Postdoctoral position in computational structural biology
Dept. of Medical Biochemistry and Biophysics, Karolinska Institutet
A postdoctoral position is available immediately in the Molecular
Structural Biology group at the Karolinska Institutet in Stockholm
(http://phillips.mbb.ki.se/). The
Hi Nicolas,
several possibilities are available for you:
- use rigid_bod_refine_zone
(http://www.biop.ox.ac.uk/coot/doc/coot/rigid_002dbody_002drefine_002dzone.html#rigid_002dbody_002drefine_002dzone)
- use rigid_body_refine_by_atom_selection (see e.g.
In Coot:
Centre on the atom/place of interest.
Extensions-Modelling-New Molecule by Sphere
then select the molecule and sphere radius.
B
I would like to specify a target atom in a pdb file and then isolate all atoms
within a given distance of the target. The selected atoms are then to be
Of course (sort of):
Extensions-Maps-Export Local Map Fragment
B
This is nice. Can it do the same for the map?
Thanks
Jim Brannigan
On 18 November 2012 15:52, Bernhard C. Lohkamp bernh...@chem.gla.ac.ukwrote:
In Coot:
Centre on the atom/place of interest.
Extensions-Modelling-New
d if you do so, be sure to tell us which versions of refmac and coot
you are using
I use Win Coot-0.7-pre-1 (version 4039), and Refmac5 from CCP4i.
It seems you are using an 'old' CCP4 (you dont specify the version,
6.1.3?) with an old(er) dictionary. WinCoot currently uses its own (up
Dear Ros,
I believe I have fixed this in the newer versions. So please update to
the latest pre-release
(http://www.ysbl.york.ac.uk/~lohkamp/coot/wincoot_newest_download.php)
and it should work fine. If the problem persists please let me know.
B
Dear All:
I am having trouble with Coot.
Dear Raj,
please follow exactly what is written in the FAQ
http://www.ysbl.york.ac.uk/~lohkamp/coot/wincoot-faq.html#mozTocId860510. I
just updated it slightly to hopefully make things even clearer (*). You
seem to be mixing different possible setups. Either you move the files
to WinCoot\bin
You can try the scripts
user-define-restraints.scm/user_defined_restraints.py which allow you to
specify restraints. These are not available in the distribution (yet)
but from google code:
http://code.google.com/p/coot/source/browse/trunk/scheme/user-define-restraints.scm
Adding to Tim's comment. In Coot use:
Extensions-Modelling-Arrange Waters Around Protein...
B
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Hash: SHA1
Hi Jacob,
to semi-answer your question: coot runs under windows, as far as I know,
but it may not be in the gui.
Tim
On 10/19/2011 08:41 PM, Jacob
Coot:
Extension - Modelling - Residues with Missing Atoms...
Or watch out for the blue bars in the rotamer validation graph in Coot.
B
Dear all,
Does anyone know a program that will check a PDB file for missing
atoms and output a list of the corresponding residues?
Many thanks in
Eric,
That IS the way to do it. Please make sure you have the dictionaries in
the path and check your coot startup script in case it sets
COOT_REFMAC_LIB_DIR back to nothing (and hence falls back to the ccp4
one). Do you get any message in your start up console? BTW which
version of Coot
Thank you for the comment. You are correct that there are being backups
made in the newer interruptable fit function (they were't previously in
the uninterruptable fitting). I wasnt thinking about that (*). This may
(especially on windows) slow down things a great deal as we write and
gzip these
Dear all,
I found the step refine speed of wincoot is much slower than that of linux
coot (with the same pc). Is it normal or I need to configure something with
the wincoot?
There are a number of things that might explain this, for example
1) You linux system is intrinsically faster
Section 4.4 Atom Colouring
http://lmb.bioch.ox.ac.uk/coot/doc/coot/Atom-Colouring.html
i.e.
add to your ~/.coot file
|
(set-colour-map-rotation-on-read-pdb-c-only-flag 1)|
Or use the preferences (only in newer pre-release versions):
Edit-Preferences-Bonds-Bond Colours
tick the box:
Hi Seema,
for python scripting in Coot (and syntax) you may want to refer to the
WIKI:
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot#Python_Scripts
or the manual:
http://www.biop.ox.ac.uk/coot/doc/user-manual.html#Scripting
I meant to complete a more comprehensive
I recently got the 24 inch Zalman and when the coot window is
maximized the 3D is reversed. I know I can minimize it slightly and
move it up and down a pixel to fix it. Has anyone found a trick to
leave it maximized and correct the 3D. I have tried adjusting screen
position but have not
Wasnt there recently a similar discussion(?):
http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg16099.html
Maybe try JLigand (www.ysbl.york.ac.uk/mxstat/)
B
Hi all,
I need to create a cif file for a new ligand that does not exist in
the pdb, so far. Normally refmac created such a cif
Hi Tim,
I cannot comment on the installation/hardware problems. But I can give
you a hint on how to 'invert polarisation': Switch the stereo sides. In
pythonic Coot use:
switch_stereo_sides()
For convenience a while back I made a 'zalman stereo toggle' toolbutton
together with a 'switch
Hello Rongjin Guan,
your problem most likely comes from different pdb version formats. The
files which work are probably pre pdb v. 3.0. Although (Win)Coot is
mainly v. 3 compliant here we are not (really (*)). A fix (at least for
the files which are not working) may be to change two lines
Hi Francois,
your mtz file doesnt appear to have any phases, so Coot (or whoever)
cannot make a map. What Coot cleverly tries to do in such a case is to
use calculated phases from the given pdb (and mtz) file. So it runs
refmac with the pdb and mtz to retrieve this phase information. There is
I am wondering , do we need uninstall the previous version of coot to
install this?
No. Many group use more than one version of Coot.
Ah, but perhaps you mean WinCoot? My (limited) experience is that you
can install right over the top of the old one.
WinCoot can be installed on top of
In agreement with the previous posts and to avoid any confusion with
respect to Coot. Here is a previous post about this issue:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0901L=CCP4BBP=R94235
Bernhard
Dear All,
I see that the UK is catching up and the NVIDIA Geforce 3D Vision Bundle
*Postdoctoral position in structural biology of protein complexes in
nerve development and disease*
Dept. of Medical Biochemistry and Biophysics, Karolinska Institute
A postdoctoral position is available immediately in the Molecular
Structural Biology group at the Karolinska Institute in
Dear Geoffrey,
it seems you read the manual
(http://www.ysbl.york.ac.uk/~emsley/coot/doc/chapters/user-manual_5.html#SEC137),
but you didnt replace the imol and master-chain-id with a value. You
want to specify the molecule (imol, e.g. 0) and the chain from which to
copy to others (e.g. A),
If we are buying a system from scratch, can I get the GeForce 2 card
and 3D bundle and have it work for winCoot?
I very much doubt it. If I understand it correctly this systems only
works with DirectX applications. Since (Win)Coot uses OpenGL rather than
DirectX it is unlikely to work
You can use Coot to find the centre of mass. In the scripting window just
type:
in scheme:
(centre-of-mass yourmoleculenumber)
or in python:
centre_of_mass(yourmoleculenumber)
Bernhard
BTW the American spelling of centre (center) should work too...
Dear all,
I was trying to do a NCS
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