David J. Schuller wrote:
I have an NAD cofactor. Coordinates attached; they were generated by
running libcheck on the CCP4 dictionary file NAD.cif (standard file
taken from CCP4 6.1.0). I am trying to rotate various torsional angles.
I am using the "Edit Chi Angles" feature of Coot 0.6-pre-1. Is
Alex Luso wrote:
Hi Bernhard,
Thanks for the clarification.
commenting on this. Maybe there should be some low level implementation
without the use of fancy (scheme) widgets, so that at least scripts can
be run.. (on my - long - list now).
Ok, I think that would be a good idea. Given th
Moritz Metlitzky wrote:
Hi everybody, i just installed coot and played around a bit with my
structure and the Fit Protein command. Now to my question, i have a zinc
atom in my structure coordinated by 3 cysteines. it refines pretty well, but
when i do Fit Protein Coot always links the 3 cys direc
Oliver Clarke wrote:
I like the fit protein script - at low resolution, initial rounds of
fitting and refinement often result in my leucines/isoleucines having
fairly implausible rotamers, and fit protein is a great way of quickly
fixing up the worst of these.
However, it doesn't seem to de
Alex Luso wrote:
On Wed, 13 May 2009 23:29:28 +0100, Paul Emsley
wrote:
I meant the issue Berhard mentions as the reason scheme is not available to
Win-Coot - "missing text in scheme widgets". Just curious if that's a minor bug
or something major.
Oh I see - yes
Clare Peters-Libeu wrote:
First off, let me apologize for a really long message.
I'm trying to get Coot running on a 64-bit machine running fedora core 9. I
picked fedora core 9 because many of the graphics libraries required for
Coot are already installed. However, the autobuild script fails
hari jayaram wrote:
Hello Paul and everyone,
Since I had complained about difficulties in building coot from
subersion on Ubuntu Jaunty , I thought I should write in to say that I
tried building the subversion revision 2021 on ubuntu 9.04 from scratch
and it builds just fine and everything wo
Sebastiano Pasqualato wrote:
Hi Paul, hi all.
I have noticed that coot can't deal with spacegroup information of cns
files.
I have to substitute this:
CRYST1 87.188 49.276 132.627 90.00 108.88 90.00 P 21
with this:
CRYST1 87.188 49.276 132.627 90.00 108.88 90.00 P 1 21 1
to have t
Hi Jennifer,
Doebbler wrote:
I am running Coot 0.5.2 on an intel Mac 10.5.6. I am trying to
visualize the symmetry related molecules for a small inorganic molecule
in spacegroup P 21/C. If I load the file into swiss PDB viewer or
Mercury, the symmetry operators show that I have 4 molecule
For the record/archive I'd like to conclude this thread.
It recognizes the spacegroup as P 1 21/c 1.
Is seems that Coot indeed does display symmetry correctly for this
spacegroup, but not in the way that other programs (e.g. Mercury or
Swiss PDB Viewer) do.
coot> (show-spacegroup 0)
"P
Oliv Eidam wrote:
Hi,
I have the same problem like Robert.
And although I updated to coot-0.6-pre-1-1941-intel-10.4-10.5.tgz like Bill
suggested, the problem (displaying no or wrong bonds) persists.
Has this problem been resolved by now? I am using OSX 10.4.11.
And
source /sw/bin/init.sh
This has been an enlightening thread - I thought that I knew about
linking executables!
If I have understood correctly, then a relative rpath of $ORIGIN/../lib
(and $ORIGIN/../lib64 for 64 bit builds) is the way to go. Hopefully
that will mean that we can get rid of the script wrappers (at le
Dear Bleeding-edge binary [1] Coot users,
I would appreciate feedback on the representation of LINKs using the
output of Buster and Phenix.refine.
(The last time I saw this in action (I don't have such files myself)
(and prior to the most recent fixes) it crashed.)
Thanks,
Paul.
[1] rev
Edward Miller wrote:
Hey Folks,
I'm working on refining a full capsid containing 60 chains.
Using the chain ID column, I've numbered my chains A-Z, a-z, and 0-7.
I was successfully able to refine my capsid in refmac using this chain
ID naming scheme.
However, coot fails to read in any of th
Kevin Cowtan wrote:
Coot reads files with duplicate atom numbers
just fine (at least 0.6pre-latest does).
However Coot will ignore any lines beginning
ATOM 1?
ATOM 2?
etc
because those are not valid atom records. So that is the reason these
are being ignored.
Yes, we should say tha
http://thedailywtf.com/
2009-06-11
(I never get to see that dialog, of course :)
(Somehow they've got the mac version of this - apparently they don't fink
update-all often enough...)
Paul.
Valerie Biou wrote:
I run Coot version 0.6-pre-1 on a Macbook Pro. I used the fink
installation.
It crashes when I ask it to display a sequence
** (coot-real:764): WARNING **: Widget not found: sequence_view_dialog
/sw/bin/coot: line 5: 764 Bus error /sw/bin/coot-real "$@"
Simon Kolstoe wrote:
Dear cootbb,
When building into density I use a map generated from the FWT amplitudes
column and PHWT phases columns which I think is my 2Fo-Fc, and a second
map generated from DELFWT and PHDELWT which I think is my Fo-Fc.
Me too (more or less).
This
keeps me happy an
Frank von Delft wrote:
Hi, any particularly cogent reason why the order of symops is
different in coot and ccp4? (E.g. below: P6522.)
It's fantastically annoying, e.g. when trying to reconstruct symmetry
mates via ccp4, if the symop number is not what is shown in the coot
status bar. Or e.g
chern wrote:
Hi all,
Is it possible to separately adjust the levels of positive and
negative electron density?
No (and yes).
When I try to build a fragment with a poor density I want to decrease
the level of positive density from 3 sigma to 2 or even 1 sigma to see
more positive density, b
Maia Cherney wrote:
If I use a *map_coeffs.mtz file from the phenix.refine, how can I turn
off the negative density?
??? Confusing question. By unclicking the "is difference map?" button
(you can't do this in auto-read mode, of course).
Paul.
Leonardo Castro Palmieri wrote:
I found it, thank you all!
But, why so hidden?
Oh, really! It's not hidden. It's just a menu item away.
I use a lot this function.
I am surprised that you say that - I hadn't imagined that it was a
function that was used a lot (once per structure (if tha
Maia Cherney wrote:
Hi all, Is it possible to change residue or atom occupancies in coot?
Maia
Yes.
http://www.ysbl.york.ac.uk/~emsley/coot/doc/chapters/user-manual_5.html#SEC147
Tian, Ye wrote:
Hi All,
Hi Ye Tian/Alice,
I am trying to modify the structure of protein and save it as new PDB
file. I wonder if there’s a function in COOT to cut off a fragment?
Which way to you want it?
Cut out a fragment, discard the rest:
Extensions -> Modelling -> Copy
William Scott wrote:
Hi Paul:
On ppc but not intel, I get this for some of the window displays (eg
density fit analysis):
Yes, we (in Oxford) have seen this before on ppc too.
We didn't resolve it. I was thinking that it was somehow picking up the
wrong "fixed" font. I tried adding a fo
chern wrote:
Hi,
I am trying to find the latest version (0.6) of coot for Mac with nice
icons. Is there such a version?
Yes, the bet way to get it is to use Bill's fink coot.
http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Installing_Coot_on_OS_X
Paul
William Scott wrote:
I guess I'd better brew something newer up...
All the 0.6 are pre-releases ...
Yes, indeed (I finger fumbled and posted before I added the sentence to
that effect).
Paul.
hari jayaram wrote:
I agree with Donald, and would add my vote to a possible feature request
for coot.
Noted - slated for 0.7 then. The real fix is to make the
search+refinement do a better job at orienting the new residue, but that
is much harder than adding rotation to a peptide.
Paul.
Murray, Michael (NIH/NIEHS) [F] wrote:
Hello all,
I am thinking about purchasing a Spacenavigator from 3Dconnexion. I vaguely
remember Paul mentioning something about the device in a recent talk but I
can't quite remember the context. I was wondering if it was compatible
and/or useful with Coo
I saw this myself this morning on my Mac. I don't know what the problem
is but I think I can reproduce it.
I'll follow this up.
Paul.
Kay Diederichs wrote:
Hi Bernhard,
when I do that, the contents of the "hollow area" of the window changes
(but the sequence is still not visible). The cha
Kay Diederichs wrote:
when I do that, the contents of the "hollow area" of the window changes
(but the sequence is still not visible). The changed contents appears to
belong to other windows that I sweep across.
Thanks, it was a canvas geometry problem when there was only one chain
(not tes
Our nightly builds summary page and web server is in a state of disrepair.
As a work-around you can still get your binaries here:
http://www.ysbl.york.ac.uk/~emsley/software/binaries/nightlies/pre-release/
Paul.
Kay Diederichs wrote:
Paul Emsley schrieb:
As a work-around you can still get your binaries here:
http://www.ysbl.york.ac.uk/~emsley/software/binaries/nightlies/pre-release/
If this is the work-around, then which is the "real" one?
Seeing as you ask, the new real one is/wi
Alex Theodossis wrote:
Is it possible to change the dot density of the Probe output, when running
it through Coot?
You mean (i) the dot size? No - not yet.
(ii) the dots density? Yes, you can fiddle with arguments to
*probe-command* in the probe function in
Dhirendra K Simanshu wrote:
Hi everyone,
I am trying to refine a structure which contains acetolysine (acetyl
group attached to Lysine residue) in one of the polypeptide. I have
refined acetolysine present in peptide using Refmac after adding the
link information in the ligand cif file. After
Frank von Delft wrote:
Hi, maybe it's fixed in pre-release, but in our version of coot (v0.5.2):
When you load a monomer (e.g. NAP), and coot finds that
"monomer-NAP.pdb" already exists in the working directory, it will
simply load that file, rather than generating a new one.
This is a profoun
Frank von Delft wrote:
H...
What I read when I select from the menu is the menu label, not the
manual. Yes, *now* I know it should take 30 seconds :)
I suggest a little radio-button to select between "re-generate fresh
from library" and "use existing in working dir" or something like tha
Francis E Reyes wrote:
Is there anyway to do this? Sometimes (err I mean a lot of times) I'm
building into a low res map, trying to real space refine or regularize
several residues in a stretch and Coot gets stuck (still iterating but
not moving the atoms on screen anymore). Can I press escape
Ian Tickle wrote:
All - can anyone help me with the syntax of the 'mutate_by_overlap'
scripting command. I need to mutate a CYS to a chemically-modified
entity that I've called CYD. I made a Refmac dictionary entry for this
which I read in & it's accepted. I'm using WinCoot so I understand
Paul Emsley wrote:
Ian Tickle wrote:
All - can anyone help me with the syntax of the 'mutate_by_overlap'
scripting command. I need to mutate a CYS to a chemically-modified
entity that I've called CYD. I made a Refmac dictionary entry for
this which I read in & it
Stephen Graham wrote:
Hi all,
I'd like to add a key binding to toggle the 'Pointer distances' on or
off. I have found the scheme command "(set-show-pointer-distances
istate)" which I can use to turn them on/off, but I couldn't find an
equivalent "(show-pointer-distances)" function to get the cu
William G. Scott wrote:
The latest PyMOL and Coot both work great in stereo. I would go so far
as to say these look as good as they did on my ca. $12K (1999 dollars)
SGI R1s with Sony trinatron monitors [...]
Wow. That's pretty good. You encourage me to fix the naive stereo
"rotation".
Phil Evans wrote:
Is there a way for "Copy NCS residue range" to copy to a subset of
NCS-related chains (eg from B to only, not to A & D)?
No, there is not. I think that it should not be hard to allow the
overriding of the NCS peer chains. I'll consider it for 0.7.
Paul.
Evan Kantrowitz wrote:
Hi All,
I am having problems rotating about the chi angles of an unnatural amino acid that is in
my structure.
Urgh. Chi angles having been undergoing a big rewrite this week...
I have modified the .cif file as indicated below
_chem_comp_tor.period
HCE
Alex Theodossis wrote:
Is it is possible to configure the Probe output in Coot not to display contact
dots between atoms of the same residue?
I don't see how to do that in probe, so I guess not. If you can persuade
the authors/maintainers of probe to create such an option, then Coot
will
Federico Forneris wrote:
Dear Coot-ers,
I have a problem with CONECT records when I save PDB files with coot. I
noticed that coot renumbers the ATOM record in PDB files during save, but
does not in the CONECT section, thus showing weird connectivity on
coot-generated files opened with other visu
Scott Classen wrote:
Hello,
I'm using coot 0.6-pre release 2172
via fink
after selecting a DNA base to edit and selecting the chi angle that I
would like to move I get the following errors when I drag the mouse:
Urgh. Me too. Sorry about that (wretched chi-angle code).
I suspect 0.5.2 is
Coot will only work with Zalman with revision 2134+
Paul.
William Scott wrote:
I should add that I can only confirm that it works post revision 2134
The latest in fink is 2172. I'll make a new intel stand-alone if that
helps.
On Aug 5, 2009, at 11:46 AM, Jürgen Bosch wrote:
My coot is
Francis E Reyes wrote:
Is there a shortcut for this?
No.
I'm looking for something similar to the analysis you obtain after a
real space refine.
There is no pre-refinement analysis (i.e. validation). It would be a
nice thing. It is on the list (with 3D markup).
Paul.
Dear all,
The time is almost upon us for the Old Coot timer to go off in the 0.5
series. When we released 0.5 in Sept last year, I thought that 11
months would be comfortably enough to get 0.6 out. But alas no, there
is no new version available.
I did consider making a fake 0.5.3, and res
[Hmmm... Perhaps the mail filter eat the mail (again) - this time
without attachment]
Dear all,
The time is almost upon us for the Old Coot timer to go off in the 0.5
series. When we released 0.5 in Sept last year, I thought that 11
months would be comfortably enough to get 0.6 out. But al
Teemu Ikonen wrote:
Hi,
I recently compiled Coot-svn (manually) in Ubuntu and was somewhat
annoyed by all the Guile library dependencies which are not available
as distribution packages. [snip]
Teemu and I corresponded off-list. I will try to move Coot toward using
less unconventional packa
Victor Alves wrote:
Hi Developers
I had a pleasant surprise after installing build 2202.
I ALWAYS use side-by-side stereo (cross-eye) and before I had to
revert to mono view before resizing Coot Main window, otherwise it
would block the program. Not anymore!!
I am pleased that thi
Kendall Nettles wrote:
> coot> (ncs-control-change-ncs-master-to-chain 25 D)
Pete Meyer wrote:
I'm not sure of the exact syntax for the ncs commands, but this
backtrace is telling you that it doesn't know about a variable called
D. Unless you've created a variable with the chain id in it (aka
Phil Evans wrote:
some of the links on the (new Oxford) coot page don't work eg the
scripting manual
Oh yes, those ones slipped by. Fixed now. Thanks.
(And I believe that the scripting documentation should be part of the
main user manual now (which is why I made this oversight for the
Don Kerkow wrote:
Hi all,
I keep getting the error below when trying to calculate a map from a
mmcif file. I can convert this file to .mtz in ccp4 and then load
that into coot, which gives a sensible map, but it seems that the CCP4
intermediary step shouldn't be necessary. Any help would be
Wu, Zhongren wrote:
I am using ccp4mg to get nice graphics for presentations. I have no
problems to get movie.gif files for structure rotations. However, when
use animation, I ran into a lot problems. I followed the instructions
closely and get morph files (pdb format) from the yale.edu server
William G. Scott wrote:
The superposition GUI still reliably crashes coot in 64-bit mode for
some reason (independent of ssm vs lsq).
Hi Bill,
Thanks for your help with this.
I think that I have found the problem. It turns out that I had been
mishandling chain-ids selected from option-m
Engin Ozkan wrote:
Hi everybody,
Using the revision 2283 on 10.5, I am seeing this whenever I am
closing the application:
/sw/bin/coot: line 5: 19785 Segmentation fault /sw/bin/coot-real
"$@"
Yep, coot shuts down with a segmentation fault. I haven't tested most
functionality and it h
>> On Sep 11, 2009, at 7:36 AM, Benda, Christian wrote:
>>
>> Dear Bill,
>> Thanks for your quick reply! I installed the new revision but
>> it doesn't seem to make a difference (to my problems). I guess
>> you're right and it's because I am still running 10.4 - think
>> it's time to upgrade to 1
Miguel Ortiz Lombardia wrote:
Dear Paul and Bill,
rev 2310 from fink works properly now on mac (intel) os 10.5.8
Thank you a lot for solving this problem so quickly (and heroically)!
Some issues, then.
When launching coot I get this error:
INFO:: loading preferences file
/Users/mol/.coot-pr
Eleanor Dodson wrote:
The manual suggests the sequence view will be coloured according to
secondary structure, but that doesnt seem to be true for me
Thank you - if it is easy to fix, I'll do it shortly. If not, I'll
schedule it for 0.6.1.
Paul.
Paul Emsley wrote:
Eleanor Dodson wrote:
The manual suggests the sequence view will be coloured according to
secondary structure, but that doesnt seem to be true for me
Thank you - if it is easy to fix, I'll do it shortly. If not, I'll
schedule it for 0.6.1.
It *was* easy.
For the record, one of the 0.6.1 items is to make this (i.e. ability to
user http_proxy) a built-in feature for both versions.
Paul.
p.s. just back from HEC-2009 which was very pleasant and I'd definitely
recommend future meetings (particularly for germanophones) (I've been
out out touch bec
Also, note that the modelling tool-bar can be hidden with
(hide-modelling-toolbar).
Paul.
Abhinav Kumar wrote:
Thanks for the advice.
I had managed to reduce the size by detaching the tool bar as you
suggested. I can try unticking icons to see if this can do the job for me.
Thanks
Abhinav
Ed Pozharski wrote:
Coot consistently crashes when I try to show the sequence of the
pdb-file where some residues are labeled with insertion codes (column 27
of the ATOM record). I tested it on 64-bit Jaunty and 32-bit Hardy.
Perhaps the problem is that there are multiple copies of the same
resi
Bernhard Lohkamp wrote:
You currently cannot create a sphere as such (certainly not
transparent). But you there is some workarounds:
1.) create a generic object and add a dot (although the dot will be a
square esp when larger)
along these lines (well, a sphere of dots):
http://www.biop.o
Francis E Reyes wrote:
Hi all
It seems that adding ncs ghosts and then ncs maps is broken for my
model / coot combo.
Coot is at ver 0.6-pre-1 rev 2334.
The critical issue here is:
> WARNING:: no points to do matching
At which point Coot cannot make a sensible matrix, and gives up graceles
Pierre Aller wrote:
Hi all,
I am using coot 0.6-pre-1 (revision 2334) on mac os X 10.6.1, and I
encountered a problem with the rotamer function. When I clicked on
rotamer and then then on a residue, the graphic window closed
immediately and I have this error message:
*/
/*
*/Click on an ato
vincent Chaptal wrote:
we are refining a low resolution (3A) membrane protein using coot
0.6_pre2228.
In alpha helical regions, coot in doing a very good job but we have more
trouble in loops or kinks in helices.
Typically, in those regions, we just have density for the main chain
carbonyls and
Schubert, Carsten [PRDUS] wrote:
Hi,
On redhat El4 with coot 0.6-2283 (Centos-python-gtk2) the rot-trans
button in the toolbar does not show up.
Indeed.
Toggling the button in the preferences produces the following warning:
*** (coot-real 4220: WARNING **: Widget not found:
model_toolb
Meghan Miller wrote:
Hi,
I recently updated my iMac to 10.6. After updating the OS I installed fink,
which I used to install and compile coot (version 0.6 pre). However, when I
try to do any refinements (i.e. rotamers, mutate and align, etc.) the screen
closes and I get the error message
termin
Bryan Krantz wrote:
Does anyone know of the proper patches to apply to the ia386-libs to
allow Coot to run properly on Debian Lenny AMD64? It appears that the
32bit libraries under ia386 have serious flaws and issues.
I would advise that you build 64 bit binaries yourself. I develop Coot
on
Mark Nance wrote:
Hi Cooters,
I have a pair of disulfide bonds which link two monomers in separate asymmetric units. There is a single monomer in the asymmetric unit, and two monomers come together to form disulfides between Cys 26-Cys45, and Cys45-Cys26.
For the record, you can't refine s
Johan Hattne wrote:
Dear all;
My coot, 0.6-pre-1-revision-2312 running on Gentoo, seems to be leaking
memory when switching the NCS master. Anybody else notice leaks here or
while doing superpositions (which I guess is the underlying cause)?
OK, thanks for the info. Yes, there could well
Ian Tickle wrote:
is there an easy way to turn off the display of the negative contour
level for a difference map after it has been read in?
I found a function 'set_map_is_difference_map()' to effectively turn
on the negative level, but I couldn't see one to turn it off, maybe
something lik
Ben Eisenbraun wrote:
On Fri, Nov 13, 2009 at 10:56:55PM +, Judit Debreczeni wrote:
2009/11/13 Ben Eisenbraun :
I'm trying to add a keyboard shortcut for Rotate/Translate Zone.
Try this:
(add-key-binding "Rotate-Translate Zone" "r" (lambda () (do-rot-trans-setup 1)))
Original Message
Subject:Re: fit RNA/DNA
Date: Sat, 14 Nov 2009 01:59:14 +
From: Paul Emsley
To: ray brown
References:
ray brown wrote:
Is there any way to real space refine RNA/DNA base-pairs while constraining
the W-Crick H-bond distances and
Andreas Förster wrote:
I have a structure with three chains in the asymmetric unit. When I
select "Refine/Improve Ramachandran Plot" from Extensions/All Molecule,
coot does its thing until it reaches the end of the second chain, then
stops with the errors pasted below. ...
Any ideas why t
S. Shunmugasundararaj wrote:
Is it possible to mutate a residue to a non-standard residue in coot?
Yes. Section 5.6.13 of the Coot User Manual. You could have found it by
searching for "mutating to a non-standard residue"
Extensions -> Modelling -> Replace Residue...
Paul.
Schubert, Carsten [PRDUS] wrote:
is there a way to toggle the use of Hydrogens in the mutate and add
terminal residue commands?
No.
Currently coot (2486) does not seem to allow
building of Hydrogens upon changing or adding residues.
Right.
If that is not currently possible, what are
pebbleped...@gmail.com wrote:
Hi all
I am trying to find out if coot can export a map file that in text format.
I have created a difference map from two cns maps and want to export
it also in cns format (can be read in text eidtor). But till now, I
can only save it in xx.map format that in ASCI
pebbleped...@gmail.com wrote:
Hi all
I want to know possible method to get electron density map for ligand only.
The material are 2mFo-DFc map downloaded from EDS server and also
coordinates from PDB.
The electron density map contains protein, water and ligand. I want to
build a electron den
We are please to announce the release of coot-0.6
Source here:
http://www.biop.ox.ac.uk/coot/software/source/releases/coot-0.6.tar.gz
Binaries from here:
http://www.biop.ox.ac.uk/coot/software/binaries/releases/
Paul.
--
Release 0.6
o FEATURE: User-defined clicks [Joel Bard].
o
Dear All,
Our new paper has been accepted and is now "in press". Please (if you
want to cite coot) update your citation.
About -> About -> References
I think that this is particularly important for users of WinCoot and
Coot on Mac OS X, because the paper includes Bernhard Lohkamp and Bill
Ed Pozharski wrote:
In Ubuntu 9.10, coot appears to be fully compatible with compiz when
running on Intel graphics card. So there is no need to disable the
visual effects anymore.
Hoorah! So will we get to see a youtube video of coot running an "all
molecule" script (say), each face of t
Ed Pozharski wrote:
Coot severely slows down the system when I try to generate the density
fit graph using multi-model (NMR-style) pdb file [snip]
Thanks, I'll make a note to investigate this.
Paul.
pebbleped...@gmail.com wrote:
hi all,
I have a question about how does coot mask the electron density map.
I have a ccp4 electron density map file with parameters like this:
Parameters as read from the map file
Origin .. -167 -36 -35
Extent
Maia Cherney wrote:
I suggested some time ago to
include "Go to atom" button in the bar beside Display manager, as this
is one of the most used buttons. Paul liked the idea, but I don't see it
in the new release.
For the record, I should reply to this.
I did consider this option. I thoug
Arnaud Basle wrote:
Is it possible to tell coot to use a proxy server?
No.
Well, yes, strictly, but it won't listen.
Ask again in a few days though.
Paul.
Bernhard Lohkamp wrote:
Is it possible to tell coot to use a proxy server?
No.
Well, yes, strictly, but it won't listen.
Ask again in a few days though.
No.
Well, yes if you have a build with python enabled. The python functions
will pick up the http_proxy properly.
In your ca
Victor Alves wrote:
The thing is I can't find neither a stable 0.6 binary for ubuntu (32
bits) with python AND gtk2,
Not all the target platforms built 0.6 correctly. We are
investigating. I think that the Ubuntu 32-bits build is a virtual
machine in York. It's a bit non-trivial to debug
Sara Zueger wrote:
Hi everybody,
Hi Sara,
as I did not find a final solution to the hydrogen restraints problem
(flying or exploding during real space refinement) in any of the mailing
lists, I wanted to pick this topic up again.
If one adds hydrogens by phenix.ready_set or reduce the lab
Phil Evans wrote:
How does the Extensions->Dock sequence command work?
I've got a polyAla model, so I open the dialog, import a sequence file, click the "Sequence
closest fragment" or "Sequence all fragments!"
Then I get in the terminal window something like
Sequence: ??QKDIGVKPEFSFN??
Confid
Ben Eisenbraun wrote:
Hi Cooters,
I have a user running Coot from the official binaries (coot-0.6-pre-1-
revision-2486-binary-Linux-i386-centos-4-python-gtk2) on Red Hat Linux 4.6.
Using Gnome Terminal, when coot runs, the shell output is garbled. It
looks like this:
(⎽␊├-⎽≤└└␊├⎼≤-␌⎺┌⎺┤⎼ 0.1
Or to put it slightly differently: the masking of symmetry-related
density works (only) when the cell and symmetry of the map is the same
as the cell and symmetry of the atoms for the mask.
Paul.
Bernhard Lohkamp wrote:
Hi,
you dont say how you obtained you map. Usually in Coot, thanks to
wtempel wrote:
Hi all,
judging from what I see being used by my colleagues, COOT is well on
its way to world domination.
Like Linux (haha).
Anyway, suppose I have "split" a residue, say lysyl, to model
alternate conformations of its side chain. Suppose further that I
would like to remove
det...@uoxray.uoregon.edu wrote:
Paul Emsley wrote:
wtempel wrote:
Anyway, suppose I have "split" a residue, say lysyl, to model
alternate conformations of its side chain. Suppose further that I
would like to remove NZ from conformer B. Upon doing so, the current
COOT impl
Ed Pozharski wrote:
I have a reproducible crash when using SSM on a particular structure.
It has 4 chains and coot crashes only if I try to SSM chain B on top of
chain A (but not A on top of B or any other chain on top of A).
What's the general procedure to report such bugs - do I turn on core
d
Anonymous wrote:
> We have the following system and have found that Coot (0.5.2 and 0.6) runs
> very slowly:
>
> -Dual Xeons @ 3 GHz
> -4 GB RAM
> -nVidia 256 MB Quadro FX 3450/4000 SDI
> - >250 GB hard drive space
> -Red Hat Enterprise Linux WS release 4 (Nahant Update 7)
>
How does g
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