al other different Scientific
> Linux versions of coot. However, it is still not working. I'm wondering if
> it's more of a cenos8 issue in general or some other local set-up.
>
> Any suggestions are warmly welcomed. Thank you all again.
>
> best,
> Ming
>
> On Mon, Feb
Hi Ming:
I got some similar errors on my Ubuntu install. Removing some of the non-coot
libraries (like libpng) that are duplicated might help. Also, make sure you
have the appropriate processor architecture.
Bill
> On Feb 22, 2021, at 8:14 AM, Ming Sun wrote:
>
> Hi all
>
> I'm trying
Hi Leonard et al:
I want to apologize to you and everyone for dropping the ball on this. Between
a massive wildfire that almost took out our house (and destroyed those of
several colleagues), the pandemic, a forced lab move on short notice, and a
pile of new teaching assignments, I haven’t
kind of have burned
out on this stuff in the last few years.
We will figure something out. Compared to all that is going on in NYC right
now, these problems will hopefully be minor.
Take care.
Bill
William G. Scott
Professor, Department of Chemistry and Biochemistry
and The Center
, but from
what I understand, it has the latest coot (and refmac), so if you need the new
version, I suggest you do that.
If we can’t have a more recent version of coot in fink vs. ccp4, and can’t have
refmac, it kind of makes it pointless to maintain coot in fink.
Bill
William G. Scott
Try re-installing Xquartz.
https://www.xquartz.org
William G. Scott
http://scottlab.ucsc.edu
> On Apr 4, 2018, at 4:52 PM, Elena Zehr <zehr.el...@gmail.com> wrote:
>
> Hi,
>
> After upgrading my MacOS to High Sierra, coot stopped running giving me the
> error
For those using fink, I’ve updated the fink package info file
http://fennario.ucsc.edu/~wgscott/coot/finkinfo/coot.info
I still need to figure out how to get it into fink.
Meanwhile, you can put the file in /sw/fink/dists/stable/main/finkinfo/sci and
build it.
William G. Scott
Director
I wonder if coot might be able to take advantage of this:
> https://arstechnica.com/science/2017/11/new-hardware-lets-any-computer-run-an-interactive-3d-interface/
>
> <https://arstechnica.com/science/2017/11/new-hardware-lets-any-computer-run-an-interactive-3d-interface/>
W
might get better responses asking about pymol on the pymol mailing list.
(Asking questions about PyMOL on the coot email list is kind of like ordering
flowers for your mistress on your spouse’s cell phone and credit card.)
William G. Scott
Director, Program in Biochemistry and Molecular Biology
Sorry. I forgot to change one occurrence in the build script. Should be fixed
now.
William G. Scott
Professor, Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
University of California at Santa Cruz
Santa Cruz, California 95064
USA
http
,
Bill
William G. Scott
http://scottlab.ucsc.edu/~wgscott
-gtk_2.1-1_darwin-x86_64.deb”
sudo dpkg -i *.deb
This is the same package with a later epoch label so fink updates won’t touch
it.
On Sep 3, 2014, at 10:40 AM, William G. Scott wgsc...@ucsc.edu wrote:
On Sep 3, 2014, at 5:33 AM, Dimitry Rodionov d.rodio...@gmail.com wrote:
Hi Jianghai
}”.
Thanks.
Bill
William G. Scott
Professor, Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
University of California at Santa Cruz
Santa Cruz, California 95064
USA
http://scottlab.ucsc.edu/~wgscott
Dear Oliver et al:
On Jul 20, 2014, at 8:54 AM, Oliver Clarke oc2...@columbia.edu wrote:
WARNING:: No coot.py file found! Python scripting unavailable.
It looks like this is the problem. For some reason it is no longer getting
copied from the src to python directory. If I do this manually,
On Jun 19, 2014, at 9:33 AM, William G. Scott wgsc...@ucsc.edu wrote:
If the user has set $DYLD_LIBRARY_PATH (perhaps via ccp4), it is possible
this gets over-ridden.
I can reproducibly mess coot up with this:
export DYLD_LIBRARY_PATH=/Applications/ccp4-6.4.0/lib
and un-mess it up
anyone tell me what I'm doing wrong?
Thank you so much in advance.
Nacho
William G. Scott
Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
University of California at Santa Cruz
Santa Cruz, California 95064
USA
http://scottlab.ucsc.edu/scottlab/
I am updating the “stable” coot in fink to rev. 4965 which should work fine
with the latest rkdit.
On Mar 14, 2014, at 11:11 AM, William G. Scott wgsc...@ucsc.edu wrote:
Dear Nacho:
The “coot-pre” package should work. In updating that, I think I probably
broke the “stable” coot package
I am clueless on this one, so I'll post it to the coot mailing list in case
anyone else has seen this ….
On Oct 8, 2013, at 9:53 PM, Felix Frolow wrote:
Hi Bill, I regularly update coot using FINK ( from your repository)
Since one of the recent versions of coot ( difficult to say from when,
DYLD_LIBRARY_PATH
on tcsh should do it.
Also, you could try installing coot from here, as a control (or an alternative):
http://scottlab.ucsc.edu/~wgscott/xtal/wiki/index.php/Stand-Alone_Coot
Good luck.
Bill
William G. Scott
Professor
Department of Chemistry and Biochemistry
and The Center
On Sep 5, 2013, at 3:43 AM, Steffen Schmidt steffen.schm...@tuebingen.mpg.de
wrote:
coot0.7.1.0-7 Crystallographic molecular graphics
coot-pre0.8-pre-4749Crystallographic molecular graphics
refmac 5.7.0032-3 CCP4 refmac5 standalone update
Great,
Crystallographic molecular graphics
refmac 5.7.0032-3 CCP4 refmac5 standalone update
Great, it works for me also!
Do you plan to have it also available for 10.6?
Steffen
Yes, I'll try to get it done (tested) today.
Bill
William G. Scott
Professor
Department of Chemistry
On Sep 4, 2013, at 7:42 AM, Steffen Schmidt steffen.schm...@tuebingen.mpg.de
wrote:
Hey Bill,
I noticed that coot complains that
WARNING: in init_refmac_mon_lib file
/sw/share/coot/lib/data/monomers/list/mon_lib_list.cif not found.
WARNING:: energy lib
On Sep 3, 2013, at 1:04 PM, Dale Tronrud det...@uoxray.uoregon.edu wrote:
I was looking for the download site for Coot but the links have
have found point to
http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/
but there is nothing there. Where do I go to find prebuilt coot
binaries?
On Apr 24, 2013, at 1:40 AM, Andreas Förster docandr...@gmail.com wrote:
Dear Özkan and all,
this question was asked by Dave a month and a half ago
(https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1303L=cootP=R286), but
there was no reply.
Snow Leopard is deprecated, even though 25%
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.
I'm having python mis-match problems on 10.6.
On Feb 19, 2013, at 7:21 PM, Dmitry Rodionov d.rodio...@gmail.com wrote:
This seems
and crashed my computer with the main website on
it. Sorry. I can't drive due to a broken ankle so it might be awhile before it
is up again.
Good luck.
Bill
William G. Scott
Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
228 Sinsheimer Laboratories
On Feb 8, 2013, at 3:29 PM, Arto artop...@berkeley.edu wrote:
/Users/pulk/.coot-preferences/0-coot-history.scm
Try moving or deleting that file and see if it works again.
Which button in COOT do I press to print a PDB file represented as a
ball-and-stick model to get a 3D printout from someplace like this?
http://www.shapeways.com
William G. Scott
Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
228 Sinsheimer
a chance to unpack.
-- Bill
William G. Scott
Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
228 Sinsheimer Laboratories
University of California at Santa Cruz
Santa Cruz, California 95064
USA
On Nov 12, 2012, at 12:25 PM, Paul Emsley pems...@mrc
Additional OS X builds are linked here:
http://scottlab.ucsc.edu/~wgscott/xtal/wiki/index.php/Stand-Alone_Coot
On Sep 29, 2012, at 2:49 AM, Paul Emsley paul.ems...@bioch.ox.ac.uk wrote:
Mac 10.8:
http://psbmini.ucsc.edu/~wgscott/coot/stablereleases/Coot-0.7-stable_64bit_10.8.2.pkg.zip
that can be used
for coot and the ccp4 suite, to prevent users from having to install two sets
of what should be the same libraries.
Peace and joy,
Bill
William G. Scott
Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
228 Sinsheimer
/python2.7/site-packages/gtk-2.0:/sw/share/coot/python
and it should work.
Coot is inheriting $PYTHONPATH from some other location, probably CCP4, and is
getting messed up. I'm about to update the fink package, as soon as I confirm
today's svn (r4386) compiles and behaves.
Sorry.
Bill
William G
What happens if you try to display a pdb and map downloaded from the EDS? I
believe that uses the same auto-open sequence, and it would help in figuring
out whether the problem is with a refmac incompatibility or something else…
On Aug 2, 2012, at 8:13 AM, Pernigo, Stefano
On Jul 17, 2012, at 6:25 AM, Felix Frolow wrote:
I will wait for fink version if it will be one… :-\
Does anyone use or want this anymore?
-- Bill
William G. Scott
Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
228 Sinsheimer Laboratories
I don't, but I will try to get it done by the time 10.8 is released, if not
sooner.
Bill
William G. Scott
Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
228 Sinsheimer Laboratories
University of California at Santa Cruz
Santa Cruz, California
COOT_SBASE_DIR=$CCP4/share/sbase
export
PYTHONPATH=/Library/Coot/lib/python2.7/site-packages:/Library/Coot/lib/python2.7/site-packages/gtk-2.0:/Library/Coot/share/coot/python:$PYTHONPATH
/Library/Coot/bin/coot-real $@
William G. Scott
Professor
Department of Chemistry and Biochemistry
and The Center
/refmac/data/refmac_experimental/refmac_dictionary_v5.35.tar.gz
William G. Scott
Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
228 Sinsheimer Laboratories
University of California at Santa Cruz
Santa Cruz, California 95064
USA
phone: +1-831-459
Howdie:
Has anyone had success using coot with a 3D stereo projector?
If so, any recommendations?
Thanks.
Bill
William G. Scott
Contact info:
http://www.chem.ucsc.edu/~wgscott/
this for ubuntu already. Is
anyone reading this a maintainer
for ubuntu and/or debian?
Bill
William G. Scott
Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
228 Sinsheimer Laboratories
University of California at Santa Cruz
Santa Cruz, California
refinement.
Bill
William G. Scott
Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
228 Sinsheimer Laboratories
University of California at Santa Cruz
Santa Cruz, California 95064
USA
phone: +1-831-459-5367 (office)
+1-831-459-5292 (lab
On Jan 26, 2012, at 5:36 AM, Bernhard Lohkamp wrote:
Hope this resolves the problem,
B
Seems to fix it on OS X
-- Bill
Well, I just build a version for 10.6, and haven't had a chance to point anyone
to its web location, so I am guessing you installed the one I compiled for
10.7….
So please try this one and lemme know if it works please.
Bill
http://sage.ucsc.edu/~wgscott/coot/
William G. Scott
Professor
Hi Phil:
I haven't been able to compile coot since 11 September, due to a change in the
code.
I've got a 10.6.8 version of that too, but nothing newer I am afraid.
Sorry.
Bill
On Oct 31, 2011, at 5:11 AM, Phil Evans wrote:
As I understand it, Bill Scott now only builds Coot for OSX 10.7:
On Oct 24, 2011, at 8:01 AM, Paul Emsley wrote:
I have switched from the COOT I compiled from fink to Bill's binary COOT,
the situation has not changed.
They are both compiled with fink. The only difference is the top-level
directory is /LIbrary/Coot instead of /sw
Hi Andrew:
I don't have the hardware to test it on, but as far as I am aware, it will do
active stereo. At least that is the intention.
Bill
PS: I'm compiling various versions of 0.6.2. Somehow I missed the fact that
the stable release had come out two weeks ago. Sorry.
On Jul 7, 2011,
Dear Phil, Paul, Ben, Bernhard et al:
Sorry to arrive 8 hours late to the party, but first my apologies to Phil. I
thought I had fixed this problem by excising from the coot wrapper script the
path in /System/Library, i.e.,
export
I'm hosting nightly builds now, and none of the more recent versions should
have this in the wrapper script. Please let me know if somehow that isn't the
case.
Bill
On May 4, 2011, at 9:10 AM, Phil Evans wrote:
I did delete the *.pyc files in the system directories, and they have now
Nice. Seems to work fine in the OS X version as well... in my 60 seconds of
testing.
Bill
On Mar 31, 2011, at 12:58 PM, Kevin Keating wrote:
I've just released a new Coot plugin to help with building RNA structure,
so I wanted to make a quick announcement to the mailing list for any
I'm attempting to generate automated builds of coot pre-releases for OS X
10.6.X users. These are 64-bit. If all works well, there should be a new one
every day (assuming a new source tarball is available).
http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Stand-Alone_Coot
Please let me
Has anyone managed to compile a recent version of coot on OS X 10.4.X via fink?
Thanks.
Bill Scott
Dear Antony:
First, allow me to apologize for this. I was hoping this would help make
everything seamless.
Mark Brooks suggested updating X11 from http://xquartz.macosforge.org/trac/wiki
. Although this might help with such a problem on 10.5 with ppc., in this
case I believe it shouldn't
Sorry I haven't done this until now. Been distracted by the struggle for
survival.
http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Stand-Alone_Coot#Version_0.6.2-pre-1-3072
Check /usr/local/xtal/coot64/bin/coot
to see if I set $PYTHONPATH right.
It should have /usr/local/xtal/coot64/lib/python2.6/site-packages/gtk-2.0
Nathaniel Echols wrote:
When I use the 0.6.1 package from Bill's web site, I get this error when I
try to start the Python scripting GUI:
Did you issue
source /sw64/bin/init.sh
(or init.csh if you are a tcsh user)
first?
This sets $PATH and some other needed environment variables.
On May 4, 2010, at 6:01 AM, David Lisgarten wrote:
Dear Coot,
I recently installed Coot version (0.6.1 64 intel) on a
iMac
If you can define a SMILES string for your ligand, you can get coot to
build the ligand with the press of a button in a fraction of a second.
If the SMILES syntax is a PITA, use this:
http://www.molinspiration.com/cgi-bin/properties
If you need more options, phenix.elbow also permits you to use
On Feb 8, 2010, at 2:07 PM, Nathaniel Echols wrote:
On Mon, Feb 8, 2010 at 1:51 PM, William G. Scott wgsc...@chemistry.ucsc.edu
wrote:
This is available to install as a binary from here:
http://molprobity.biochem.duke.edu/get_molprobity.php
Although probe and MolProbity3 are said
Any ideas?
-Sam
Try something more recent.
Dear Richard:
It looks like I neglected to add this as a dependency.
Please try installing libcurl4-shlibs, and hopefully that will solve the
problem.
If not, please let me know as soon as possible.
Bill
On Jan 17, 2010, at 12:33 PM, Richard Kingston wrote:
Hello Bill
After updating
On Jan 11, 2010, at 4:38 AM, Andreas Förster wrote:
Every time I'd ask a question
You really ought to update. 0.1 is a bit long in the beak.
Yo:
Several people wrote to me in the last couple of days about different problems
with respect to the latest coot update in fink. This all happened at the
beginning of term so I haven't really had enough time to deal with this
systematically.
Briefly, I put coot 0.6 is in the stable and
Are you using the 32-bit or 64-bit coot? I have to confess only having checked
the 64-bit version (which worked ok in my hands).
On Jan 7, 2010, at 9:31 PM, Jan Abendroth wrote:
Hi all,
I am trying to update coot on osx 10.6 from a 0.6-pre version to the current
fink version (0.6.1-pre).
No problem. The hope is that with fink, anyone can compile and install coot
without drama on OS X ppc or intel, 10.6, 10.5, 10.4 (there is no 10.6 ppc).
On Jan 5, 2010, at 6:13 AM, Huw Jenkins wrote:
On 5 Jan 2010, at 13:57, William G. Scott wrote:
If you use what is in fink
See if this works:
http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Stand-Alone_Coot#Stable_Release_for_Intel:__coot-0.6_for_64-bit_Intel_10.6
On Jan 4, 2010, at 2:58 PM, Huw Jenkins wrote:
On 4 Jan 2010, at 22:21, Nathaniel Echols wrote:
The package distributed by CCP4 was not compiled
Just get a $300 Zalman LCD monitor and use coot with that. No special
hardware required and it is OS independent. I'm using it also as my
primary monitor as I type this.
Michael J Miley wrote:
I have a linux workstation with a nvidia quadro graphics card and
matching emitter/lcd glasses
On Nov 2, 2009, at 3:59 PM, Bryan W. Lepore wrote:
http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Installing_Coot_on_OS_X
Be sure to use the so-called unstable branch of fink to get the
latest pre-releases of coot
do i read this correctly : it means ONLY pre-releases, right? and
then
This happened on a new snow leopard install. It looks like that
Apple decided not to include any .la with their X11 SDK.
Yes, unfortunately the only way to deal with this is to delete all the
*.la files in /sw that make reference to the nonexistent libs or other
*.la files.
I found the
Hi Folks:
On OS X, 10.6, I have been playing around with hfsCompression. I can
decrease the size of /sw/share/coot significantly:
% cd /sw/share/
% du -h -d 0 coot
180Mcoot
% sudo mv coot coot.1
% sudo ditto --hfsCompress coot.1 coot
% du -h -d 0 coot
31Mcoot
This can also be
On Sep 14, 2009, at 3:23 PM, Paul Emsley wrote:
So the last couple of days have been a bit frustrating for me, but a
good deal of credit goes to Bill of course.
This can be read in at least two ways.
As anyone who knows me could tell you, the only thing I really can
take credit for is
Paul just pulled off a heroic fix (rev 2310). Please try that.
On Sep 11, 2009, at 7:40 AM, William G. Scott wrote:
Dear Christian:
I'm getting it now too. I forgot to cc you. I get it on 32-bit but
not 64-bit SL. I've sent the crash report to Paul .
Check to see if you have
On Sep 11, 2009, at 7:36 AM, Benda, Christian wrote:
hink it's time to upgrade to 10.6, finally!
10.6.1 now.
:D
.
Engin
On 9/8/09 7:14 AM, William G. Scott wrote:
Hi Christian:
I just committed coot 0.6-pre-1-revision-2283 to fink cvs. It
fixes a bug on 64-bit where the menu would freeze when
superposition is invoked. I suppose there is a 0.001 chance
that it fixes the other problem too. I have
Hi Christian:
I just committed coot 0.6-pre-1-revision-2283 to fink cvs. It fixes a
bug on 64-bit where the menu would freeze when superposition is
invoked. I suppose there is a 0.001 chance that it fixes the
other problem too. I have no way to test on 10.5 intel (I still have
The good news is I can reproduce your error:
checking for GtkGLExt - version = 1.0.0... no
*** Could not run GtkGLExt test program, checking why...
*** The test program failed to compile or link. See the file
config.log for the
*** exact error that occured. This usually means GtkGLExt is
I just started a stereographics section on the coot wiki, but need
help, specifically with the hardware stereo part from someone with
firsthand experience, but feel free to improve all of it:
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot#Stereographic_Display
On Aug 19, 2009, at 1:14 AM, Lutz Schmitt wrote:
Dear Bill,
I am probably one of the many people out here who asked you a
question concerning the Zalman 3D monitor.
We got one yesterday and I upgraded coot to coot 0.6-pre-1 (revision
2215) running on a Quad-Core Intel with a NVidia Qudro
On Aug 19, 2009, at 8:21 AM, Paul Fyfe wrote:
(set-hardware-stereo-angle-factor 1.3)
This is I think the command I was after.
Thanks.
.
Lutz
Am 19.08.2009 um 20:41 schrieb William G. Scott:
Hi Lutz:
Yeah, that is definitely the problem. That kind of hardware
stereo is for a CRT and the special video card it needs.
Fortunately, we don't need any of that.
Try issuing the scheme command
(zalman-stereo-mode
Dear Jürgen:
I've been using the DVI cable provided and full resolution (I had to
set this manually in display preferences). I assume what works with
my mini and my airbook would also work with a macbook pro. I haven't
tried the VGA option, but assume that would work too.
One thing I
Dear Bernhard:
Thanks very much for implementing Zalman stereo into coot. I
apologize for neglecting to say so in my earlier email, and after
previous cootbb emails, I have no excuse (except maybe fatigue).
Thanks also for pythonizing coot, by the way, too.
All the best,
Bill
On Jul 29, 2009, at 3:34 AM, Paul Emsley wrote:
For me, the reference stereo image is Frodo on a ES PS390.
I'm old(e) enough to remember having used that.
You might like to tweak the eye angle:
set_hardware_stereo_angle_factor(1.45) # or some such
(I am presuming that you are using the
Hi Jason:
For some reason that I don't understand, some users find they need to
issue the command
source /usr/local/xtal/coot/bin/init.sh
prior to issuing the command
coot
(coot in this context actually invokes a wrapper shell script that
has that first source command in it, so that is
I have the following guile-like stuff installed, if it is of any help:
diablo-% which dpkg-list
dpkg-list () {
dpkg --list \...@\*
}
diablo-% dpkg-list guile | grep ii
ii guile-1.6-libs
1.6.8-6.3ubuntu1 Main Guile libraries
ii
On May 5, 2009, at 3:16 PM, CK wrote:
Hi all,
I am refining a structure that contains RNA. I've added hydrogens
in the riding positions to help with maintaining proper geometry
during refinement. However, when I go to adjust the model between
refinements in coot using Real Space Refine
Could you (or we) set
LANG=en_US.US-ASCII
in the coot wrapper script?
On Apr 29, 2009, at 8:01 AM, Steffen Schmidt wrote:
Hi,
I experienced a weird error (amino acids are not connected) when
setting the environmental variable LANG to de_DE.UTF-8 (on a OS X
10.5 machine). I guess this
On Mar 29, 2009, at 2:34 AM, Phil Evans wrote:
On 29 Mar 2009, at 04:42, William G. Scott wrote:
This I hope will address previous grievances:
http://tinyurl.com/coot1941
... except I get a load of errors I didn't have before :-(
and no splash screen or icons. The files all seem
On Mar 2, 2009, at 4:25 AM, Vellieux Frederic wrote:
Any idea?
Is it there?
http://www.mail-archive.com/ubuntu-b...@lists.ubuntu.com/msg663049.html
As far as learning scheme,
My $0.02:
From a purely practical standpoint, if, like me, you have limited
time, energy and mental capacity, python would probably yield a better
investment payback. There are numerous extensions available that make
parsing things like pdb files very simple,
What happens if you turn off all compositing effects?
On Feb 23, 2009, at 8:37 AM, David Schwefel wrote:
Dear Coot community,
I encountered some problems using Coot on fedora core 10. I
installed the
binaries, and upon starting, the system crashed just in the moment
when the
Coot window
On Jan 30, 2009, at 10:50 AM, Nathaniel Echols wrote:
the binaries I was using of coot-0.5-pre1
had this problem, while coot-0.5.1-pre1-1661 used the correct
interpreter.
That sounds like something I made, in which case I am even more puzzled.
The interpreter is actually supposed to be
)4.67.41.79.13
==
- Original Message - From: William G. Scott wgsc...@chemistry.ucsc.edu
To: COOT@JISCMAIL.AC.UK
Sent: Friday, January 16, 2009 6:04 PM
Subject: Re: Glossy_P gtk+2
That would be my fault.
On Ubuntu, I have this:
% more /etc
the best
Valerie
William G. Scott
Contact info:
http://chemistry.ucsc.edu/~wgscott/
:57 AM, William G. Scott wrote:
Woops. I didn't see that. I auto-generated the list of
dependencies from the output of ldd on the coot binary, upon which I
then used dpgk -S to find the corresponding packages. For some
reason it generated this falsely (the library is also present, but
ldd
Hi Enrico:
I have this:
% dpkg -S svg_loader.so
librsvg2-gtk: /sw/lib/gtk-2.0/2.10.0/loaders/svg_loader.so
The package that provides this is librsvg2-gtk, which should be a coot
dependency.
Could you please check, and maybe try reinstalling it, ie.
fink reinstall librsvg2-gtk
and let me
Another idea:
If you have $DYLD_LIBRARY_PATH assigned, try unsetting it before
invoking coot, i.e., issue
DYLD_LIBRARY_PATH= ; coot
On Nov 17, 2008, at 8:09 AM, Enrico Malito wrote:
Hello,
I was wondering if anybody observed this before. When I start coot I
get this messages (a long
/fink_intel_10.5_only stable main crypto
deb http://sage.ucsc.edu/fink_intel_10.5_only unstable main crypto
deb http://sage.ucsc.edu/fink_intel_10.5_only local main
Then issue
fink selfupdate-rsync
sudo apt-get update
fink -b update-all
On Oct 14, 2008, at 9:43 AM, William G. Scott wrote:
Dear
I agree, but why do you want to build B-form RNA?
On Oct 10, 2008, at 8:48 AM, Daniel Holloway wrote:
I'm using the 'Ideal DNA/RNA...' function. When I try to build A-
form RNA,
I get what I want. When I ask for B-form RNA, I get DNA! Looks like
something to fix...
Many thanks
in the C2'-endo conformation) and using it as the basis for a
novel
ligand.
On Fri, 10 Oct 2008 09:13:57 -0700, William G. Scott
[EMAIL PROTECTED] wrote:
I agree, but why do you want to build B-form RNA?
On Oct 10, 2008, at 8:48 AM, Daniel Holloway wrote:
I'm using the 'Ideal DNA/RNA
Hi Citizens:
I can't remember who was working on pre-compiling the OS X 10.4X intel
coot. Could someone remind me? Thanks, and sorry.
Bill
run the pdb file through ccp4's pdbset, which will canonicalize it (if
that is a word).
On Oct 5, 2008, at 5:59 PM, Masaki UNNO wrote:
Hi Colleagues
I am using CNS for structural refinements. I have installed
COOT_0.5 but I
think the new version of COOT cannot display CNS coordinate
Does anyone have a copy of libgmp.3.dylib from OS X 10.4.X built on
a G4 ppc, preferably with a single processor, that works with coot?
If so could you please email it to me?
Thanks.
Bill
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