On 13/10/2020 17:36, Frank von Delft wrote:
That video is rather dramatic...
:-)
did it do that on its own, or was there dragging-by-mouse going on?
"No, she went of her own accord."
(no dragging)
The jelly/morphiness seems to allow a greater radius of convergence than
rigid-body
? What happens when you reduce the map weight?
Fitting RNA with a conformational change is one of the things that Coot
now does well (if I may be so bold).
Paul
On Oct 12, 2020, at 8:11 PM, Paul Emsley <mailto:pems...@mrc-lmb.cam.ac.uk>> wrote:
On 12/10/2020 13:44, Sorbhi Rath
On 12/10/2020 19:11, Paul Emsley wrote:
On 12/10/2020 13:44, Sorbhi Rathore wrote:
Dear all,
Could anyone please suggest the best way to decide which German-
McClure Alpha value to use during refinement (both at a higher
resolution and lower resolution areas for a cryo-EM map)?
I am
On 12/10/2020 13:44, Sorbhi Rathore wrote:
Dear all,
Could anyone please suggest the best way to decide which German-
McClure Alpha value to use during refinement (both at a higher
resolution and lower resolution areas for a cryo-EM map)?
I am using coot 0.9.1 pre EL(ccpem).
A
On 08/10/2020 17:11, Clemens Grimm wrote:
I just lost my Coot settings and startup files.
rsnapshot!
I did this some months ago, but have a hard time finding this info.
Could someone point me to how to enable the interactive dots during RS
refinement and the Ramachandran polyeders?
http://legacy.ccp4.ac.uk/html/maplib.html
This doesn't mention skew -
I meant: This *does* mention skew...
Paul
p.s. something hideous happened to the image between sending and
receiving. Something down-sampled it - I' guess jiscmail.
On 30/09/2020 11:50, Pranav Shah wrote:
I am trying to visualise my model in coot 0.9 and after turning the
stereo mode the model appears to have a flipped hand. Is there a way
to fix this?
Turn it off and turn it on again?
If that consistently fails you can try a negative stereo separation
On 25/09/2020 15:28, Yong Tang wrote:
When we read in an NMR model that has an ensemble of 23 structures, how do we display only one of them
for clarity and simplicity?
The only command that I found related to NMR models is "n-models 1mol" in this link:
I have recently learned that Ana's "Coot for Cryo-EM" talk is now
available on YouTube:
https://www.youtube.com/watch?v=HJr-hJEF8oA
Paul.
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On 24/09/2020 10:03, Manoj saxena wrote:
I have built a DNA into a cryoEM map and I want to change the
directionality of the chain.
Is there a simple Coot option that I can use or do I have to build the
model again.
Not that I can think of.
Another question is: can Coot add DNA in both
On 23/09/2020 19:05, Kevin Jude wrote:
I'm using coot 0.9.1-pre for OS X from ccpem-20200722. I find that
while I can hide hydrogen atoms as expected using Edit>Bond
Parameters, when I change my molecule representation to Bond (Colour
by Chain), the hydrogens return as individual atoms.
uye
On Sun, Sep 20, 2020 at 10:41 PM Paul Emsley
mailto:pems...@mrc-lmb.cam.ac.uk>> wrote:
On 20/09/2020 19:27, Qiuye Li wrote:
The protein is a filament and the reconstructed map is in a
512*512*512 box. I segmented this reconstructed map in Chimera
using Seg
,
Qiuye
On Sun, Sep 20, 2020 at 1:29 PM Paul Emsley <mailto:pems...@mrc-lmb.cam.ac.uk>> wrote:
On 20/09/2020 17:29, Qiuye Li wrote:
>
> Thanks for the suggestion, it looks map segmentation and coot do
not
> work well with each other, see the tests I did below:
On 20/09/2020 17:29, Qiuye Li wrote:
Thanks for the suggestion, it looks map segmentation and coot do not
work well with each other, see the tests I did below:
1. .mrc map directly from relion:
in Chimera: OK
in Coot: OK
2. segmented map generated from Chimera:
what do you mean by
That looks odd. I wonder if the problem lies with Coot or the program
that generated the map. How does this map look in PyMOL or Chimera (for
example)?
Paul.
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On 09/09/2020 20:28, Guenter Fritz wrote:
Dear all,
just a simple question, but I could not figure it out:
In coot 0.9 (vers. Marina Bay from CCP4 7.1) osx.
Can somebody point me to the option to select the map to attach to the
scroll wheel?
(in 0.89 this was HID -> ScrollWheel -> Attach
On 17/08/2020 09:37, Clemens Grimm wrote:
Dear All,
mutating RNA bases to Tr gives me the following error:
"This should never happen - badness in get_standard_residue_instance, we selected 0 residues looking for
residues of type :Tr:
Oops - can't find standard residue for type Tr"
Other
Hi Luise,
On 13/08/2020 08:36, Luise Kandler wrote:
I'm a beginner in programming and I am trying to write a plugin for coot, that
sets up a window using gtk.
OK.
I
already downloaded gtk+3 and pygobject and managed to run a simple example from the Terminal, that works
perfectly fine
On 26/07/2020 13:29, Victor Tobiasson wrote:
Dear fellow modellers,
Hello Victor,
I am using a fresh install of coot 0.9 from ccpem version
1.4.1-nightly (git: 1.4.1-93-g9873763) and am having some problems.
Whenever I add terminal residues any subsequent refinement of the
region will
On 24/07/2020 14:42, Yong Tang wrote:
Dear all, I have a loop truncation that could be explained as
ProteinName(1-20)-GSSGSS-(40-500), where residues 21-39 was replaced
with a GSSGSS linker. Now the problem is in Coot, how do I define this
mutant in a way that I could still preserve the
To find variants of nucleic acids:
File -> Search monomer library
"guanosine 3' " (without the double quotes) -> Search
for example.
Once you know the 3-letter code/label_comp_id, you can use Replace
Residue. Maybe you want 3GP or 3DA.
Paul
On 24/07/2020 21:47, Yong Tang wrote:
Thank
On 25/07/2020 04:37, 陈喆 wrote:
I use coot to calculate my protein channel . it worked well .then I
want to generate a figure using pymol with small dots calculated by
coot. I noticed the output file hole_surface_dots.dat cannot work in
pymol. Is there any way to export the coordinates of
On 15/07/2020 09:48, Vijay Jayaraman wrote:
I wanted to use the Jiggle fit option in coot. I initiated coot from the CCPEM
interface (I made sure CCP4 is working). Whenever I try to open my map (size
350 MB) coot crashes with the following error message:
terminate called after throwing an
On 15/07/2020 08:16, Clemens Vonrhein wrote:
Hi Paul,
On Fri, Jul 10, 2020 at 11:16:55AM +0100, Paul Emsley wrote:
Maybe you could give today's reversion a bash
(efde451d59318f6f58c7f8295c93c86f764126e5)
What does that mean? I guess it is meant as a git commit ID, right?
Yes
On 10/07/2020 15:56, Andrew Sharff wrote:
On Fri, 10 Jul 2020, Paul Emsley wrote:
Thank you for the reply.
I hope that the recent commits you have made address the issues.
It seems to me that they are not going to be easy to diagnose,
especially our script visualise-geometry-coot, which
On 07/07/2020 14:37, Andrew Sharff wrote:
Dear All,
Since moving to ccp4 7.1 (and Coot 0.9), we have been seeing several
issues on MacOS with some of our utility programs, which start Coot
with both distributed and automatically generated Coot scheme
scripts.
I don't really follow what
On 04/07/2020 06:03, Kevin Jude wrote:
Using Coot 0.9 from the most recent CCPEM nightly for Mac. When I do a
"triple refine" against an EM map or X-ray of any peptide triplet that
includes one-half of a cysteine pair at position i+-1, I get a "Failed
- Error: No Progress". Same when I do a
On 26/06/2020 21:01, Haji-Ghassemi, Omid wrote:
Dear fellow WinCoot users,
I recently updated my Wincoot to the latest 0.9 beta and changed the
start-up script to load all of the library and dictionary files
required for refinement (as Bernhard suggested).
Everything seem to work fine,
On 23/06/2020 19:35, Andrea Thorn wrote:
with which scripting command can I rotate the view with each move when I
forward through a chain (for example, using the space bar)?
set_reorienting_next_residue_mode(1)
To
On 18/06/2020 09:15, Pedro Matias wrote:
Hi Christoph,
The .coot file must reside in your root directory, not in
.coot-preferences, .i.e., ~/.coot
in your home directory, that's right.
Also, I think you should only have either .coot or .coot.py there.
Yes
The .coot-preferences file
On 09/06/2020 09:34, Guillaume Gaullier wrote:
On 9 Jun 2020, at 02:39, Paul Emsley mailto:pems...@mrc-lmb.cam.ac.uk>> wrote:
Keen as I am for people to (successfully) compile the source code, I don't think that it's necessary in
this case - you just need to activate the relevant m
On 09/06/2020 10:04, Clemens Grimm wrote:
I am very happy to see the new refine tools running on six cores.
:-)
However, since I have 80 cores available,
:-(
By default, coot will try to use as many cores as you have. I have not been able to get the refinement past
about 60% occupancy
Turtle Bay is the 0.8 series
Marina Bay is the 0.9 series
On 08/06/2020 18:42, Clemens Grimm wrote:
Dear All,
I wonder how to
(1) undisplay and
(2) remove
restraints generated with ProSMART and displayed for a particular
molecule. I do not see any entries for that purpose, neither in the
On 08/06/2020 03:51, Ahmad Khalifa wrote:
The Coot sequence view window assigns different colors to residues. What does
this coloring mean exactly?
Here's a bit of source code:
case mmdb::SSE_Strand : s = "firebrick3"; break;
case mmdb::SSE_Bulge : s = "firebrick1"; break;
case
First, Coot doesn't do much with masks (which is are maps with only 1s
and 0s). I think that it can read them in, but not write them out.
On 28/05/2020 19:17, Bernhard Rupp wrote:
Maybe I should explain an example: Say coot detects an unmodelled blob
(maybe a ligand). Now, I would like to
On 19/05/2020 14:06, Erwin Pannecoucke wrote:
Dear all,
My apologies for this 3^rd email in such a short time, this will be the last
one.
I restarted building in the refinement branch, and encountered the following:
-Again I had to manually declare $coot_version=coot-0.9. This time I did it
On 14/05/2020 12:39, Arto Pulk wrote:
Hey,
Yo.
I have been trying to install Coot 0.9 from source or autobuild for Ubuntu
18.04.
Good.
1) Tried autobuild script but it gives me error:
https://raw.githubusercontent.com/pemsley/coot/master/build-it
OK, that's a bit decrepit
On 14/05/2020 00:00, Daniel Asarnow wrote:
Hi Paul,
Hi Daniel,
Is there a list of functions that can be used in the preferences file?
Yes. Chapters 11 through 14 of the Coot User Manual.
Are there other files besides coot.py that define them?
Yes. Typically,
On 13/05/2020 10:04, Nikos Pinotsis wrote:
I noticed that other non bonded atoms (Na, Cl etc ) have a sphere and
cross which is quite ok.
OK.
I can see a possibly reason why this is not the case for water molecules.
I liked the way that PyMOL does it.
In any case larger spheres
On 12/05/2020 14:42, Pedro Matias wrote:
Hi,
Hi.
Is there a way to control stereo separation / depth in the new COOT? The
picture is excessively deep in comparison with the previous version.
What you are mostly seeing, I think, is that the transformation between
the eyes is no longer
On 08/05/2020 18:34, Kevin Jude wrote:
I have a Fab with an interchain disulfide that I'd like to refine with
sphere refine, but SG atoms repel each other. I have no trouble with
intramolecular disulfides. Is there anything I can do to restrain this
bond in coot? I'm using coot 0.9 for OS X
On 05/05/2020 14:47, Xavier Brazzolotto wrote:
I’ve recently installed Coot 0.9 from CCP4 7.1 us OSX Catalina.
The program works okay except for the glycan module :
Trying to add a « complex mammalian » glycan chain it stops at the
addition of the second residue with the following error
This is perhaps not the best venue for CCP4 questions.
On 04/05/2020 11:10, Eleanor Dodson wrote:
I am running CCP4I2 on my rather ancient MacBook Pro and worry that I will use
up all the disk space.
Crystallographic projects are rarely big these day compared to disk sizes. Use
$ du -s --si
On 29/04/2020 01:11, Jade Shi wrote:
Hi,
Hi Jade.
I'm interested in writing a script (run from the command line) that reproduces the
Find Ligands functionality from the Coot GUI, as I have several protein/ligand pairs that I'd like to
process automatically without manually running Fit
Steady on. I hope that Bill and I can finagle coot into working with
whatever gtk+ it has been provided.
FWIW, Gtk+3 in the works and Gtk+4 is on the horizon.
Paul.
On 25/04/2020 03:35, Edward Miller wrote:
Thanks, Bill, as always for the dedicated support.
I've been a fink user,
On 20/04/2020 09:41, rainfieldcn wrote:
I still couldn't locate the button.
:-) Oh yes. Sorry. It's been ages since I used 0.8.x ...
There, you can find it under Extensions.
(I hope)
FWIW, the windows (python, actually) version didn't work well for me
last time I tried it.
Paul.
On 20/04/2020 09:12, SUBSCRIBE CCPEM Lei wrote:
Thank you Paul.
I've got winCoot 0.8.9.3-pre installed. But I still cannot find the glycan tool.
Where is it supposed to be?
Calculate -> Modules -> Carbohydrate
To
On 19/04/2020 23:54, SUBSCRIBE CCPEM Lei wrote:
I am trying to build a long glycan in WinCoot 0.8.9.
I heard there is a glycan tool in coot described in
http://journals.iucr.org/d/issues/2018/04/00/ba5284/index.html.
But I can't find it in my Coot.
You are using an Old Coot.
So which version
On 08/04/2020 12:11, Jason wrote:
I am using the latest version I can find of wincoot
I think the version that I would recommend is 0.8.9.3-pre from
Bernhard's github. 0.8.9.3 will be out soon (I am a bit inundated ATM.)
and I am trying to follow the tutorial/webinar.
I am not sure
Coot 0.9 is released.
This release has been a long-term effort (4 years according to my
notes). It is powerful but not as
clean and stable as I would have liked, but I don't want to delay any
longer. Many of the additions
and updates have been focused on the problems posed by cryo-EM
On 29/03/2020 10:04, Clemens Vonrhein wrote:
Dear all,
given that nearly everything seems to be possible with Coot (apart
from making a good cup of coffee ... but who knows), maybe someone
could help me out here.
(1) When working with a hydrogenated molecule (not riding hydrogens!)
in
On 25/03/2020 07:40, Daniel Larsson wrote:
I guess I could deal with the file opening from my python script. How do I load
a dictionary or CCP4-style map from a python script?
read_cif_dictionary("dict.cif")
handle_read_ccp4_map("test.map", 0) # the additional argument tells coot that
On 24/03/2020 15:09, Daniel Larsson wrote:
I tried the latest CCPEM nightly build of coot and can no longer use the
command line options. A command such as this:
coot --dictionary ligands.cif --map map1.ccp4 --map map2.ccp4 --map3.pdb --em
--pdb model1.pdb model2.pdb --command coot_render.py
On 05/03/2020 21:56, Dale Tronrud wrote:
I wanted to get some experience with a large model so I am exploring
4YBB.
Problem 1
If I select "Fetch PDB using Accession Code..." in the file menu and
ask for 4YBB the download fails with
PDB Accession Code: 4YBB
BL WARNING:: Retrieve of url
On 25/02/2020 20:52, Kenneth Satyshur wrote:
V 0.9 Pre drops the map out of display when going from mono to stereo. This does not happen in 0.8 V. I have
enclosed the output of coot from the run in stereo.
OK, thanks. I'll try to come up with a fix the next time that I'm in the
lab.
Paul.
On 14/02/2020 15:29, Dorota Kubacka wrote:
I assume that Modeling=Make Link in WinCoot is not making the covalent bond, do
I am right?
It adds a link (a covalent link, presumably) to the model. But that part is easy - the tricky part is
generating the dictionary for the link and that
On 13/02/2020 12:49, Dmitry Semchonok wrote:
> Dear colleagues,
>
> We are doing the model building using COOT.
Jolly good - CCPEM latest nightlies Coot, I hope.
>
> We got our cryo-em map using SCIPION (running relion software inside the
> SCIPION)
>
>
> The problem is that when we open the
Hi Dorota,
On 12/02/2020 16:40, Dorota Kubacka wrote:
I would like to mutate one aa into non standard residue, namely GLU with ribose
covalently linked.
I already have mol file of the new structure (GLU+ribose), I've generated pdb
and cif files in PRODRG program, changed the type of molecule
On 12/02/2020 11:46, igor tascon wrote:
I am having some problems to open a mrc cryoEM map in coot. I received the map as a spi volume file and I
converted it into a mrc file using xmipp_image_convert command in scipion to perform some
real_space_refienement, that worked fine. However, when I
On 10/02/2020 11:23, Christian Becke wrote:
> I am currently testing coot built from the refinement branch (revision
> 9786) on Gentoo linux.
are you using ccpem jhbuild or using the build-it script? Or something else?
> I would like to display maps and models using
> hardware stereo. Stereo
On 23/01/2020 01:45, Emilia C. Arturo (Emily) wrote:
This is a follow-up from a thread from May 2018
(https://www.mail-archive.com/coot@jiscmail.ac.uk/msg04199.html )
That thread was mostly about running coot remotely. From the rest of your message, that seems not to be the
case for you.
On 02/01/2020 16:21, SUBSCRIBE CCPEM Lei wrote:
I used coot to calculate the pore profile of a channel. It worked great.
Glad to hear it.
Then I wanted to make a figure using pymol with the small dots calculated by
coot.
I found the output file hole_surface_dots.dat didn't seem to be a pdb
On 20/12/2019 16:35, Colin Levy wrote:
Morning,
Can anyone suggest the correct method for introducing a non natural amino acid into a protein backbone? I am
aware of the modelling, replace residue option but in this instance I am having no joy in creating a protein
chain that can subsequently
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.
To unsubscribe from the COOT list, click the
sigh. This one has actually been tested...
To unsubscribe from the COOT list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT=1
(let ((seq "DVSGTVCLSALPPEATDTLNLIASDGPFPYSQD")) ;; or
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
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 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
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 20/11/2019 20:06, Dale Tronrud wrote:
The sampling of a map on a grid is a computational simplification of
the map. This approximation is made for the convenience of the computer
software. I presume that Coot's real space refinement includes
corrections for the course size of the grid,
On 20/11/2019 13:28, Karim Rafie wrote:
>
>
>
> I have a question regarding the map smoothening option in coot
> (Calculate -> Map Tools -> Make a (very) smooth copy). If I understand
> correctly, the Shannon sampling factor applied by default is 1.5 and
> that the smoothening process adjusts
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
On 04/11/2019 10:45, Daniel Larsson wrote:
... But one still lands on the P atom of nucleotides when using "Ctrl-g" (go to residue). For
consistency, I think these two mechanisms should focus you on the same atom.
agreed.
Paul.
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 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
On 22/10/2019 13:41, Stránský Jan wrote:
I have proceeded on to building own coot,
Great!
but I am not very successful...
:-(
Would any one share with his build-it wrapper on
CentOS7, and what exact extra packages had to be installed?
I have looked in INSTALL, and did not find
On 23/10/2019 05:07, Ahmad Khalifa wrote:
Is there a limit to the number of chains that Coot can display in a
structure?
Not as far as I know.
A lot of the chains in my structure weren't loaded.
:-( Are you sure that you were using a bona fide input file?
The missing chains appear to be
On 18/10/2019 20:54, Robert A Grant wrote:
Recently I noticed that my installation of COOT can no longer fetch PDB files.
The program reports the following error:
PDB Accession Code: dps
(get-ebi-pdb "dps")
DEBUG:: in get-url-str: "dps"
"http://www.ebi.ac.uk/pdbe-srv/view/files/dps.ent; pdb
On 14/10/2019 13:39, Daniel Larsson wrote:
ProSMART restraints does not work with lower-case chain IDs. Perhaps the coot
scripts could swap the chain IDs to facilitate easy access to restraints for
large complexes. (Yes, I know that lower-case chain IDs are not really part of
the PDB
On 16/10/2019 12:40, Daniel Larsson wrote:
Is there an easy way to select multiple ranges for refinement in coot? I have
some long-range (in sequence) interactions and want to refine two different
regions at the same time (e.g. residues 1-10 and 100-110).
refine_residues(0, [["A", r, ""]
On 16/10/2019 09:42, Daniel Larsson wrote:
This really annoying thing kept happening to me where the H5' hydrogen would fly off when I refined RNA.
This is on my todo list, sorry that you were affected before I fixed it :-(
Paul.
On 14/10/2019 13:46, Stránský Jan wrote:
>
> I am probably missing something, but how can I activate this feature? It
> is not on by default, and I cannot find it anywhere in menus.
It is now on by default - you can't centre on the P any more :-)
>
> I have tried coot from CCP4, and the latest
On 09/10/2019 08:20, Daniel Larsson wrote:
> Hi,
>
> Is there an easy way to customize Coot so that the view is centered on the
> C3' atom instead of the P atom when navigating RNA (e.g. when using
> space/Shift-space or Ctrl-g)? Often the density at the P is the best, so it
> makes sense to
On 07/10/2019 08:14, Daniel Larsson wrote:
I'm wondering what is the preferred way to add hydrogens when (re)building
parts of a model? I start by running phenix.ready_set and then I want to
rebuild stuff in coot. Is there an easier way than running ready_set again?
I don't quite follow
On 20/09/2019 06:16, Ahmad Khalifa wrote:
> How does Coot guess the direction of the chain? How confident is this
> assignment?
It tries to fit it both ways and gives you the model that has the
highest fit to density score. I don't have numbers for the confidence -
sorry - I don't think I've
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 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
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 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 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 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 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 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 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 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 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 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 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
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