On 06/11/13 23:59, David Shin wrote:
HI all,
Just went back to a project and oddly having about the same problem
(which I do not think existed before):
Coot 0.8-pre revision 4792 on 10.6.8
I have a modified residue, but has partial occupancy, so the residues
have different names for A and
On 06/11/13 14:50, Oliver Clarke wrote:
Hi all,
I would quite like to try out the PISA interface in COOT, but it complains that
I require a newer version than 1.06.
I have the version distributed with CCP4 6.4.0, which I believe is 1.18, and I
am running the nightly coot build (r4818) on a
On 18/11/13 13:26, Felix Frolow wrote:
I have a very large complex of proteins and I would like to use COOT
to apply NCS edits in the case where the “master copy” is not chain A
of my complex but any given chain.
The script that I currently use (example only, actual number of
molecules is
Hi Wei,
First a note on style: Your reply style leaves something to be desired.
I had some difficulty in understanding the answers to my questions.
Generally speaking, if the response style is interleaved, you should
follow that style, rather than top posting. Also, you should quote the
On 26/09/13 08:03, Lau Sze Yi wrote:
Hi,
I just recently downloaded the stand-alone coot 10.8 from Scott Lab
Pages. When I try to open my mtz files it doesn't load with the
following warnings in my terminal:
sys:1: GtkWarning: Unable to find default local directory monitor type
sys:1:
On 28/08/13 10:48, Winfried Meining wrote:
Another question aside: Is it possible to switch left/right sides in
hardware stereo mode by system wide configuration?
Yes. Add to your .coot or elsewhere:
(hardware-stereo-angle-factor -1.5)
or something negative that pleases your eyes.
On 23/08/13 20:57, Tim wrote:
Hi,
I'm running into trouble when trying to add an alternative conformation to a
non-standard residue type and subsequently trying to do real-space refinement.
I am working on the structure of a fluorescent protein that cyclizes three
residues in the middle of
On 14/08/13 07:37, John Bruning wrote:
Hi,
I have CentOS 6.4. I am trying to use the autoinstaller script to
install the 0.8 pre-release. After the ./configure command it fails
saying it can’t find clipper. Yum says I have the most recent release
of clipper (2.1.11) and I have all the
On 07/06/2013 07:21 PM, Marcin Wojdyr wrote:
My first target is to build from the svn with
there are tarballs at:
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/coot/source/
BTW it seems that ver. 0.7.1 was released a week ago.
Hmm... thanks for that.
./autogen.sh
don't
./configure
On 07/06/2013 09:30 PM, PICCA Frédéric-Emmanuel wrote:
Hello Marcin
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/coot/source/
is it the official location for the source packages ?
No.
./autogen.sh
don't
I was speaking for a fresh svn checkout of coot, not from the source package.
On 07/08/2013 03:25 PM, PICCA Frédéric-Emmanuel wrote:
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/coot/source/
is it the official location for the source packages ?
No.
So where can I find the 0.7.1 official source package ?
On 07/03/2013 10:54 AM, Tim Gruene wrote:
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Frederic Picca,
in case it helps packaging, you find the tar-files of coot both for
jessie and wheezy on my web-site.
(http://shelx.uni-ac.gwdg.de/~tg/coot_deb/)
Why does Frederic have a problem
On 02/07/13 19:36, PICCA Frédéric-Emmanuel wrote:
Hello, I am working on a coot package for the DEbian distribution.
During this work I found a few problems. I reported them on the google core
issue system of coot [1]
But until now I got no answer.
So I would like to know if you are reading
On 24/06/13 14:13, Alan Cheung wrote:
Dear All - How does coot assign secondary structure? It seems
different from DSSP and pymol.
It uses mmdb's CalcSecStructure() function (which was written by Liz
Potterton, I believe).
I text searched the manual but couldn't find anything about it...
On 06/19/2013 09:16 AM, Dirk Kostrewa wrote:
... and I've seen two different Coot mt leucine rotamers: the one that
I've reported with Chi-angles -65, 51 (which would be closer to the mp
rotamer), and one with Chi-angles -65, -60 (which would be mm).
Apparently, Coot changes something else.
On 06/18/2013 02:30 PM, F.Xavier Gomis-Rüth wrote:
Hi all,
how do I prevent that when reading in a new molecule, e.g. by PDB
fetching, the screen is centered on the new molecule's center
but stays where it was before?
pressing the 'U' key will undo the move
but if you think about it in
On 06/12/2013 08:39 PM, Nat Echols wrote:
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.
I wonder if you are
On 09/05/13 18:17, Yahui Yan wrote:
Dear all,
I installed coot 0.6.2 in Ubuntu. I can't merge molecules using the
button 'calculate'--'merge molecules'. Have anyone met this before?
Thanks.
Doesn't ring a bell - what does it say in the status bar and/or console?
Paul.
On 30/04/13 22:49, Webmaster wrote:
Attention,
As a matter of urgency,we are upgrading our Electronic mail service this
season in order to reduce hoax and spam mails
in our email log and change in our user webmail interface..
This is BS of course. Jiscmail seems a bit leaky - sorry about
On 04/26/2013 09:37 AM, ing. Jan Stránský wrote:
Hi all,
i'm recently experiencing that File-Fetch PDB using acession code
doesn't work. It downloads file with *.pdb extension, but inside there
is html code with link to the structure.
Is that our bad local setup of coot, or is it global
Hi Alexander,
On 03/29/2013 04:33 PM, Alexander Scouras wrote:
While scripting up a keybinding to toggle fixed atoms (via
mark_atom_as_fixed()), I discovered that closest_atom (and also active_residue)
does not actually return the closest atom for an amino acid, but actually the
CA. This
On 04/02/2013 09:04 PM, hari jayaram wrote:
Hello,
I auto-upgraded my system to Ubuntu 12,04 and my old coot setup (
from 10.04) works just fine on the new system .
There is just one problem in that the coot multicriterion charts
generated by Molrpobity no longer behave the same way .
On 22/03/13 15:16, F.Xavier Gomis-Rüth wrote:
Dear Paul The Cooters,
some questions:
(i) Is it possible to tell the program in a rather straightforward
manner to connect two chains within a model
that have different chain identifiers? This is very useful when
rebuilding models created by
On Wed, 2013-03-20 at 13:24 +, Anat Bashan wrote:
Hi All,
I build a ligand that is partly RNA and Partly a protein chain. In between I
have a special nucleotide with a N bound to C3' (instead of O3'). it is :
CC-PPU-Ala-Phe-Val. I have links in the .pdb file and the PPU is a known
On 13/03/13 19:36, Thomas, Leonard M. wrote:
Hello all,
I am haveing a problem with running coot on an older Linux RHEL 5 workstation.
I downloaded the following binary from the CCP4 website, can't get the coot
site.
coot-0.6.2-binary-Linux-i386-rhel-5-python-gtk2.tar.gz
Once all is set I
On 15/03/13 16:39, Ed Pozharski wrote:
Say I have 5bp long stretch of double helix DNA that I want to dock into
the density manually. Rotate/translate zone does not work, presumably
because the fragment is made of two chains. I can get around this by
renumbering one of the strands and then
My understanding was that Tim uses pythonic extensions - I guess that
this is one of those (rare, I think) functions where the python
preference is not accounted for. I'll take a look - it should be a
simple fix.
I intend to update to guile-gnome at some stage - it was the major
On 20/02/13 03:33, William G. Scott wrote:
Sorry. I just got my 10.6 computer back up and did another build a few hours
ago.
I haven't been able to reproduce the issue, but was only trying on 10.8.
OK
I'm having python mis-match problems on 10.6.
:-( that was the only thing that
Hello Marian,
On 12/02/13 16:58, Marian Oliva wrote:
Sorry to bother you with this question but I´m having some troubles when
loading smiles of new synthesize ligands for fitting.
First I was using an older version of Coot and after File=smiles, an error
message showed up (related to ccp4
On 14/02/13 21:54, Paul Swartz wrote:
I am attempting to use coot0.7 installed using the yum archive on Fedora 18 and
a computer with intel HD graphics 4000 driver. When coot starts initially, the
rotation and translation is nearly at the speed that I am used to with Fedora
16 install. If I
On 08/02/13 23:29, Arto wrote:
Hey,
My coot does not start up anymore. Yesterday I done fink selfupdate and added:
(define *probe-command* probe)
(define *reduce-command* reduce)
(set-find-hydrogen-torsion 1)
(set-do-probe-dots-on-rotamers-and-chis 1)
(set-do-probe-dots-post-refine 1)
On 15/02/13 15:11, Nat Echols wrote:
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
On 06/02/13 01:11, Ethan Merritt wrote:
Since the pdbe has apparently changed its URL, breaking the download
capability in the version of coot I've been running, I decided to try
to build a current copy from source.
I downloaded the autobuild.sh script,
customized AUTOBUILD_BUILD and
On 28/01/13 10:38, Pedro M. Matias wrote:
Hi,
Is it possible to deactivate the nomenclature errors check in the new
Coot ? Sometimes this check is not very useful and it becomes rather
annoying when one has several molecules loaded only wants to look at
the structures...
I agree.
Add to
On Thu, 2013-01-24 at 11:35 +, Paul Emsley wrote:
On Wed, 2013-01-23 at 19:17 -0500, hari jayaram wrote:
Hi I am trying to build the subversion coot on a Ubuntu machine
running 12.10 using the build-it-gtk2-simple python script.
I get all the way to compiling the final coot
On 24/01/13 19:10, hari jayaram wrote:
Sorry Paul ..
Didnt understand your suggestion. In which makefile do I have to move
the -ldl after -lpython2.7
PYTHON_LIBS in src/Makefile
I checked out tag 4546 and not I get a different error Py_Initialize
, PySys_SetArgv not declared in scope. (
On Mon, 2013-01-21 at 17:57 +, Petra Lukacik wrote:
I am using Coot 0.7 Clayton (revision 4459) on Linux CentOS 6.3.
My ccp4 is ccp4-6.3.0 and is up to date.
I am interested in running lidia but I get an error when I push the activate
prodrg flat mode:
(info-dialog Something went
On Tue, 2013-01-22 at 12:42 +0100, ing. Jan Stránský wrote:
So when I just download precompiled coot, it won't work?
It depends. The builds use the OS version of the widget library - if
this is sufficiently up to date, then the ligand builder can be built.
If not, not. IIRC, RHEL4 is not
On Wed, 2013-01-23 at 11:23 +0100, Tim Gruene wrote:
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear all,
The attached python script works fine when I call it as 'python
test.py', i.e. the cells of the tables are filled with text
(python.jpg; Python 2.7.3, Debian testing).
When I
On 21/01/13 14:21, Clemens Vonrhein wrote:
Dear all,
On Thu, Jan 17, 2013 at 07:48:34AM -0800, Nat Echols wrote:
If I had to guess, I'd say that the output from Refmac is on an
approximately absolute scale, i.e. the volume-scaled density values
resemble the actual electron densities expected
On 08/01/13 12:27, ing. Jan Stránský wrote:
Hi everybody,
I think, I have some problem with JLigand. Recently on CCP4-weekend's
lunch bytes I saw in Bernhard's (or Paul's) JLigand window one extra
toolbar (see my window in attachment). I remember ther was icon with
+ to show close contacts of
On 20/11/12 21:22, Scott Classen wrote:
When I turn on Pointer Distances or Environment Distances or manually measure a
distance or angle I am not seeing any distance labels only the dotted lines
between atoms.
I'm running 0.7 build 4459 on OS X 10.8.2 and XQuartz 2.7.4 (xorg-server 1.13.0)
On 19/11/12 10:22, Rex Palmer wrote:
Does anyone know why the ligand alpha lactose in COOT has at least one
sugar ring that is not fully symmetrical.
You mean from Get Monomer LBT?
Molecules such as that are directly imported from the Refmac Monomer
Library. And I think they are generated
Thank you all for you kind comments.
Sushi and sake always welcome (as long as it's not still moving).
Paul.
On Fri, 2012-11-02 at 17:07 -0500, Jeffrey Van Voorst wrote:
Greetings,
Greetings. Sorry for the delay.
I have poked around the Coot GUI and code (a little). I have asked
others in the same lab, but am unable to find a good answer for
selecting a range of residues using the mouse and/or
So would I, but it does sound like a graphics driver bug.
Paul.
On Mon, 2012-11-05 at 07:15 +0100, ing. Jan Stránský wrote:
Hi Grant,
first of all, I would try the last release, the 0.7 version of Coot.
Jan
On 11/05/2012 02:22 AM, GRANT MILLS wrote:
Dear all,
I have been using both
On Fri, 2012-10-12 at 12:55 -0400, Ben Eisenbraun wrote:
On Fri, Oct 12, 2012 at 12:42:23PM -0400, Ben Eisenbraun wrote:
Howdy Coot-ers,
Clicking Extensions-Modelling-Jligand launch results in:
Environment variable JLIGAND_HOME not set
jligand java jar file: ./jligand.jar not found
On Sat, 2012-11-10 at 16:08 +0100, Jon Agirre wrote:
Starting in October, I noticed that Paul changed his e-mail address
from ox.ac.uk to cam.ac.uk. I wonder if it has anything to do with the
lack of updates.
Yes. Everything (actually MRC-LMB (and what that has to do with
cam.ac.uk I have no
On Sat, 2012-11-10 at 13:15 -0500, McCully, Dwayne (NIH/NLM/LHC) [C]
wrote:
When running Coot 0.6.2 from CCP4 6.3.0 or running the Coot 0.7-pre-1
standalone, I get illegal instruction errors (see below).
If I comment out the tips.scm and tips-gui.scm files from within the coot.scm
file then
On 11/10/12 07:45, Bernhard Lohkamp wrote:
Have you tried 0.7? And checked md5sum?
0.7 for Ubuntu 10.04 64-bit not available ATM. I'll do it today.
Maybe your download was compromised?!
I think the upload was compromised.
Paul.
On 09/10/12 23:47, jpd wrote:
hi,
i am not sure if this is a coot or phenix problem, but i'll start here.
we work on large complexes and after refining in phenix
we try to open it in coot and get avalanched with
INFO:: found bad VAL chiral atom: B 14 CB
we get so many of the warnings that
Hi Bobby,
I am trying to refine a protein with two ligands. One of the
ligands apparently will not allow me to do real space refinement in
coot after I import it as a cif file, created from sketcher.
It is not clear to me what reason you have for using sketcher (it is
not the first tool
Hi Coot-users,
We are pleased to announce Release 0.7 of Coot.
Source:
http://lmb.bioch.ox.ac.uk/coot/software/source/releases/coot-0.7.tar.gz
Binaries:
http://lmb.bioch.ox.ac.uk/coot/software/binaries/releases/
Mac 10.8:
On 07/09/12 11:03, Nicholas M. Glykos wrote:
Dear developers,
A quick note to say that thymines added using 'simple mutate' in coot v.0.6.2
appear to be missing the C7 atom. Apologies if it turns out that I should have
checked the list contents before sending this message ...
Yes, sorry
On 04/09/12 10:23, Martin Montgomery wrote:
Hello,
I'm having trouble with 0.7-pre-1-4305 installed through fink on osx
10.8.1
I updated to fink 0.34.3 then coot 0.7-pre-1-4305.
Coot now crashes after the launch of the splash screen with the
following message:
Spacegroup: P 1
Cell: 40.631
On 30/08/12 19:47, Seth Harris wrote:
Hi all,
I and others have occasionally been plagued by the Add Terminal
Residue function placing the new residue somewhere distant. While
there are various workarounds (reject and try again, do more searches,
real space refine or regularize after it's
On 23/08/12 13:46, Steffen Schmidt wrote:
Hi,
I noticed that the rigid body fitting (Extension - Rigid body fit molecule…)
doesn't work anymore ( segfault)
I am using coot 0.7-pre-1-433 on linux or 0.7-pre-1-4305 (fink installation) on
os x. It used to work in 0.7-pre-1-632 (fink
On 23/08/12 17:49, Jeff Headd wrote:
Hi everyone,
I'm working with EM maps in .mrc format, and I'm having trouble
loading them in recent versions of Coot running on Mountain Lion. I'm
able to load the same .mrc files using rev 3697 on Linux just fine,
but using any of the recent builds for
On 15/08/12 00:24, Scott Classen wrote:
Hi Paul,
I received this message after the crash: [snip]
Hi Scott,
Thanks for that.
There will be a fixed binary (revision r4323) available shortly.
Regards,
Paul.
Hi Stefano,
Sorry for the delay, I was coming back from the ACA.
On 02/08/12 16:13, Pernigo, Stefano wrote:
I've tried to auto-open several MTZ files without success.
The MTZ files were produced using REFMAC5 (restrain refinement). After
loading the PDB file in coot (successfully) I tried
On 25/07/12 16:20, Sebastiano Pasqualato wrote:
Hi there,
I'd like to model a thioester bond, starting from protein A with an
exposed Cys, and having juxtaposed the carboxyl group of a C-terminal
residue of protein B.
The way I would like to proceed is by:
1) telling coot that there's a
On 25/07/12 18:38, Jonathan Grimes wrote:
Is there a quick tool in Coot to calc the RMSD of N atoms from the best
plane
through those atoms.
Yes.
Measures - Plane Distances
but happily found the renamed file and continued.
Best wishes,
Alex
On 16 Jul 2012, at 19:10, Paul Emsley wrote:
On 16/07/12 18:08, Alexander Batyuk wrote:
Dear all,
I'm trying to build coot with build-it-gtk2-simple/wrap-build-it scripts on
Ubuntu 12.04 64bit but the script stops
On 21/06/12 17:21, Phil Evans wrote:
Why is is that when I add an OXT atom I lose my colour by chain?
Because I wanted to make sure that you could see the added atom. If you
were in CA mode, then you might wonder what happened.
Hmm I suppose that I could add a check for all-atom mode
On 20/06/12 10:04, Luca Pellegrini wrote:
Is there a way to flag up residues that have been modelled with different side
chain rotamers in two NCS-related molecules? I can use the NCS Ghost Control
tool to check individual residues but it would be useful to be able to produce
a list, so that
--auto filename for auto-reading mtz files (mtz file has the default
labels FWT, PHWT)
Is there an easy way to join these up? I just want to be able to
inspect the map. I use this already to automatically show results from
refmac, which works very nicely indeed.
Off the top of my head
On 24/05/12 11:03, Ian Tickle wrote:
Hi Graeme
This has nothing to do with Randy's 1986 paper on minimally-biased map
coefficients from partial structures (which I assume is the one you're
referring to) since as you said yourself these are experimental, not
partial structure, phases. Rather,
On 24/05/12 10:52, graeme.win...@diamond.ac.uk wrote:
coot --python -c 'make_and_draw_map(sad.mtz, F, PHI, FOM, 1,
0)' --no-guano
gives
INFO:: preferences directory /home/gw56/.coot-preferences
does not exist. Won't read preferences.
(filter-fileselection-filenames-state)
On 20/04/12 22:45, Ed Pozharski wrote:
The build-install-coot-from-scratch script mentioned here
http://www.biop.ox.ac.uk/coot/build-install-coot-from-scratch.html
has a bug. It should be AUTOBUILD_INSTALLED, not AUTOBUILD_INSTALL, and
binaries end up in ~/autobuild no matter how you define
On 09/04/12 09:12, Kelly Hew wrote:
Hi,
I have recently upgraded my coot version from 0.6 to 0.7. But when I open my
mtz files, I am very puzzled why the 2Fo-Fc maps doesn't load. All the green
and red blobs I see in the old 0.6 version does not seem to be present in both
0.6.2 and 0.7.
Hi
On 21/03/12 22:02, Ed Pozharski wrote:
When using Fit protein extension the memory consumption by coot goes
steadily up. On 200 aa protein the memory consumption by coot just went
up from 120Mb to 320Mb. Stepped refine adds another 40Mb but
immediately and it does not grow as the refinement
On 03/04/12 11:18, Antony Oliver wrote:
I am really enjoying the functionality of LIDIA in the recent versions of Coot
— thank you Paul.
Glad you like it :-)
Just a couple of questions / ideas / feature requests though...
A) LIDIA doesn't always seem to show all hydrogen bonds, i.e.
OK, Done now, r4092.
Cheers,
Paul.
On 03/04/12 10:55, Paul Emsley wrote:
Just for clarity, that is a temporary fix.
Coot needs to be fixed - hopefully there will be a new revision in
place by the end of the day (previously I didn't know what a P-peptide
was - now I do).
Cheers,
Paul
On 26/03/12 19:58, Alok Shenoy wrote:
Hello,
Problem:
1) Chain A has a couple of residues missing. The numbering shows 231 232 234.
Clearly marking out the spot where the residue is missing. Sequence shows that
there is an aspartic acid missing in position 233. Problem is - both 232 and
234
On 21/03/12 22:02, Ed Pozharski wrote:
When using Fit protein extension the memory consumption by coot goes
steadily up. On 200 aa protein the memory consumption by coot just went
up from 120Mb to 320Mb. Stepped refine adds another 40Mb but
immediately and it does not grow as the refinement
On 15/03/12 14:52, Paul Emsley wrote:
On 15/03/12 14:31, Ed Pozharski wrote:
set-go-to-atom-chain-residue-atom-name fails when the residue number has
the insertion code (e.g. 33A, 76B, etc.). The method only allows the
iresno to be an integer as described here
http://www.biop.ox.ac.uk/coot
On 12/03/12 16:17, Engin Özkan wrote:
I have trouble seeing certain symmetry-related molecules sometimes.
This is extremely acute when the molecule being solved is very
elongated. In one bad case, with display radius turned to 63 Angstroms
and Calpha being displayed, I can see a million
Baah. The documentation [1] generation system needed reworking.
Fixed now.
Thanks,
Paul.
p.s. dots now have pretty pretty colours (and corrected atomic radii).
[1] which *should be* up to date with latest pre-release
On 07/03/12 15:48, Miguel Ortiz Lombardía wrote:
Le 07/03/12 14:58,
I think that 0.7 is almost ready for release.
Bleeding-edgers please bash on it now.
There is one problem that I have not been able to reproduce. That is the
space doesn't take me back problem. In fact, I am not sure if that is
the proper description.
So, if you experience this, please give
On 05/03/12 13:56, Ian Tickle wrote:
Hello, I just installed WinCoot_0.7-pre-1-4040 (because I kept getting
the message this is an old Coot from version 0.6.2.1 !).
Sorry about that. We're just slower at making released that I thought
we'd be.
I am considering a dynamic check, rather than
On 02/03/12 14:13, Bryan Lepore wrote:
On Fri, Mar 2, 2012 at 6:24 AM, Paul Emsleypaul.ems...@bioch.ox.ac.uk wrote:
On 02/03/12 09:37, Dirk Kostrewa wrote:
is there a way in Coot to get the density fit analysis as a table? I
want to use these values in comparative plots using gnuplot.
use
On 02/03/12 09:37, Dirk Kostrewa wrote:
is there a way in Coot to get the density fit analysis as a table? I
want to use these values in comparative plots using gnuplot.
use the command line program density-score-by-residue
Paul.
On 09/02/12 07:10, Bernhard Rupp (Hofkristallrat a.D.) wrote:
Dear Cootsies,
following Paul's advice I started to autobuild coot using
http://lmb.bioch.ox.ac.uk/coot/build-install-coot-from-scratch.html
It is a little bit like whacking hamsters - it needs swig, which needs
pcre...
Sorry
On 31/01/12 11:53, PRASENJIT BHAUMIK wrote:
Dear Miguel,
I tried the following
cd /usr/lib32
sudo ln -s libldap-2.4.so.2 libldap-2.2.so.7
cd /usr/lib/x86_64-linux-gnu
sudo ln -s libldap-2.4.so.2 libldap-2.2.so.7
Now if I want to start COOT, I am getting the following error message.
For the record, I hope/think that this is the same problem that is
currently affecting the RedHat 5 builds too about which one or two
others have contacted me. (We don't catch it because the automatic
testing doesn't start the gui.)
Paul.
On 26/01/12 13:36, Bernhard Lohkamp wrote:
Hi Kay,
On 26/01/12 21:48, Ezra Peisach wrote:
Personally, I like the ability to at least have a sanity check of the
HETNAM with the dictionary - and if they do not match - do not use
it... Assuming people provide a unique name in their dictionary - even
if it is FOO1, FOO2, etc - this could catch the
On 25/01/12 16:46, Kendall Nettles wrote:
I know my message was not very clear. I'm thinking of occasions where the
ligands are symmetrical, or we have a mixture of compounds and are not sure
which regioisomer to fit. We would load the maps and models of other structures
with related
Now that Coot uses the restraints dictionary to render ligands it has
become apparent that the method of doing so is problematic for typical
working situations.
Say for example your read in
complex-XYZ00123456.pdb in which the ligand is called LIG
You read in the dictionary for XYZ00123456 and
On 18/01/12 17:26, Ed Pozharski wrote:
On Wed, 2012-01-18 at 17:10 +, Paul Emsley wrote:
Here's a possible solution: When the refinement map become undefined
the
map-using functions down the right are greyed-out (and inactive) and
the
tooltips for these icons say how to define the map
On 17/01/12 08:33, Dayana Nisbar wrote:
How to change the map level from rmsd to sigma?
You can't. Electron density levels should not be expressed in terms of
sigma. Sigma refers to probability distributions - and an electron
density map is not one of those. I used to not understand this
On 17/01/12 12:01, Takaaki Fukami wrote:
Dear Coot experts,
I have a protein with an N-acetyl group at its N-terminal, and
want to refine it with coot refmac5.
Refmac recognize the LINK and applied restraints in
$CLIB/list/mon_lib_list.cif.
In Coot, when I refine zone from B0 to B1, the
I can address some of these...
On 17/01/12 12:14, Charles Finley wrote:
is there anything like an optimal hardware setup for a new installation of coot?
I don't know - it would be a useful thing to track, I think - updating
one a year or so...
(I am a bit behind the times, hardware-wise)
On 17/01/12 18:19, David Schuller wrote:
Welcome to Coot. 0.6.2 (revision 3566) [with guile 1.8.8 embedded]
[with python 2.7.2 embedded]
Installed via yum: coot-0.6.2-8.20110715svn3566.fc16.x86_64
On Fedora 16 Linux
I am trying to view a PDB file with a centrosymmetric space group. It
doesn't
On 17/01/12 18:19, David Schuller wrote:
Welcome to Coot. 0.6.2 (revision 3566) [with guile 1.8.8 embedded]
[with python 2.7.2 embedded]
Installed via yum: coot-0.6.2-8.20110715svn3566.fc16.x86_64
On Fedora 16 Linux
I am trying to view a PDB file with a centrosymmetric space group. It
doesn't
On 13/01/12 12:00, Takaaki Fukami wrote:
Dear Coot experts,
I'm working on a peptide with an N-methyled amino acid in the middle.
How can I connect this residue to previous/next residues?
To simplify the problem, first I changed the residue to MVA
(N-methyled-L-VAL),
because its library
On 22/12/11 00:01, Sabyasachi wrote:
I am trying to mutate my protein with a cy3-dye modified cysteine amino acid.
Is there any way to do it in coot?
I think that it's a mistake to try to mutate the protein.
I don't think that this is really a coot issue. Have a look at the
JLigand
On 22/12/11 16:11, Prashant Singh wrote:
Hi Everyone
I am new to COOT and don't have much idea about the shortcuts in it.
Is there a way in COOT for some windows like Display Manager, Go To Atom,
Ramachandran Plot to open up automatically every time I start COOT?
Start coot, open your
On 20/12/11 11:42, Miguel Ortiz Lombardía wrote:
Hi again,
This time a feline OS of the king-type on a MacBook Pro 64-bit machine
is giving trouble with Coot. Compiled using fink (freshly installed by
the bootstrap procedure on a fresh Xcode 4.2.1, itself installed from
scratch, i.e. no
The go to blob thing was not in this user .coot file. I will add it,
along with other useful keyboard bindings.
Just a related FYI: I have changed the binding for h recently - it's
better now (because it does on-the-fly link analysis) and has proven
useful when working with carbohydrates.
Hi JED,
On 09/12/11 13:29, Judit Debreczeni wrote:
I used to use delete-residue-with-altconf in an extension, looping
over a subset of residues returned by residues-with-alt-confs.
As delete-residue-with-altconf no longer exists,
I must say that I was unaware of the disappearance of
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