On 26/01/2017 22:23, Oliver Clarke wrote:
Hi all,
I wrote a little jiffy to highlight missing segments and color by length (breaks
with <15
missing residues are gray; 16-50 orange; and 51+ red).
It is included in this script
(https://www.dropbox.com/s/0b4bebwxw0p9x0e/oli_custom.py?dl=0), and
On 23/01/17 15:40, Oliver Clarke wrote:
Hi,
Delete zone (delete_residue_range()) is extremely slow when deleting large
selections, often taking many minutes to delete a single large chain, even when
backups are disabled. Is there an alternative function that is faster, or the
possibility of
On 23/01/17 16:29, Susana GONCALVES PIRES wrote:
Hello everyone,
maybe this question came out already, but I would like to know if
there is a way to do "rotate/translate zone" of several chains at the
same time?
If you want to rotate/translate zone on several chains (A,B,C), but not
the
On 13/01/2017 10:10, Christoph Parthier wrote:
Since version 0.87 starting C-alpha baton building (after map skeleton
creation) crashes
COOT. In version 0.86 it still worked. Occurs in Coot for Windows and Linux
(Scientific
Linux 6.7).
dictionary-related again, I guess.
We use the c-alpha
On 11/01/2017 10:10, Luca Pellegrini wrote:
The ‘Edit Chi Angle’ command makes Coot crash (the Coot window implodes), the
instant I
start adjusting manually the side chain. This only happens when I launch Coot by
double-clicking its icon; when I run it from a terminal window, with
On 05/01/2017 17:52, Luca Pellegrini wrote:
I have created an unnatural amino acid (ua1.pdb, ua1.cif) in JLigand, I have
added it to
my structure and fitted it into the density. Now how do I tell Coot, when I
regularise
the local structure, to keep the peptide bond stereochemistry with the
On 19/12/2016 08:44, Andrea PICA wrote:
Hello everyone,
I was wondering whether it would be possible in coot to include symmetry
related atoms in
sphere refinement.
I've thought about it. It's tricky and probably slow. It's a nice feature to have, but not
scheduled at the moment.
Paul.
ut this problem in the "right" COOT way?
It sounds that you are thinking the right thoughts. I'm not sure about the details for the
particular problem though... perhaps a cis-model for a cis pre-Pro that won't stay cis?
Paul.
On Mon, May 23, 2016 at 3:28 PM, Paul Emsley <pems...
Quite Right Folmer,
I am pretty sure that this was fixed in 0.8.2:
Release Notes has this item:
o BUG-FIX: Resetting of Own font colour on opening the preferences
dialog fixed.
Paul.
On 02/12/2016 10:45, Folmer Fredslund wrote:
Dear Andrea,
I would suggest, if at all
On 30/11/2016 10:25, Folmer Fredslund wrote:
As was mentioned, there were some problems with COOT and mutations
after a recent CCP4 update.
I've seen crashes after "Add OXT to Residue..." (from Calculate->Other
Modelling Tools) in revision 6498 provided by CCP4-7.0 (update 24),
but I don't see
On 11/11/2016 03:32, Edwin Pozharski wrote:
I had an opportunity to build coot executable on a fresh ubuntu box. It
compiles fine after
you install few dependencies but I noticed the following:
1) it seems that coot won't work without CCP4.
"Without CCP4" is slightly ambiguous. Let's
Coot 0.8.7 is released.
Binaries and source code from
http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot
For those who compile from source, this version works with CCP4SRS (not currently enabled in
my standard binary builds).
Release 0.8.7
o FEATURE: Lidia now has canvas scaling
o
On 04/11/2016 15:55, Tim Gruene wrote:
I would like to draw the surface of a (small) molecule, e.g. at VdW-radius,
and display by colour the map values from an mtz-file at the surface.
There is no interface to do this.
Ideally I would like to set surface distance from the nuclei, the
On 12/10/2016 13:43, Kevin Jude wrote:
I am frequently getting distortions of proline residues during real space
refinement -
specifically, close approaches between C and CD (pictured). It's hard to nail
down exactly
what is happening but it seems like planar peptide restraints aren't working
On 28/09/16 10:51, Matzov Donna wrote:
Hello,
Hello Donna,
For RNA modelling I used to have a "user-defined-restraints.scm"
script which allowed me to maintain proper base-paring geometry while
I did real-space refinement and regularization.
Unfortunately, my script doesn't seem to work on
On 09/07/15 13:38, David Briggs wrote:
Dear all,
We have encountered some problems when using the carbohydrate module
in coot.
When I centre on an Asn which has NAG density, invoke the Carbohydrate
module and select Add ASN-NAG NAG, Coot crashes and dumps the core.
Dear David,
Thank you
It seems to me that Rachel's answer is somewhat unclear. To rephrase
then: if I deposit a new structure with a new ligand and I give it an
as-yet-unassigned three-letter-code, will the RCSB/wwPDB keep the code I
gave it? Actually a straight reading of Rachel's answer is no - but I
On 13/06/15 18:12, Oliver Clarke wrote:
I realize this is somewhat of a niche concern, but figured I would report it
anyway. The sequence viewer is broken for long protein chains, it doesn't show
anything after residue 2241.
No, it's not broken - there is a limitation in the X11 window
On 05/06/15 14:50, Sheriff, Steven wrote:
At BMS we do many hundreds of structures a year with ligands and we
assign the same, already assigned, three-letter code for all of our
ligands (unless we have two or more different ligands in a single
structure...)
(I have plans to improve
On 29/05/15 21:15, Emilia C. Arturo (Emily) wrote:
Hello.
I am struggling with an old question--old because I've found several
discussions and wiki bits on this topic, e.g. on the PyMOL mailing
list (http://sourceforge.net/p/pymol/mailman/message/26496806/ and
On 27/05/15 16:16, Oliver Clarke wrote:
Hi all, dragged refinement doesn't seem to work for structures with riding
hydrogens - see linked screen recording showing dragged refinement of the same
structure with and without hydrogens.
On 24/05/2015 16:57, Ian Tickle wrote:
Hello, does anyone know how to simultaneously display negative
positive contours for a neutron 2Fo-Fc map?
For example, as in Fig. 2 here:
On 28/04/15 10:41, Lau Sze Yi (SIgN) wrote:
Hi,
I fitted small molecule ligand into observed electron density using
the Find Ligands function and did a density fit analysis. What is
considered an acceptable score?
You want a density correlation of greater than 0.89 to be better than
the
On 23/04/15 23:13, Marie Elizabeth Fraser wrote:
Hello,
Is there a way to change the bond colour for the second (or subsequent)
chain in a PDB file when the models are represented as Calphas? I use Edit
Bond Colours to change the colour of the carbon atoms, so that the first
subunits
On 22/04/15 15:17, Andreas Schedlbauer wrote:
Would like to know how the new feature in coot 0.8 'Add parallel
planes restraint' (Extensions/Modules/User defined restraints) really
works. If defined does not seem to have any effect in real space
refinement.
The method is described here:
be the issue here?
Cheers,
Jose
On 03/27/2015 07:13 PM, Paul Emsley wrote:
On 25/03/15 22:27, nih\mayerm wrote:
Deal Paul.
Recently I had an unusual case of dual occupancy of a ligand binding
site by two different ligands. I refined this by giving same resids
to the two ligands (here C1
On 28/03/2015 15:47, Ian Tickle wrote:
On 27 March 2015 at 19:16, Paul Emsley pems...@mrc-lmb.cam.ac.uk
mailto:pems...@mrc-lmb.cam.ac.uk wrote:
There might be a python version of these available from the
Molprobity server. It should be straightforward for them to make
On 27/03/15 17:04, Ian Tickle wrote:
Hello All
I'm trying to read the script from multichart into WinCoot. I do:
multichart-coot reduce.pdb reduce.scm
but when I select Calculate - Run Script absolutely nothing happens,
there's no error message on the console, nothing.
Hmm... that needs
On 25/03/15 22:27, nih\mayerm wrote:
Deal Paul.
Recently I had an unusual case of dual occupancy of a ligand binding site by
two different ligands. I refined this by giving same resids to the two ligands
(here C1 in coordinates below), refining their occupancy (in Phenix) - worked
very well.
On 24/03/15 22:01, Roberts, Sue A - (suer) wrote:
I'm wondering why this was changed. Does the optimum elasticity change with
resolution, map quality, or another experimental limitation? Or does it more of
a user preference?
Because cis-peptides. My worry was that in the previous regime, it
On 17/03/15 14:10, Peter Stogios wrote:
Hello,
In Coot's directory/file open dialog window when opening any file type, the
directory sorting doesn't make any sense and I cannot find what directory I
need without pulling teeth.
Directories are not sorted directories by name, date modified,
On 09/03/15 11:47, Andrea Ilari wrote:
I changed the operating system automatically from ubuntu 12.04 to Ubuntu 14.04.
My version of COOT is still working but the validate routine doesn't work properly, I can't open
the ramachandran plot, the geometry analysis .. and also the HID scrollwheel,
On 11/03/15 00:06, Kenneth Satyshur wrote:
After using 7.1 for a while, it was easy to 'real space refi zone' a
amino acid. Pull on it and it will drag everything
else with it. On 8.1 when I try this, it just rips an atom away from
the residue and does not move the whole residue.
There
Sorry for the late comment, I somehow missed this while I've been away.
Yes, this is very horrible - and noted by Airlie last year.
It's on the Must-Fix list for 0.8.2.
Paul.
On 23/02/15 09:24, Phil Evans wrote:
So why is the option to change it presented in the dialog? You can change it
On 18/02/15 23:31, Tc Cheng wrote:
Hi all,
Hi Tc,
Happy goats?
I am currently using coot 0.8.2 pre-release on Centos 5.
good for you!
I have a ~ 4.4A EM map
OK! Not bad!
(in mrc format) that I want to build a model in coot.
OK!
The map shows up properly in chimera but not in
On 08/02/15 16:43, Gabriele Balducci wrote:
hello,
while building r5551 from source, I get the following error:
8888
In file included from phenix-geo.hh:3:0,
from phenix-geo.cc:6:
../coot-utils/residue-and-atom-specs.hh:37:19: error: 'mmdb' has not been
On 30/01/15 18:14, Murpholino Peligro wrote:
hello everybody!
Hello Murpholino Peligro,
I was just getting a better structure from the 193L.pdb with coot
(Fetch PDB and map using EDS) Everything was ok,...but the last
residue (129) could not be refined ...The warning that appeared was
On 24/01/15 17:11, Kenneth A. Satyshur wrote:
Is it possible to output a list of peak pick coordinates? I want the top 100
peaks in a list
so I can display them and determine if I want to keep them or not.
(list-head (reverse (map-peaks imol 2) 100))
HTH,
Paul.
On 19/01/15 14:56, Christoph Parthier wrote:
Hi,
I noticed when adjusting the 'bond colours' using the slider in
'Edit/Bond Colours...' when an molecule (1 chain) is 'coloured by
chain') with activated check mark 'Change colours for Carbons only'
only the colours of the first chain (chain A)
On 19/01/15 14:45, Christoph Parthier wrote:
Hi,
I know the 'baton building' feature of COOT is rarely used, but - believe it or
not - we use it in teaching quite a lot and there is a bug which every time
results in desperate students (and supervisors...), so high time to report:
Once 'Ca
On 20/01/15 16:53, Rex Palmer wrote:
My protein has 4 separate chains A,B,C and D but the pdb file has the
chains in order C,D,A,B. Is there any existing software that would
rearrange my pdb file as A,B,C,D?
Extensions - Modelling - Reorder chains.
This should work in 0.8 and 0.8.1, but
On 14/01/15 05:13, Satyabrata Das wrote:
Thank you for this kind reply, the font sizes are not much but they
are bold,
however sometime they are normal, please see the attached image.
Dear Satyabrata,
It looks like you are using a binary built by CCP4. Do you see the same
problem with
On 12/01/15 15:49, Marcin Wojdyr wrote:
Dear Satyabrata,
I think the gtk messages can be ignored.
They can be ignored. I don't know why you are seeing them.
How the bold fonts look like? Like this:
On 21/12/14 21:37, Scott Horowitz wrote:
Hi all,
Is it possible to display only one alternate conformation at a time? I
have a situation where I have several alternate conformations, and
it's hard to see with them all displayed at the same time.
Hi Scott,
No it's not - sorry.
You might
We are pleased to announce Coot Release 0.8.1.
(Basically a bug-fix release.)
Redhat, CentOS, OpenSuse and Ubuntu binaries will appear here shortly:
http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/binaries/release/
WinCoot here hopefully:
On 09/12/14 14:47, PC wrote:
Hi guys,
Sorry for the repost in COOT/CCP4/PHENIX.
It is possible on of the users in one of these communities might know the answer
I was wondering if there is a small script I can use to generate the outline of
the allowed regions of Ramachandran map on to which
On 20/11/14 16:48, Tobias Beck wrote:
Hi Paul and Huw,
Thanks for your emails.
That is all I get in the terminal too (Coot 0.8.1-pre rev 5423 on OS
X 10.9.5) but the table of “Questionable Waters” does appear (hidden
underneath the main window). Is that not happening for you? X11
window
On 19/11/14 20:22, Tobias Beck wrote:
Hi all,
I am using Coot 0.8.1-pre rev 5445 on Mac (OS 10.9.5) and would like
to validate waters. However, after selecting the criteria and hitting
'Ok', the terminal only gives me
(command-in-path-or-absolute? *probe-command*)
Interestingly, all the
On 19/11/14 13:26, Frank von Delft wrote:
Hi all - does coot have a way to let me see the pdb header?
There is a remarks browser under About
(Yes, I know I can open a text browser - but that's typically about 20
clicks, especially if I pulled the coordinates directly from the PDB.)
Hi ... err.. bbc :)
On 14/11/14 12:52, bbc wrote:
I'm trying to build latest coot source on a CentOS 6.5 machine, but I get a
compilation error for coot-0.8.1-pre/protein_db.cpp, namely it looks like it
complains that a class is undefined. Here is the compilation line and error
output:
On 04/11/14 20:35, Jan Stransky wrote:
Hi Dorothy,
this dashed lines represent links.
Yes - you can tell this because they are drawn in the same colours as
the molecule with the half-bond colour scheme.
You can delete them in PDB-file, look for keywords LINK and LINKER.
LINK and LINKR.
Hi Mark,
Sorry for the delay.
On 01/10/14 11:22, Mark A Saper wrote:
I am running the standalone version of Coot 0.8-stable version on Mac
OS X 10.9.4 compiled for 10.9 only. I encountered 2 errors (I can
live with them, but I thought you should know).
1. Upon exiting Coot I receive these
On 13/10/14 15:31, Oliver Clarke wrote:
Just an update to the first of these issues - this only seems to be the case when I
select Jones Rainbow using the change_model_molecule_representation_mode()
function, which I bind to keys as below so that I can quickly cycle between
representation
On 07/10/14 15:37, Schmitzberger,Florian wrote:
Hi everybody,
Is it possible in COOT to change the designation of an atom?
Specific case, I downloaded an CSX with terminal carboxy group oxygen
designated OXT. I would like to change it to a simple ‘O’.
No, you can't do that. Not easily,
On 08/10/14 09:37, Lau Sze Yi wrote:
Hi,
I tried to open SMILES in COOT under Files -- SMILES but did not get any
response. What is wrong?
Is there any other way of getting around this problem? I am trying to build
Jeffamine-ED2003, currently not available in ligand library.
Hi,
On 07/10/14 11:35, Vijaykumar Pillalamarri wrote:
Dear Paul,
I downloaded the binaries from coot official website only.
:)
I think I have to link the monomer library to coot after installation
for it's proper functioning.
That should not be needed...
When I tried to load GOL from
On 01/10/14 16:32, Doeke Hekstra wrote:
As a novice to making electron density difference maps, I am curious about the
algorithm underlying the “make a difference map” option in Coot. My impression
is that the subtraction occurs in real space rather than at the level of
structure factors.
On 01/10/14 13:40, Marcin Wojdyr wrote:
A few days ago I've reported the issue with squares to freeglut
developers and they removed the points:
https://github.com/dcnieho/FreeGLUT/issues/19
For the coming ccp4 release we'll go with stroke-characters enabled by
default (for Linux only) and with
We are pleased to announce the release of Coot 0.8. New binaries should
be on their way shortly:
http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/source/releases/
http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/binaries/release/
o FEATURE: Added an interface for Cootilus
o
On 23/09/14 19:12, Vijaykumar Pillalamarri wrote:
Dear all,
I have recently installed COOT 0.7.1. When I tried to load monomers
(like Glycerol), nothing is loaded onto the GUI. Do we have to link
monomer library to COOT to be able to load monomers on COOT? if so,
please help me to get
Dear All,
As of revision 5285 the coot dependencies, as thus coot code itself has
undergone an overhaul.
The build script builds new versions of python, mmdb, clipper and ssm
and is now called build-it rather than build-it-gtk2-simple.
I'd recommend scrapping the current installation
...@crystal.harvard.edu
mailto:z...@crystal.harvard.edu
Cc: William G. Scott wgsc...@ucsc.edu mailto:wgsc...@ucsc.edu,
Paul Emsley pems...@mrc-lmb.cam.ac.uk
mailto:pems...@mrc-lmb.cam.ac.uk
Subject: Re: extensions menu is gone
Hi Jianghai,
I think I solved the problem at the time by downgrading
On 02/09/14 23:59, Mark A Saper wrote:
Is there anyway to prevent the rotate-translate fragment from showing the
hydrogens in the model?
The answer, I'm sad to say, is no, not yet.
It would be a good if Coot followed the current drawing mode of the main
molecule for the temporary atoms (I
On 02/09/14 15:06, amit sharma wrote:
Hi,
Density fit analysis in Coot plots the real space R-factor for each
residue. Is it possible to import these values for each residue?
If you are using the coot package, you can use density-score-by-residue
to get these numbers as text.
Paul.
Hello Dale,
Sorry for the delay.
On 26/06/14 17:30, Dale Tronrud wrote:
You will be distressed to hear that I'm back to refining my model
which has broken every crystallographic program. Today seems to be
Coot's day. As you see in the screen shot I have two pytol tails from
Bchl-a
On 21/07/14 19:20, jesu...@uci.edu wrote:
Hi Everyone,
I am trying to model an acyl serine residue. What is
the easiest way to input the modified amino acid into the structure so I
can refine the structure? The modification on serine
is propanoyl and butanoyl. Thank you in advance!
Centre on
On 18/06/14 19:09, Thomas, Leonard M. 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.
Now the latest version of Coot crashes when loading
On 19/06/14 11:29, Paul Emsley wrote:
On 18/06/14 19:09, Thomas, Leonard M. 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.
Now
the following reply by Paul Emsley:
*/It scales all amplitudes (whichever you chose when you read in the
mtz file) by the application of a negative (or positive) B-factor. So
the scale factor is a function of resolution and nothing more (at the
moment)./*
*/Paul./*
So just to clarify
On 02/06/14 16:15, Thomas, Leonard M. wrote:
Hello All,
I just upgraded my Mac to 10.9. I have tried both the stable version of coot
0.7.1 and also a daily build of 0.8 and still have the same problem of no
graphics window showing up. The terminal output ends at
On 30/05/14 00:17, George Devaniranjan wrote:
Thank you for your reply, Dale.
Let me rephrase the question:
Essentially I want to use COOT's Calculate--map sharpening
OK, so you know how to do that, I presume
but only use the backbone atoms in the process.
So mask out the other atoms:
On 27/05/14 22:42, RiC wrote:
HI,
Does anyone have a step by step guide to go from a structure factor file from
the PDB to a CCP4 map (understandable to a biologist) like the one I can
download on the electron density server?
Hi Patrick,
Depending on the program with which you will view
On 20/05/14 15:10, George Devaniranjan wrote:
Hi,
Hi George,
Sorry for the delay.
I am new to COOT
Hello. Welcome.
and electron density analysis and I have been reading the manual and
the tutorials so far. I have a question to which I have yet been
unable to find an answer.
It's
This adds a key-binding (Shift+L) that removes all the current atom labels:
(add-key-binding Remove labels L (lambda () (remove-all-atom-labels)))
(Not for Windows, of course.)
HTH,
Paul
On 17/04/14 08:05, Bernhard Lohkamp wrote:
Hi Grant,
to remove all labels (via GUI Measures-Clear atom
Hello Renate Gessmann,
On 11/04/14 04:19, Renate Gessmann wrote:
How do I complete a residue when I have only one atom (for example
the SG in Cys as part of a disulfite bond), but nice density without neighboring
residues? So, a 'add terminal residue' is not possible,
If I understood
Hello Renate Gessmann,
On 11/04/14 04:19, Renate Gessmann wrote:
How do I complete a residue when I have only one atom (for example
the SG in Cys as part of a disulfite bond), but nice density without neighboring
residues? So, a 'add terminal residue' is not possible,
If I understood
On 03/04/14 04:45, Oliver Clarke wrote:
Hi all,
Is the functionality of ‘Calculate--Merge Molecules’ available from the
scripting interface?
Yes.
I couldn’t find it in the manual. There is a function named merge_molecules,
but I don’t know what arguments it takes and it does not do what I
On 28/03/14 15:27, Oliver Clarke wrote:
Hi all,
Is it possible to access from the scripting interface the symmetry info in the
atom_info_text string displayed when a user clicks on an atom?
I would like to write a little function that creates a new copy of whatever
symmetry molecule the user
On 29/03/14 19:13, Oliver Clarke wrote:
Hmm, that’s a good idea, I’ll try it… I don’t think symm shift
reference chain takes an atom spec though does it? It doesn’t seem to
take any arguments so I assume it just takes the current cursor
position - I guess I could use go to atom and
PM, Paul Emsley pems...@mrc-lmb.cam.ac.uk wrote:
On 29/03/14 19:19, Oliver Clarke wrote:
Hi all,
I was wondering if anyone could shed some light on what the scale factor in
jiggle fit represents? Empirically, I’ve found that a value of 0.1 with
1000-1 trials seems to work pretty well
On 28/03/14 08:35, Kay Diederichs wrote:
Am 28.03.14 08:44, schrieb Folmer Fredslund:
Hi Kay, Ethan and Dale,
I don't want to turn this into a me too thread, but I can confirm that
I also see this issue.
My system is a 64bit Ubuntu 12.04 kernel 3.11, with the HD3000 graphics
on an i7-2640M
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 a
similar directory to COOT_PYTHON_EXTRAS_DIR but just for scheme commands. It
On 06/03/14 23:11, Schubert, Carsten [JRDUS] wrote:
Hi,
Hi Carsten
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
On 22/02/14 22:12, Oliver Clarke wrote:
When I mutate the selenomethionine residues (which for some reason
have HETATM records rather than ATOM coming out of BUCCANEER)
That is what the PDB format requires, FWIW.
to METs in coot, coot changes the records of the side chain atoms, but
leaves
On 14/02/14 00:07, Mark A Saper wrote:
The scheme command setup-auto-fit-rotamer is not documented.
Indeed, it is a widget function that I didn't think was useful when
scripting.
Which setting is with backrub off? What is the default?
On 14/02/14 19:40, Oliver Clarke wrote:
Hi all,
I’m running coot 0.8-pre r4912 on a macbook air, Mac OS X 10.9.1.
Up to date! I approve! :-)
I’ve also reproduced this in an earlier version of coot running on
Ubuntu 12.04.
Yeah... the thumbnail problem has been there since the
I've started installing the latest nightly builds of Coot that Bill
Scott maintains. They go into /usr/local/bin/coot. It will open but
the screen is white, if you move the window around on the Mac it
seems to duplicate and worse, if you load coordinates or a map,
nothing appears. I must
On 10/02/14 13:24, Balaji wrote:
Dear Coot Users
I am using Coot v0.7.2.1.
To adjust the outliers in the ramachandran map, I use edit backbone (phi/psi).
By clicking the above panel opens up the phi/psi and dynarama window.
In my case, it opens only the phi/psi panel not the dynarama panel
On 13/01/14 21:42, Seth Harris wrote:
I guess (without testing) that adding the following should do what
you want:
(set-pointer-atom-molecule 0)
I first tried adding that line to my .coot file. That didn't seem to
work, but it was functional if I typed it into the scheme
On 10/01/14 02:30, Seth Harris wrote:
Hi all Paul,
Sometime back I found or was taught or given this:
(add-key-binding Add Water w (lambda ()
(place-typed-atom-at-pointer Water)))
(Probably from Pauls-key-bindings-for-coot...)
I was looking for a quick way while browsing map peaks to add
On 23/12/13 17:15, Ian Tickle wrote:
Paul, I'm having trouble accessing the md5sums on
http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/binaries/release/
, though the tar.gzs themselves seem to be OK. I get source file
could not be read. on all of them. Could you check it out?
Hi Ian,
On 31/12/13 16:31, Oliver Clarke wrote:
Another note - what is active_atom_spec() supposed to do? I guessed it was an
equivalent of active_residue() but returning the specific atom rather than the
CA,
That's right.
but it returns this when called:
On 30/12/13 17:42, Oliver Clarke wrote:
And here is a more compact/elegant version courtesy of Paul that accomplishes a
similar function in half the code - morphing with a radius decreasing from 12
to 6 Å over an arbitrary number of cycles, using a map initially blurred with a
B-factor of
On 30/12/13 22:45, Oliver Clarke wrote:
Great! Next scripting question that I’m puzzling over - how to take a set of
sequences (present in a single fasta file), in arbitrary order, match and align
them to their corresponding homologous subunits in a PDB file, and use
align_and_mutate to
On 31/12/13 01:39, Mark A Saper wrote:
The regularize command (without a map) tends to move things more than I think they
should. Perhaps the end atoms should be fixed. How would one restrain atoms to their
starting coordinates? From the old days I recall Frodo's REFI command being
better
On 29/12/13 02:51, Oliver Clarke wrote:
I agree that normally rigid body refinement of each chain wouldn’t be
very useful - I’m using this script in a situation where we have a
large complex of many subunits that we need to fit to a quite
low-resolution map (of a related complex from
On 29/12/13 14:51, Oliver Clarke wrote:
Thanks Paul - Initially I tried rigid body + 10 cycles of
morph_fit_chain at a radius of 11 Å - that seemed to work better than
rigid body alone, although some of the larger domain shifts are still
not corrected.
Perhaps I need a larger radius for that
On 04/12/13 21:10, Robert Oeffner wrote:
Hi,
I'm customising a small script for displaying the Patterson map from an MTZ file. As the
names of the columns is arbitrary I wonder if there is a function available in Coot that
lists the names of the columns in the MTZ file. It should be similar
On 04/12/13 21:10, Robert Oeffner wrote:
Hi,
I'm customising a small script for displaying the Patterson map from an MTZ file. As the
names of the columns is arbitrary I wonder if there is a function available in Coot that
lists the names of the columns in the MTZ file. It should be similar
On 25/11/13 03:46, Oliver Clarke wrote:
Hi all,
I get the GUI error “something went wrong running cprodrg” when I try to view a
ligand in LIDIA - I’m guessing some incompatibility between coot and the
version of cprodrg distributed with CCP4 6.4.0? I am running the latest coot
nightly build
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