Hi All
Thank You very much for the response and suggestions.
I have used Robetta and ITASSER for structure prediction followed by
truncating the part according to the rmserror or loop region. However, I
was not able to go anywhere after a certain point. R-free is stuck at 40.
Even the loop region
Yes, I should have mentioned the truncation by estimated RMS error, which was
part of the protocol we used in the paper with David Baker’s group. The error
estimates are calibrated, I believe, for just the C-alpha atoms, so they are
probably generally underestimates of the errors in the rest of
I agree that RoseTTAFold would be a good idea! We've been looking at the models
for MR recently and in many cases they're excellent. We've found it can be
useful to truncate the models based on the predicted rms errors with AMPLE
(clearer solutions or even the difference between success & failur
That paper is jaw-dropping...
On 03/07/2021 10:33, Randy John Read wrote:
If there isn’t already a suitable model, this looks like a good opportunity to try
out the powerful new RoseTTAFold deep learning algorithm by Minkyung Baek in David
Baker’s lab. It can be used through the Robetta serv
If there isn’t already a suitable model, this looks like a good opportunity to
try out the powerful new RoseTTAFold deep learning algorithm by Minkyung Baek
in David Baker’s lab. It can be used through the Robetta server
(http://robetta.bakerlab.org, choose Structure Prediction->Submit and then
Dear Jan,
for some reason the ccp4 update manager will not pick our libraries if they
are not included in your installation from the start. The same libraries
can be downloaded directly from our web page:
http://chango.ibmb.csic.es/download
and then the interface lets you input a path to any custo
Dear Daniel,
All three Arcimboldo programs run only on Linux or Mac machines, so it is
not a problem with shelxe. We should change the appearance on the windows
interface and give a more sensible error message. Thanks for pointing it
out.
Best,
Claudia
El 8 jul. 2017 23:40, "Bonsor, Daniel" es
Dear All,
Does Arcimboldo actually run on WIndows as I can see it is installed and so is
ShelxE, but I have a warning in the GUI saying "ShelxE is not found and option
to run on 'this machine' is disabled. Is this a bug, do I need alter something
so get it to recognize ShelxE or it does not ru
.
Many thanks,
Sebastian
-Original Message-
From: clmil...@gmail.com on behalf of Claudia Millán Nebot
Sent: Tue 7/30/2013 4:24 PM
To: Kraatz Sebastian
Subject: Re: [ccp4bb] ARCIMBOLDO
Hi Sebastian,
we have to hold the new ARCIMBOLDO release until publication, the paper is
in press and
Dear Sebastian,
our new release, planned around the ECM in Warwick, runs on a single
workstation having access to a local or remote grid, supporting either
condor or SGE/Opengrid.
Coiled coils should be particularly suitable and we have solved a number of
them, including twinned structures. Depen
Dear,
Because this can certainly be of interest to other crystallographers,
I would like to post the following positive comment:
The recently developed software ARCIMBOLDO: Crystallographic Ab
Initio protein solution far below atomic resolution,
(Rodriguez et al., Nature Methods, 6, 651, 2
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