On 24/05/2023 14:24, hari jayaram wrote:
>
>
> CAUTION: This email originated from outside of the LMB.
> Do not click links or open attachments unless you recognize the sender and
> know the content is safe.
> *.-owner-c...@jiscmail.ac.uk-.*
>
> Hi All
> I am making some
Hi All
I want to get back to using coot to build some models after a gap of 8
years.
I have access to a Linux laptop and can put any OS version on it.
I was wondering what the easiest way forward is —get the most recent
Ubuntu and pull the latest binary ( 0.9.8.6 with binary for 20.04) or put
happen (because,
> clearly, it isn't).
>
> A few days.
>
> Paul.
>
>
>
> On 27/06/2022 03:12, Paul Emsley wrote:
>
>
> That clipper is old clipper. You need the clipper from the build script.
>
> Paul.
>
>
>
> On 27/06/2022 03:10, hari jayaram wrot
Dear Paul and the coot community
It's been 6 years since I posted on any coot forum . I saw the exciting
news around coot-1 and am itching to dive back in.
I am trying to compile coot-1 on Ubuntu 20.04
After installing a series of dependencies, which I can gladly report back
to you on...the
this on my list to do (somewhere on the top ;-) ).
B
On 05/04/2014 15:04, hari jayaram wrote:
Hi all,
I like running my refmac from inside coot and having the loggraph blt
graphs popup on completion.
loggraph graph pop ups seem broken on 64 bit redhat enterprise running
ccp4 6.3 and ccp4 6.4
Hi all,
I like running my refmac from inside coot and having the loggraph blt
graphs popup on completion.
loggraph graph pop ups seem broken on 64 bit redhat enterprise running ccp4
6.3 and ccp4 6.4 , both 64 bit versions. The window for the graph pops up
and then crashes with an error complaining
I have a question about the expanded syminfo labels in coot and the menu
item : Extensions-Modelling-New Molecule from symop.
I have a dimer in the assymetric unit in which the two molecules that
phaser picked as the solution do not share any contact area . I want to put
chain A together with a
Hi all,
When I build a custom ligand using the coot Ligand Builder (0.7.1-pre
(revision 4650) [with guile 1.8.8 embedded] [with python 2.7.3 embedded]).
Coot then runs cprodrg and generates restraints which I can use inside of
coot to do all my refinements and even run refmac from within coot.
Hi all,
I generally run refmac from inside coot.
The older coot version would automatically pick the newest maps that
resulted from refmac as the map to use for refinement..so it would go from
one FWT map (say map 0) to the newest FWT (map 2) map that resulted after
refmac..
However the auto
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 .
When I read in a scheme or python based Molprobity
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 and get an error in the
final linking part.
(dynload_shlib.o
Hi,
I just upgraded to the newest CCP4 version 6.3 and noticed that libcheck
which coot uses to produce restraints from a SMILES string produces garbled
coordinates in ccp4 version 6.3 , but the same SMILES string works just
fine with CCP4 version 6.2.
I tried to get it to fail on public
Hello All,
I upgraded to svn 4245 on ubuntu 64-Linux 10.04 .
I used to have the probe dots get redrawn following a refine prior to
this update. ( I was running svn 4222 or something like that).
However somehow the coot probe dots are not shown dynamically when
picking rotamers, and routine
Thanks Bernhard,
Sorry for not reading your very clear instructions properly.
..My monitor resolution was set crazy high and I missed the dot before
the coot.py
Once I renamed my key-bindings to dot-coot-dot-py (.coot.py) and
placed them into the C:\Wincoot directory..the key bindings work on
Hello Bernhard,
Thanks for your email .
It turns out that my file was not called coot.py and I also had a few
hidden new-line characters due to a copy paste from your wiki python
key bindings.
Once I named the file coot.py and corrected the python syntax..I see
the following behavior:
At startup
Hi recently found myself using coot on windows and was wondering where
the user specific key bindings are to be introduced to coot.
This was windows 7 and I think it defines the users home directory as
C:\Users\user.name\ , but I know that other Windows versions use
C:\Documents and
dir is much tidier
this way.
Thanks
Hari
On Thu, Jan 20, 2011 at 3:40 PM, hari jayaram hari...@gmail.com wrote:
Hello ,
I am running coot svn revision 3315 on Ubuntu Lucid 10.04
When I run refmac5 from within coot with this version of coot , it competes
perfectly and displays the new pdb
Coot does not seem to be passing its libcheck-SMILES generated cif file to
Refmac when the refmac button from inside coot is clicked and refmac is run.
IS there someway to have the refmac button be aware of the cif file that is
typically in the present working directory.
Thanks in advance
Hari
Hi I have the habit of using the subversion build of coot and decided to
switch to ubuntu 10.04 a few days before it comes out.
I am building it using the build-it-gtk2-simple python script
The build progresses till the final stage and the 16-coot.txt indicates
checking for pkg-config...
Hello everyone,
I know that coot reads in the pdb file and figures out the ncs
relationships upon loading . When you run refmac from inside coot and click
the button, I am assuming it uses the computed NCS relationships as
restraints during refinement . My pdb file does have the NCS definitions
Hi,
I noticed that the coot distributed by ccp4-6.1.3 does not have python built
into it. Is there anyway to add in the python support post installation ?
I am running the ccp4 supplied coot on OSX Leopard 10.5.8
I am cc-ing the coot mailing list as well .
Thanks
Hari
Hi ,
I am seeing this problem only on a particular 32 bit machine.
On this machine when I try to make a map using a Dano column and PHIC or
PHIDM , coot chugs through the calculation. Creates the map object in
Display manager and then no map shows up. Despite any extent of attempting
to scroll the
that allows me to get stereo on
this setup.
Monitor : Viewsonic FuHzion VX2265wm 120Hz
Graphics card: Quadro FX 4600
OS: Ubuntu Linux X86_64 - Hardy Heron 8.04
Stereo glasses: Crystal Eyes 3 with 3pin mini din connector
Thanks for your help in advance
Hari Jayaram
Brandeis University
On Tue
Hi I have a very low resolution map in which I can barely see side chains .
I want to set to zero occupancy many residues and residue side-chains before
I do a refinement.
Currently I am using the Residue-Info menu item to set each occupancy to
zero residue by residue . And in cases where part of
9.04 box.
Regardless I am happily cooting with the latest build on Jaunty jackalope.
Thanks a tonne
Hari
On Tue, May 12, 2009 at 11:11 AM, hari jayaram hari...@gmail.com wrote:
Hello ,
The jaunty 32 bit build seems to fail ( with subversion revision 2002 as
well)
It seems like based on what
/Custom_building_Coot_from_source_codeof
separately compiling all the coot dependencies . But though I would
wrote
in to inquire if there was already a simpler fix.
Thanks
Hari
On Fri, May 8, 2009 at 7:35 PM, Paul Emsley paul.ems...@bioch.ox.ac.ukwrote:
hari jayaram wrote:
Hi ..I tried a coot subversion
Hi ..I tried a coot subversion (revision 1994) built-it-simple python on the
newest ubuntu 9.04
The build crashes just after it builds guile and ( 16-coot.txt in the build
directory ) reads :
checking for Clipper... yes
Congratulations, you are using Guile
checking for guile... no
configure:
: creates all atoms as stars in ncs mates
Thanks
hari
On Thu, Apr 23, 2009 at 4:34 PM, Paul Emsley paul.ems...@bioch.ox.ac.ukwrote:
hari jayaram wrote:
Hello ,
I just noticed that rigid body fit zone in revision 1950 stops expecting
user mouse clicks after clicking on the first atom
Hi I am using the latest build (1947 0.6 pre) of coot
Coot lsq superpose does exactly what I want it to do i.e superpose all the
atoms from one set of fragments to the ncs symmety other set of fragments.
Is it possible to have coot output to stdout the transfomation matrix like
it does when it
Paul's build-it-gtk2-simple script, which should build all
the dependencies for you.
http://www.ysbl.york.ac.uk/~emsley/build-logs/build-it-gtk2-simplehttp://www.ysbl.york.ac.uk/%7Eemsley/build-logs/build-it-gtk2-simple
hari jayaram wrote:
Hi , Bill,
Sorry I skipped this mail and have not yet
Hi I am using coot 0.5 pre 1 on linux .
I am trying to correct the model after molecular replacement into a 3.3 A
map and I have a few questions
The map is quite good for all the helical regions but the loops are
expectedly hard to build. Thanks to prime-and-witch I have a remarkably bias
removed
against leopard and X and I agree with Bills sentiment..makes
me want to go back to gentoo-linuxbut then we just spent almost 3K on
this machine and I am sure hoping these problems will soon disappear
A willing guinea pig
Hari Jayaram
On Sun, Mar 23, 2008 at 6:19 AM, Phil Evans [EMAIL
in a multi-user setup that I need to do
differently
Thanks a lot for your help in advance
Hari Jayaram
Brandeis University
rotamers still a known issue?
Thanks for your help and sorry to add to this thread with a unrelated
question
Hari Jayaram
Brandeis University
On Thu, Mar 20, 2008 at 12:45 PM, William Scott [EMAIL PROTECTED]
wrote:
They keep changing the name of the damn plist file.
Try
org.x.X11
same
34 matches
Mail list logo
