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 server
(http://robetta.bakerlab.org, choose Structure Prediction->Submit and then
choose the RoseTTAFold option). It’s already been used to solve a number of
unsolved structures, including the ones discussed in a paper on the algorithm
(https://www.biorxiv.org/content/10.1101/2021.06.14.448402v1) and others I’ve
heard of through the grapevine.
Best wishes,
Randy
On 2 Jul 2021, at 12:52, Eleanor Dodson
<[email protected]> wrote:
Yes - nothing very significant in the self rotation list of peaks..
Is the resolution really 2.6A though - if so it will be very difficult to find
a single helix which would be quite a small fraction of 70x2 residues Iwould
think..
Is there no suitable model?
Eleabor
On Fri, 2 Jul 2021 at 12:45, leo john <[email protected]> wrote:
Thank you all.
I have tried both space groups. I am attaching the required file.
Cheers
John
On Fri, Jul 2, 2021 at 12:40 PM Eleanor Dodson <[email protected]>
wrote:
I presume you have tested both P41 and P43 space groups?
It is a bit hard to check peak heights in the self rotation. Could you attach
the molrep output - I think it is called xxxmolrep.doc.txt in the
job directory..
Eleanor
On Fri, 2 Jul 2021 at 12:33, leo john <[email protected]> wrote:
Hi Group;
I have collected data at approximately 2 Ang and automated softwares at Diamond
have processed it in spacegroup P41.
My peptide is 70 residues long with 3 helices of minimum 17 residues in it.
According to Mat. Coeff. there are 2 molecules. I am also attaching the
self-rotation function output map (please give some opinion on it also i.e
number of molecules, symmetry).
Since the molecule has mainly alpha-helices, I am trying to use Arcimboldo but
with no luck.
I have used both the coiled-coil mode and normal mode for it and maximum value
of CC after 5 cycles I get is closed to 20 that is not great for a solution.
Even upon looking the structure solution by Arcimboldo, I found a lot of loops
and I do not get any density for sidechains. A few of the parts of the helices
and loops are overlapping.
I have used CCPi2 with the following options:
The assymmetric unit contains 1 molecule of mol wt 7300
search for 3 helices of length 14 residues
Any help will be appreciated.
<image.png>
Thank you
John
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-----
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research Tel: +44 1223 336500
The Keith Peters Building Fax: +44 1223 336827
Hills Road E-mail:
[email protected]
Cambridge CB2 0XY, U.K.
www-structmed.cimr.cam.ac.uk
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