Hello Teresa,
I need to disagree with Graeme over the idea that ccp4i 'hides' what is
happening. If you care to you can see all the gorey details of command files,
log files etc.. You can run the programs one step at a time and with various
modes with ccp4i and iMosflm and learn something of
Norbert,
Sorry for this late reply. SSM will find multiple alternative matches
but most implementations just show you the 'best'. The Superposition
tool in CCP4mg uses ssm and has an option to look through the non-
optimal matches - hopefully one of these will be the one that you want.
L
Miri,
For matching similar small molecules you can try in CCP4mg as
described at
http://www.ysbl.york.ac.uk/~ccp4mg/ccp4mg_help/superpose.html#interactive_selection
the 'user defined' superposition option with 'monomer' mode. This
does 2D graph isomorphism for the atoms in one residue.
Hi Mattias,
CCP4mg will list contact areas in the form of the attached file.
This is evaluating the buried area (ie difference is solvent accessible area
with and without the ligand bound).
It ought to be possible to run a script if you have a significant number of
structures - contact me for
Hello Manfred and CCP4bb,
Funny, you are not the only person trying to something like this, so I have a
CCP4mg script (attached) which does the job. You do need a recent version of
ccp4mg for it to work - contact me for details.
Liz
On Thursday 08 March 2007 15:33, Manfred S. Weiss wrote:
>
Dear CCP4bb,
The intention with CCP4i GUIs is that those folders which are open by
default (after you have chosen the mode of action from the top protocol
folder) are for everyone and those that are closed by default are for
experts OR difficult cases. Unfortunately that is an OR not an AND; t
Tim & Yanming,
Our first suggestion is to try the latest version (1.0) - a few startup
issues were fixed between the two versions.
Normally I would encourage you to use the python version distributed
with ccp4mg. The C++/Python interface was built against a particular
version of Python and pro
Sebastiano,
I can suggests one approach to finding core residues..
CCP4mg will calculate the total asa buried per residue and residues can be
selected by the criteria of their buried area. One way to define the protein
core would be to select residues with, say, <5.0A*2 asa. You can easily se
Hello David,
In CCP4mg you can display any arbitrary vector in a variety of display styles
- there is an example in the the online documentation:
http://www.ysbl.york.ac.uk/~ccp4mg/ccp4mg_help/vector.html
Liz
On Tuesday 18 September 2007 10:00, David Briggs wrote:
> Good morning ccp4bb-ers!
>
James,
CCP4mg will allow you select a set of atoms and draw a surface over them
in whatever colour scheme that you choose.
The tutorial explaining this is at
http://www.ysbl.york.ac.uk/~ccp4mg/ccp4mg_help/tutorial/surfaces.html
Cheers
Liz
James Thompson wrote:
Dear CCP4'ers,
Any Window
Hi Anders and CCP4bb
Would something like
http://www.ysbl.york.ac.uk/~ccp4mg/index_info_5.html
(done with CCP4mg) be useful? In that image the molecule surface is coloured
by electrostatics (but could be any other property) and the contact area to a
ligand is indicated by dots on the surface.
Jan,
CCP4mg uses the same MTZ->map code as COOT - one thing that will make a
difference in time is the resolution of the map.
Overwise I'm not sure that ther is much that you can do - on the other
hand the developers are busy converting CCP4mg to use Qt rather than
Tcl/Tk for the GUI and this h
Dear CCP4BB,
For further research of a particular structure wouldn't hints on
expressing, purifying and crystalizing the protein often be more
useful than images or amplitudes?
Liz
On 18 Mar 2009, at 17:00, Ethan Merritt wrote:
On Wednesday 18 March 2009 09:41:59 Garib Murshudov wrote:
Miguel,
CCP4 are intending a major project on the ccp4i database and one of
the requirements will certainly be enabling multi-user access to
databases. I'm sure we will be looking for your input on other
requirements when we have someone in post.
Liz
On 22 Mar 2009, at 08:11, Miguel Orti
Hi Oliv,
I'm sorry, I think you will need to edit the output file from Sketcher
_mon_lib.cif - the torsions section ( _chem_comp_tor) will have
something like
test CONST_1 C1 C2 C3 C4 180.0 0.0 0
the 180 needs changing to 0.0.
I think that is all you need to do - no doubt someone
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