Seth Harris wrote:
Actually I do have a map button.
Hmm... I see.
But I'd rather write something in a script somewhere once than click
the button and confirm the click EVERY time I start the program!
OK, I'm not understanding you then. If you start from fresh and you
read in more than
Ed Pozharski wrote:
1. This does not include autobuilder bugs, right?
sigh yes, I do mean autobuilder bugs too - as long as it's not about SuSe.
2. What is the bug reporting procedure - just email the list?
Yes - or me, or coot-dev at ysbl dot york dot ac dot uk if you wish.
Craig Smith wrote:
Hey gang,
Hey indeed. Buenos días, in fact.
I have an ethylene glycol that I trying to build into my structure. I
used File - Get monomer and entered EDO and deleted the hydrogens. I
can move EDO into density using rotate/translate zone but I'm having
problems
Andreas Förster wrote:
Hey cooters,
I'm trying to replace my current coot (centos4 binary, version 0.6,
revision 2540 with guile 1.8.7 and python 3.6.0 embedded) with a more
recent binary. The OS is RHEL 5.2 to 5.4, 32-bit.
I download version 0.6.2, revision 2939, python, unpack but can't
Christian Benda wrote:
Hi,
we have a recurring problem with our coot installations (coot version 0.6.1rev
2740 on Mac OS X 10.6.3).
For some users when they start coot, they get a list of error messages in the terminal (see below) and structures are displayed without most of the bonds drawn
Jan Dohnalek wrote:
I have noticed that Coot puts me in irrelevant places when I use the
Unmodeled blobs validation. It does its job but then the list of blobs
sends me to perfectly interpreted places and I cannot see any
uninterpreted blobs...
I don't know why this should be, I have not
Francis E Reyes wrote:
What kind of maps are produced in coot when refmac is run from within
it? Sigma-weighted 2fo-fc's ?
SigmaA, yes, Standard refmac maps: 2mFo-DFc, mFo-DFc.
Ed Pozharski wrote:
It appears that when loading model/map from command line (via --pdb and
--auto options) coot ignores the parameters defined in $HOME/.coot .
Mine has the (set-map-sampling-rate 2.5) setting for smoother maps, but
when I use the command line to load pdb/mtz files, the maps
Jan Abendroth wrote:
since a few versions, the linux distribution of coot seems to have
lost the handy rotate/translate button in the toolbar on the right
side of the main window. It is not an option under preferences
either. However, it is still around in the osx version from Bill.
Are there
SIPPEL,KATHERINE H wrote:
Hi all,
I am running Coot 0.6.2-pre-1(revision 2816). The OS is Open Suse
11.1. Every time I try to open a SHELX refined pdb file with
ANISOU cards I get this error
ERROR 14 READ: Unmatch in different records for the same atom
Then it lists the line number of the
SIPPEL,KATHERINE H wrote:
Thanks for all of the replies. It turns out with the updated COOT
that ANISOU cards require an element type (column 77-78).
For the record, it is not fundamentally the update of Coot that has
changed things, it's that recent versions of Coot use recent versions of
Dear Dirk,
Dirk Kostrewa wrote:
another point for your wish-list: when I add a terminal residue, an
alanine is added that I have to mutate into the proper amino acid type
in a second step. I would find it very useful, if a popup-window would
ask me, which amino acid type I want to add. This
Maia Cherney wrote:
Hi Paul,
the format of the file got screwed. I am resending the file in the
attachment.
I would like to repeat the description of the problem.
There is a difference in recording of water molecules in coot and in
phenix. The example is given in the attached pdb file.
Dear Eleanor,
Eleanor Dodson wrote:
When converting from CA to Main chain it would be wonderful to just have
to select a CHAIN - not click on the first and last residues..
In that I cant think of any time when you would want to only convert a
limited span of residues..
On reflection, I
Alice Dawson wrote:
I'm running Coot 0.6.1 on a Mac (running 10.5.8), installed via Fink.
I'm running some Shelx refinements. When I try to save the coordinates
(as a .ins, from a .res that I read in) I get this error
(first-coords-imol)
(first-unsaved-coords-imol)
INFO:: Setting
Garib Murshudov wrote:
Just for info:
There is new version of the dictionary that is compliant with pdb v3.
It works with new version of refmac and should work with phenix also.
It seemed to work with coot also.
Eleanor Dodson wrote:
This seems to be lost ??
/y/programs/xtal/coot/coot-Linux-i386-fedora-10-gtk2-python/share/coot/python
reads pdb and says:
...
INFO:: NCS chain comparison 306/307
INFO:: NCS chain comparison 304/307
INFO:: NCS chain comparison 306/307
INFO:: NCS chain comparison
Sebastiano Pasqualato wrote:
Hi Paul, hi all,
besides for the principal task of building molecules, I like using coot for
studying structures.
I would however be very happy to give a given chain a determined color, rather
than having colors attributed by the program.
Well, you (only)
Kay Diederichs wrote:
I was under the expression that coot automatically calculates an anom
diff map when the DANO label is used.
Depends what you mean by automatic, but I would say not. Open MTZ,
use the Expert button, that will enable anomalous labels (as I suspect
that you know).
subh wrote:
Hi,
I am trying to open my phased mtz file in coot to see the anomalous
difference map.But it does not open when I choose Open mtz, .cif etc.
While I can open the map by choosing auto open .MTZ it doesnot give me the
choice to select the maps that I want to see.
I knew that if I
Norman Zhu wrote:
This email is a continuation of an inquiry I post last week. The
problem I had and still is i can't use the real space refine
zone and regularization zone functions on a DNA structure. Whenever i
ask the computer to fit the bases into the electron density it would
Miguel Ortiz Lombardia wrote:
Le 4 févr. 2010 à 04:37, Norman Zhu a écrit :
hello there
I am in the process of refining a protein structure complexed to DNA
promoter site. I ran into difficulty as i try to move a few bases into
patch of electron density that is obviously meant for
Marko Hyvonen wrote:
(transform-map-using-lsq-matrix 1 A 1 200 0 A 1 200 2 (molecule-centre
1) 10)
All seems to go fine, except that the map matches correctly only part of
the transformed molecule, and it looks like when the map is extended by
symmetry, things fail
Yes, the
david lawson (JIC) wrote:
Dear All,
I would like to set up a key binding to delete the water molecule I’m
centred on, but I can’t get the guile syntax right. Can anybody help?
A good question for bioklatch, http://www.bioklatch.com/ IMHO. I'll
answer it there too, if someone asks
Hi Martin,
Martin Moche wrote:
Dear Coot Users,
I am trying to run, coot-0.6.1-binary-Linux-i386-fedora-4-gtk2, at my
Fedora10 Linux machine...
Eeek - Stop right there! The correct solution is to use the Fedora 10
binary.
... which seems not to to be in place yet...
OK, it is now,
Goodness, sounds like fun.
Coot does have an alignmutate function of course, but you don't get to
fiddle with the sequence alignment - Coot uses its own alignment [1].
My understanding is that should be fine for ~70% sequence identity or
better. My feeling though is that it is not widely
Kevin Cowtan wrote:
Ezra Peisach wrote:
I move that the names in the scheme scripts be changed to the american
names and that a new script British.scm be put in place.
Well, that's just crazy talk. The scripting interface should clearly use
the established language of science, which
We are pleased to announce the release of Coot-0.6.1
Source code:
http://www.biop.ox.ac.uk/coot/software/source/releases/coot-0.6.1.tar.gz
Binaries
http://www.biop.ox.ac.uk/coot/software/binaries/releases/
(the building on additional platforms is underway):
Paul
--
Release 0.6.1
o
Victor Alves wrote:
About Auto-save.
I tried it, after modifying the PDB model I was working on, but
apparently this didn't save those changes to my current opened PDB
file. It just writes a coot.state.scm file.
Am I right?
Well, I can't say that you're wrong, but for me, modified
Dear Andrew,
Having worked with O for many years I am only now getting
serious with COOT. There are a couple of things that I would
like to do that don't seem to be available (as far as I can
tell), but which may well be possible using Macros.
Unfortunately a quick
Miguel Ortiz Lombardia wrote:
Dear all,
Is there a way to ask Coot to write pdb coordinate files with nucleic acid
residue names in 'standard' PDB format? That is: DA, DC, DG, DT, A, C, G, T...
No. It's on the list. I will use the PDB-approved nomenclature.
Sorry, this may have been
Antony Oliver wrote:
I'm using Coot on OS X - so I don't know whether this is a 'feature' of this
version (fink built) - but the dialog boxes, particularly the save dialog,
always appear behind the main window. It is possible to change this
behaviour, so that it appears in front?
Apple
Lei Jin wrote:
I have two questions here:
1. Where is the COOT for MAC OSX? I just could not find it,
although I could find COOT for Windows and Linux at
http://www.biop.ox.ac.uk/coot/software/binaries/releases/
See the FAQ:
Katarina M wrote:
Hi all,
I am running coot version 0.6 pre on Mac OS X 10.5.8. Everything was working fine upon
installation for couple of months and all of the sudden after trying to real space refine a
residue funny looking dots would appear around it (as is shown in the attached
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
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??
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
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
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.
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
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
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].
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
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
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
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.
Ben Eisenbraun wrote:
On Fri, Nov 13, 2009 at 10:56:55PM +, Judit Debreczeni wrote:
2009/11/13 Ben Eisenbraun b...@crystal.harvard.edu:
I'm trying to add a keyboard shortcut for Rotate/Translate Zone.
Try this:
(add-key-binding Rotate-Translate Zone r (lambda ()
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
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
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
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
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):
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. Rev 2339
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
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 10.6, finally!
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
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
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
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
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.
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
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
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.
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
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
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
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
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/will be here
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
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
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
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.
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
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
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.
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
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.
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
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 $@
I
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.
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
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
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
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
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
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
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
Dear Maia,
Maia Cherney wrote:
I would like to use only one-button keys, so that I could use only
one hand when fitting.
Why!? Because the other one is needed to prop up your head, maybe? :-)
http://linuxoutlaws.com/files/dan-jaunty-party-thumb.jpg
I find using my left hand for
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
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
Ed Pozharski wrote:
After recent upgrade to Ubuntu 9.04, coot binaries that worked fine
before started reporting the ELFCLASS64 error when loading a
particular library, namely /usr/lib/libguile-srfi-srfi-1-v-3.so.3.
I understand that the real root of this problem is my bizarre obsession
with
hari jayaram wrote:
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
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Dear Eleanor,
Eleanor Dodson wrote:
1) The check on GLN and ASN and HIS? for likely hydrogen bonding is very
useful. Do you think it would be worth extending this to THR?
HIS is not part of the ASN/GLN check. And indeed the ASN/GLN check
works by B-factor analysis, not hydrogen bonding.
From: Christian Roth christian.r...@bbz.uni-leipzig.de
Hi all,
I am not sure but If I remember correctly Bernhard mentioned on the
last CCP4
study weekend in Nottingham that Coot is able to merge the
different water
chains, generated through repeated refinement runs, in one. If this
Maia Cherney wrote:
The general torsion function is not as good as the torsion in old X-fit.
Are you or have you ever been a member of the von Delft Pressure Group?
In x-fit you click on two atoms of a single bond and you can rotate the
rest of the molecule around that bond. This bond can
CK wrote:
I think perhaps I should clarify what I've been doing. I've been
refining my structure using phenix.refine and had reached a fairly
satisfactory point with suitably low R-factors (21/25) and very
reasonable RMSDs for bonds and angles. At this point I ran my structure
through the
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