16:52, Murpholino Peligro wrote:
> I installed coot from here
> (https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/devel/build-info.html).
>
>
> After installing a few libraries with `sudo dnf whatprovides
> missinglib` got coot working. But it does not feel the same as ccp4's
>
On 06/06/18 17:27, Marcin Wojdyr wrote:
>> After installing a few libraries with `sudo dnf whatprovides missinglib` got
>> coot working. But it does not feel the same as ccp4's coot. It feels a
>> little bit slow.
> It's generally the same, but CCP4 applies a few patches to the coot
> source, uses
On 06/06/2018 22:02, Murpholino Peligro wrote:
I went into latest builds and choose the rhel
OK. They binaries run fine.
I found out that by doing Edit->Preferences->General->Smooth recentering->No. The jumps from residue to
residue are not "hideously" slow.
OK, but the video that you
On 25/05/2018 15:26, Emilia C. Arturo (Emily) wrote:
" oops failure to construct rdkit molecule"
Hi Emily,
This is indeed the issue here. Coot needs to be able to convert your ligand from pdb/mmCIF representation
into an internal/rdkit molecule. It won't be able to do this if there is no
On 23/05/2018 23:24, Ethan A Merritt wrote:
I just updated the O/S on two of my machines (linux Mageia6) and perhaps
foolishly also ran the update tool in ccp4 before checking that everything was
working. Now I find that I have a coot problem but I don't know whether it's
due to the OS update
Dear Kamel,
As a rule, if you use binaries distributed by CCP4, you should ask them, not me.
However...
I am not able any more to scroll maps opened from .phs files with the middle
mouse button (although I can change it in the map settings).
I got the message: 'WARNING: No map - Can't
On 30/12/2017 19:32, Xiao Lei wrote:
Dear All,
I am using WinCoot 0.8.6.1 .
:-/
I find Coot fails every time when doing real space refinement of Iso-aspartic acid residue (IAS) in PDB
entries containing IAS.
For example, in PDB entry 1DY5 chain A residue 67th IAS, when doing real space
We are pleased to announce the release of Coot-0.8.9
http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/source/releases/coot-0.8.9.tar.gz
Binaries here:
https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/binaries/release/
Mac and Windows binaries will be forthcoming in due course.
On 11/01/2018 16:44, Victor Tobiasson wrote:
Following the release of coot 0.8.9 it appears some of the core controls for
"dragging" molecules during real space refinement have changed. Is there a more
comprehensive documentation of the changes than listed in the RELEASE-NOTES available?
Hello Rene,
I am analyzing and comparing more than forty structures solved in complex with
different ligands. I would like to estimate for the ligands in each structure
the fit to electron density via COOT scripting. However,
(score-residue-range-fit-to-map) function did not seem to work on
On 29/01/2018 13:11, René Wintjens wrote:
I'll take a look for map-to-model-correlation function.
In the meantime, I wonder if simply the function (density-at-point) computed at the ligand coordinates on an
omit map would be easier to compare the ligand fits to the density.
You could do
On 30/07/18 20:23, Qianglin Fang wrote:
> Dear All,
>
> I have been working on a cryo-EM map with a boxsize of 1200 pixels. But every
> time I tried to open the map in COOT, only a portion of the map was loaded.
> I was wondering whether there was any limit on the box size that COOT can
>
On 30/07/18 22:20, Qianglin Fang wrote:
> Thank you very much for the reply. I have already tried to use a large map
> display radius. Acctually, I found this problem after trying this. I also
> tried to open a map in EMDB (accession code: EMD-7472) which has a box size
> of 1280, and got the
On 31/07/18 19:23, sameer wrote:
> Hi,
> The documentation at -
> https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/web/docs/coot.html#get_002debi
>
>
> has following procedure to get model and maps from PDBe -
>
> get-eds-pdb-and-mtz id
>
I think that EDS moved between 0.8.9 and 0.8.9.1 -
On 27/08/2018 03:44, Jiapeng Zhu wrote:
Dear all,
I just upgraded my system to ubuntu 18.04 and installed the latest version
coot-0.8.9.2-pre-revision-7644-binary-Linux-x86_64-ubuntu-18.04.1-python-gtk2,
but I had a problem of real space refinement. I adjusted the model to fit the
density by
On 28/08/2018 16:20, Andrea Thorn wrote:
I would like to mark a box in an .mrc file (ccp4 format map); I know the xyz
coordinates of the corners.
Can I do something similar to "show unit cell" or draw 24 lines with some
script command in Coot?
coords = [
[0,0,0], [0,0,1], [0,1,0],
On 16/07/2018 22:15, Xiao Lei wrote:
Is there a way to measure the distance between an atom and another atom in symmetry mate models? I tried to
measure the distance usually by clicking two atoms, coot only gave very long distance between the two atoms
in ASU, even though the distance
On 30/08/2018 07:41, Andrea Thorn wrote:
Apply() could be replaced with map(function, list) in python.
for idx_pair in idx_list:
print idx_pair
# the following is inelegant, what is the python equivalent of apply?
to_generic_object_add_line(a, "green", 2,
On 22/01/2018 07:40, Marko Hyvonen wrote:
Dear Cooters,
I seem not to be able to read in coordinates which has two different residues (=heterogeneity) in a
particular position. The residues have the same residue number, but differ in residue name. They are
market as alternatives A and B
On 23/04/18 18:01, wtempel wrote:
> Hello,
> is flipping a His side chain using the button on the right-hand
> toolbar working for you as expected? In our hands, starting with
> version 0.8.9 (?), the "side chain flip", applies a 180 degree chi-2
> rotation keeping the imidazole moiety fixed and
We are pleased to announce the 14th Anniversary release of Coot: 0.8.9.1
Source Code:
https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/source/releases/coot-0.8.9.1.tar.gz
Binaries:
https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/binaries/release/
Release Notes:
o FEATURE:
On 24/03/18 18:28, Kenneth Satyshur wrote:
>
> coot 0.8.9 crashes when reading cif file. I tried reading my G4P.cif
> file and coot crashed with the following output:
>
>
For the moment try using Modern fileselector dialogs (Edit Preferences
General).
Paul.
On 01/04/2018 22:00, Paul Emsley wrote:
We are pleased to announce the 14th Anniversary release of Coot: 0.8.9.1
Mac binaries:
http://psbmini.ucsc.edu/~wgscott/coot/stablereleases/
Thanks Bill.
Paul.
On 12/10/18 11:58, Heng-Keat Tam wrote:
>
> I am wondering what's wrong with the real space refine zone for prolines in
> Coot (7658)? There are some problem with my machine (Ubuntu 18.04), when I
> refine (real space refine zone) proline. Even though the proline fits into
> the density,
Hello Jan,
first of all thank all developers for their great work on COOT and others for
their great support!
:-)
I am using the software now for years very successfully. However, today I noticed that I do one thing over
and over again - and wondered if it can't be automated. The way I
On 10/10/18 05:19, Xiao Lei wrote:
>
>
> I know in Coot there is an option called "making a link between two
> atoms by click". Is there a way in Coot to remove any link by clicking
> two atoms which have a link between them?
>
>
Sadly not :-/
Paul.
On 02/10/2018 18:22, BuddySphinx wrote:
Thank you for your reply. However, I encountered another issue. I was able to reverse my fragments and now
the first atom is at the correct position. But how do I continue to Baton mode? Because when I hit Baton
mode, it seems started a new project and
On 02/10/2018 17:24, BuddySphinx wrote:
I am trying to use the Baton mode feature to manually trace my Ca carbon. I
started on an atom within an alpha helix and hit the point where I realized this is the first atom. Now I
want to set up this as the first atom, is there a way to do that? Also,
On 02/10/2018 19:38, BuddySphinx wrote:
I see. But how to deal with the situation when I hit the C/N terminal atom of the chain when using Baton
mode? Like in my case, I started with an atom and after I mapped 38^th of the Ca atoms, I hit the first atom
(N terminus). But the Baton trades can
On 27/09/2018 22:44, Edwin Pozharski wrote:
Is there currently a way to auto-run the sphere refine on full sequence (similarly to stepped refine option,
preferably with an option to enforce Ramachandran)? If not, are there plans to add such feature? Is there
some fundamental objection to such
On 28/09/18 07:29, Mohamed Ibrahim wrote:
> Dear COOT users,
>
> For crystal structure with a metal cluster, what is the best way to
> generate and edit a restraints file.cif for the metal cluster?
>
I don't know about the best way, but if it's a single atom I'd make
distance restraints between
On 10/10/18 17:51, Yangqi Gu wrote:
>
> I am trying to dock my filaments coordinates into the map. I have
> shifted my cryomap using Chimera by changing the coordinates to origin.
In the coot world, one more typically shifts the coordinates to match
the reconstruction.
> However, when I opened
On 26/09/2018 11:29, F.Xavier Gomis-Rüth wrote:
You may also have to change the sigma contour level. When loading a cryo-EM
map, we have encountered that
COOT defaults to some very high sigma level, so that nothing is shown.
Interesting, it is my experience that the level is too low - i.e.
On 26/09/2018 04:02, Yangqi Gu wrote:
I have a question regarding to model building. I am trying to trace my protein
backbones manually. I have a helix EM map,
Do you mean "helical" - something with alpha helices in? Then I'd use "Place Helix
Here"
Or a helical reconstruction? There is
On 17/11/2018 16:11, Paul Emsley wrote:
https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/files/movies/residue-reorientation-mode.mov
https://github.com/pemsley/coot/commit/e559e4e12dee3439193b58144bd1ed769bae411d
Revision count 7699
The eagle-eyed amongst you will notice
And for those who don't want animation but do want reorientation, we have
"snap" mode:
https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/files/movies/residue-reorientation-snap-mode.mov
(example is the C-terminal fragment of the A chain of the tutorial data)
Revision count 7706
Paul.
On 11/12/2018 15:32, Andrea Thorn wrote:
Hi!
I cannot get Coot to open some EM PDBx/mmCIF files, for example 5lza, 5lzd,
5lze or 5lzs.
It says in the terminal output: "No Spacegroup found in this PDB file
There was a coordinates read error". However, the space group is listed in the
cif
On 26/11/2018 06:45, Galesa, Katja wrote:
Is the licence for Coot payable in Pharmaceutical industry (Novartis)?
Dear Katja,
Coot is free to all - including the pharmaceutical industry :-)
Regards,
Paul.
To
On 18/11/2018 16:08, Paul Emsley wrote:
And for those who don't want animation but do want reorientation, we have
"snap" mode:
https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/files/movies/residue-reorientation-snap-mode.mov
And here, because Jan mentioned it, is residue reo
https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/files/movies/residue-reorientation-mode.mov
https://github.com/pemsley/coot/commit/e559e4e12dee3439193b58144bd1ed769bae411d
Revision count 7699
Paul.
To unsubscribe
On 09/01/2019 04:27, Yong Tang wrote:
Happy New Year to all,
Happy New CCP4 Study Weekend.
I'm solving many structures of the same protein and would like to find a quick way to inspect like 10
selected residues of the 250aa protein in coot, for every structure against the matched electron
On 17/09/18 19:49, Robert Grant wrote:
> I have been using the Phenix-linked Coot to modify a MR solution calculated
> from a rather poor data set, with high merging Rs and very low absolute
> intensities. I have observed what I consider bizarre behavior in the real
> space refinement
Dear All,
We are pleased to announce the release of Coot 0.8.9.2
Source:
https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/source/releases/coot-0.8.9.2.tar.gz
Binaries:
https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/binaries/release/
More Linux binaries and Windows binaries will be
On 07/04/2019 14:02, Ahmad Khalifa wrote:
I'm working with a lattice made of a tubulin monomer that I modeled and refined
in Coot.
Sounds fine.
I have fitted other units of the monomer along the length and to the side of my monomer in a cryo-EM map to
study tubulin interactions with non
On 27/02/2019 01:52, V F wrote:
I vaguely remember there was some coot-scheme to simulate something
like centre_zone residue_a residue_b in coot. (i.e) centre between
residue ranges
I don't think that centring on a residue range is a thing. You can centre on an atom, a residue or a
On 13/03/2019 17:51, Kevin Jude wrote:
I'm using the latest prerelease build for OS X rev 7881. Although I really appreciate the new dashed lines
for missing loops, when I turn on symmetry, coot crashes immediately. This happens on my desktop computer
(OS X 10.12.6) but not on my laptop (also
On 20/03/19 19:49, Ahmad Khalifa wrote:
> I have a cryo-EM map that I want to segment.
"segment" as in what segger does? Or merely create a masked map?
> I have structures surrounding the density of interest from all sides.
> I used chimera to subtract everything and clean the density using
>
On 12/02/2019 06:01, Andreas Schedlbauer wrote:
Given two nucleotides
Given those nucleotides, I rather suspect you want base pairing restraints, not
base packing restraints.
Given a nucleic acid helix going "up the page", as it were, base stacking restraints are for
vertically-related
On 12/02/2019 09:31, Paul Emsley wrote:
On 12/02/2019 06:01, Andreas Schedlbauer wrote:
Given two nucleotides
Given those nucleotides, I rather suspect you want base pairing restraints, not
base packing restraints.
*.. base pairing restraints, not base stacking restraints
On 10/02/2019 15:01, Ahmad Khalifa wrote:
1) I like to set my structure view to show only the alpha carbon backbone. Is there a way to show the side
chains of only selected residues?
There is:
graphics_to_ca_plus_ligands_and_sidechains_representation(imol)
That, as you can see, doesn't
On 12/02/2019 02:32, Andreas Schedlbauer wrote:
Using latest build of coot for Scientific Linux (my version 7.6) get following
error when launching 'Add Parallel plane restraint' command:
INFO:: Failed to match restraint to templates:
EXTE STACK PLAN 1 FIRST RESIDUE 882 CHAIN A ATOMS { N3
On 15/01/2019 04:57, Markus Heckmann wrote:
I just want to replace the SER with a modified amino acid residue. Say
for example, SEP (Phosphoserine, O-phospho-l-serine).
I'm sorry that I have left this question unanswered for so long - but for the
archive, the answer is
Extensions ->
On 17/05/2019 17:10, Hannah Bridges wrote:
>
>
> I am using coot 0.9-pre (ccp-em) with a protein that contains Fe-S
> clusters. Although the bonds are now drawn between the Fe and S atoms
> (thanks Paul!) and the clusters no longer explode when you real space
> refine without adding your own
On 30/05/2019 18:27, Darin Lory wrote:
This an error I'm receiving with coot 0.8.9.1 Scientific Linux 7.4 with
Python2/GTK2 on RHEL 7.6 server.
I'm trying to integrate coot and PyMOL with Phenix. From my Phenix guru: For
Coot, I would recommend using 0.8.9.x series
$ which coot
On 08/05/2019 12:17, Bernhard Rupp wrote:
>
> Dear Fellow Cootsters,
>
>
>
> I am trying to use the flexibility of glycans as validation of a
> docking model (no density available)
>
> by torsioning the glycans into conformations where they do not
> interfere/clash with the models.
>
OK, but
FWIW, this message:
On 20/05/2019 23:32, Darin Lory wrote:
guile: error while loading shared libraries: libguile.so.17: cannot open shared
object file: No such file or directory
failed to launch the crash catcher
is telling you that the (guile-based) crash catcher fails to start - it is not
On 19/05/2019 21:40, Ahmad Khalifa wrote:
Hello,
I want to write a script that does the following:
for a bunch of chains and atom numbers:
go to chain letter and atom number
do sphere refinement
This should get you started:
imol = 0
residue_list = [["A", 10, ""], ["A", 20, ""], ["A", 30,
On 06/05/2019 20:10, Ahmad Khalifa wrote:
> I have a large structure loaded in Coot. The middle mouse click is
> often mistaken for a center around atom action whilst trying to
> navigate the map.
I presume that you mean middle-mouse click and drag (aka "pan" (like the
PyMOL mode)) get confused
On 03/07/2019 13:04, CRAIG A BINGMAN wrote:
This structure has been solved and refined using phenix in the hexagonal setting of space group R 3. There
is one copy per asymmetric unit in R 3.
As you can see from the attached image, coot is rendering some but not all of
the symmetry mates.
On 15/07/2019 02:48, Ahmad Khalifa wrote:
I know I can either force beta strands or alpha helix restraints while refining/regularizing, but what about
3-10 helices?!
For a 3-10 helix, you will have to add the bond restraints one by one:
Extensions -> Modules -> User Defined Restraints ->
On 12/04/2019 21:17, Edward A. Berry wrote:
What is the format for match-list in:
lsq-match imol-ref imol-moving match-list
(or where is it described).
I somehow missed this question
apply-lsq-matches is called with 2 arguments: imol-ref and imol-moving, which
are the molecule numbers.
On 21/04/2019 23:19, Shah, Pranav Nitin wrote:
I was trying to follow your tutorial on model building in cryo-em
maps. As I was following the tutorial, I tried installing extra
plugins, but found that running curlew() in Coot was unresponsive. I
am running coot 0.8.9.2 (through ccp4) on my
On 15/07/2019 10:22, Paul Emsley wrote:
> On 15/07/2019 02:48, Ahmad Khalifa wrote:
>> I know I can either force beta strands or alpha helix restraints
>> while refining/regularizing, but what about 3-10 helices?!
>>
>
> For a 3-10 helix, you will have to add the
On 03/09/2019 14:47, Daniel Larsson wrote:
Now I got 0.9-pre working (thanks Colin Palmer for the suggestion!). In the new
version, I have problem generating ProSMART restraints for RNA.
The Pro in ProSMART refers to proteins. If you actually used ProSMART (rather than following the video)
On 23/08/2019 17:05, Mark Saper wrote:
The sf-annotate_P1.cif file that I have generated for PDB submission
contains the map coefficients along with the observed structure factors.
_refln.pdbx_FWT
_refln.pdbx_PHWT
_refln.pdbx_DELFWT
_refln.pdbx_DELPHWT
Is there any way that Coot can read
On 27/08/2019 15:22, Noor Agip wrote:
> I am rather confused, can you clarify on what to download, from where and
> exactly what to put in the config file?
>
The curlew script files are here:
https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/extensions/
Put them in your
On 04/09/2019 00:12, Paul Emsley wrote:
On 03/09/2019 14:47, Daniel Larsson wrote:
Now I got 0.9-pre working (thanks Colin Palmer for the suggestion!). In the new version, I have problem
generating ProSMART restraints for RNA.
The Pro in ProSMART refers to proteins.
Oh, no it doesn't
On 13/09/2019 13:13, Edwin Pozharski wrote:
I have recently asked for suggestions on dealing with handle_read_draw_molecule crash when included in
~/.coot.py. An obvious (I am certainly getting dumber with age) workaround is to put ~/.coot.py into a
separate file and run it from Calculate menu
atom_attribs = active_atom()
returns the attributes of the atom closest to the centre of the screen.
OOps - I meant: active_residue()
To unsubscribe from the COOT list, click the following link:
On 13/09/2019 12:08, Auffinger Pascal wrote:
I wrote a python script to load several maps and structures
and would like to use a command to display only two of them
(like unchecking display in the display manager) and also to
use a command that would help me to decide which structure/map is
On 06/09/2019 14:15, Edwin Pozharski wrote:
So I wrote this script long time ago to help loading multiple models (both pdb and mtz files) at once that
also contained several useful shortcuts to navigate through the set of structures etc. I haven't used it in
quite some time, and it was pointed
On 30/07/2019 17:00, Ahmad Khalifa wrote:
> Reinstalling didn't solve the problem:
>
> https://youtu.be/jXZ5bZsuK3g
>
That's weird - not see that before. That is under the control of the
graphics driver, not WinCoot. Try turning down your graphics optimizations?
Paul.
On 29/07/2019 12:01, Luca Pellegrini wrote:
> Hello,
>
> How do I change the default setting for skeleton size, so that I can
> skeletonise a large map without crashing?
>
> Best wishes,
> Luca
>
> INFO:: making skeleton cowtan...
> GraphicalSkel input map: 385.2 385.2 385.2 1.571 1.571 1.571
>
On 20/07/2019 18:33, Ahmad Khalifa wrote:
After generating metal ion restraints using Elbow in Phenix and refining my structure, I end up with a
structure that forms two solid bonds between the GTP and Mg+2.
You will get solid bond if the GTP and Mg+2 are in the same residue (I'd recommend
On 24/07/2019 09:38, Dorota Kubacka wrote:
I installed the newest version of WinCoot-0.8.9.2 on Windows10. The option "Merge
molecules" works in a wired way. It works when I
"get monomer" like EDO form the base and then merge it with protein but DOESN'T work when
I am trying to "get monomer"
On 25/07/2019 14:46, Eleanor Dodson wrote:
> by default - how to get rid of them???
>
Calculate -> Scripting -> Scheme -> (delete-hydrogens imol) ;; where
imol is the molecule number
Or you can create a new molecule that excludes hydrogen atoms in the
selection:
Edit -> Copy Fragment ->
On 02/11/2019 15:38, 何青霞 wrote:
Is this the email of COOT developers?
As good as.
How can I help?
Paul.
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On 08/11/2019 19:51, Seth Harris wrote:
I'm sure this has been asked, but after some searching I can't find hints. Apologies if redundant, but can
someone refresh me on how to get Coot to be graceful about residues with insertion codes...particularly
during real space refinement. I have a
On 05/11/2019 19:14, Folmer Fredslund wrote:
I'm not at my machine now so can't check, but perhaps these parts of the manual
can help:
https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/docs/coot.html#Map-Contouring
non-moving residue in refinement. That was fixed here:
commit c9f19a5b9b57a97c130907fa7b00ed6d9284615d
Author: Paul Emsley
Date: Tue Dec 3 16:19:57 2019 +
If you mean a stretch is made between two moving residues, then that is
a problem that I don't recognise (and according t
On 11/12/2019 14:26, Daniel Larsson wrote:
Hi,
I can confirm that this happened to me now, using 0.9-pre build from CCPEM
1.4.1 (revision-count 855). I also tested some old binaries and the change was
introduced sometime between revision-count 819 (does not try to connect across
the gap) and
On 11/12/2019 12:30, Daniel Larsson wrote:
I have a question about the undo mechanism, especially if I undo several steps.
Occasionally, when I undo and the redo, I do not get back to where I expect to be.
Instead it seems that the I could recall a previous state. This seems to happen when I
On 16/12/2019 22:32, Karim Rafie wrote:
I am currently working on structure of a protein complex and am trying to identify the sequence of a protein
chain (24mer) that hasn't been seen/described before. Thankfully, the map is good enough allowing me to
identify two positions along this chain
sigh. This one has actually been tested...
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(let ((seq "DVSGTVCLSALPPEATDTLNLIASDGPFPYSQD")) ;; or
Well, jet-lag enables me to tinker with this script further. Now it does fitting, refinement, scoring and
sorting - not what you asked for, but it might be useful.
Paul.
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On 28/10/2019 10:57, Pranav Shah wrote:
Somewhere in my efforts to customise my coot user experience I have
managed to turn off the scroll wheel dependent change of the contour
level and now i cannot figure where that option is! Could you tell me
how I can preamble this? I am using the 0.8.9.2
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