Hi all,
Can anyone recommend software to dock previously solved domains into a (very)
low-resolution experimentally phased map?
I am working on a rather marginal case where this would be useful - very large
assembly (500kDA per ASU), native goes to 6.9A, and the best derivative goes to
8A
Many thanks for all the replies - I haven't yet tried all of them, but they all
look worth following up on, much food for thought here:
* Several people suggested SITUS COLORES, which I shall certainly try and had
not heard of until now.
* The program ESSENS, from the Uppsala software factory,
Hi all,
I have recently been trying to use the LIDIA ligand-viewer of Coot, which calls
cprodrg.
I am running CCP4 6.4.0 with all the latest updates on a Macbook Air (mid-2012
model) with OS X 10.9 installed and the latest nightly build of coot (r4833).
Unfortunately, when I run cprodrg
I had exactly the same thing happen this year to a 2008 macbook pro. Computer
still worked while attached to power but unsurprisingly the battery did not
work after that.
On Nov 18, 2012, at 7:00 PM, CCP4BB automatic digest system
lists...@jiscmail.ac.uk wrote:
There are 8 messages totaling
or denaturation. Does anyone have any
experience with reductive methylation of disulfided proteins, or know
of any references describing the same?
Thanks in advance,
Oliver Clarke.
__
The information in this email is confidential
Dear all,
Apologies for the non-CCP4 related post, but does anyone know where the HOLE
program for mapping the conduction pathways of ion channels may be obtained
from these days? Preferably in a form that may be run on Mac or Linux systems.
It no longer appears to be available from the Sansom
Dear Bing,
My best guess is that these are artefacts due to the increased noise level at
special positions (in your case a sixfold increase - see for example:
http://scripts.iucr.org/cgi-bin/paper?S0365110X66000264).
I agree with your assessment that it is best to leave such peaks unmodelled
Dear Amit,
I am not aware of an easy way to do this using Coot.
However, if you run the Comprehensive validation tool in Phenix, it will
generate a similar real-space correlation plot automatically, and the raw data
for that plot can be exported (there is an option to save results to file).
Thanks Nat, this is exactly what I was looking for and it makes perfect sense!
To make this more convenient when one has many unidentified densities of
varying lengths, I've written a little extension for Coot that generates a new
UNL residue with a specified number of carbons, makes restraints
My apologies - there was an error in that script, I forgot to delete prodrg
droppings - this one is better:
menu=coot_menubar_menu(Custom)
def make_alkyl_chain():
def make_alkyl_chain_length_n(n):
smiles_string=int(n)*c
new_molecule_by_smiles_string(smiles_string,smiles_string)
Dear Isa,
Do you have any cysteines? I assume so given you mention class B metals... If
so, and you have a ready supply of relatively isomorphous crystals, I would
consider giving native SAD a go, collecting datasets from 5-10 (or however many
you need) datasets at a reasonably low energy (say
and/or submit an abstract for a poster/short talk:
https://www.comppaa.org/comppaa-symposium-2018
See below for a list of invited speakers with provisional titles - I think the
meeting is shaping up very nicely, and we’d all love to see you there!
Cheers,
Oliver Clarke
Radu Aricescu: Human GABAA receptor
Hi all,
The deadline to register for the COMPPÅ symposium (covering production,
structure determination, functional analysis and engineering of membrane
proteins) is coming up in less than a month!
Take a look at the attached flyer for confirmed speakers - I think it’s a
pretty top notch
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