Run it for more cycles. Doesn't take long to drift far enough for it to
not find its way back when you turn x-ray back on.
This isn't just a problem in refmac, or phenix, or x-plor, or even MD
programs like AMBER. The problem is that in order to make a structure
fit into density you have to distort the geometry. Turn the geometry
weight up too high and your R factors blow up. Turn the X-ray weight up
too high and you get badly distorted geometry. I think we've all
experienced that?
-James Holton
MAD Scientist
On 12/3/2020 8:29 PM, Jon Cooper wrote:
Hello James, that's really strange - I've used refmac et al., to do
poor man's energy minimizations of models and they've generally come
out fine, unless the restraints, etc, are wildly off-target. I wasn't
playing with X-ray weights though, since there never was a dataset, of
course.
Cheers, Jon.C.
Sent from ProtonMail mobile
-------- Original Message --------
On 4 Dec 2020, 01:34, James Holton < jmhol...@lbl.gov> wrote:
It is a major leap forward for structure prediction for sure. A
hearty congratulations to all those teams over all those years.
The part I don't understand is the accuracy. If we understand
what holds molecules together so well, then why is it that when I
refine an X-ray structure and turn the X-ray weight term down to
zero ... the molecule blows up in my face?
-James Holton
MAD Scientist
On 12/3/2020 3:17 AM, Isabel Garcia-Saez wrote:
Dear all,
Just commenting that after the stunning performance of AlphaFold
that uses AI from Google maybe some of us we could dedicate
ourselves to the noble art of gardening, baking, doing Chinese
Calligraphy, enjoying the clouds pass or everything together
(just in case I have already prepared my subscription to Netflix).
https://www.nature.com/articles/d41586-020-03348-4
<https://www.nature.com/articles/d41586-020-03348-4>
Well, I suppose that we still have the structures of complexes
(at the moment). I am wondering how the labs will have access to
this technology in the future (would it be for free coming from
the company DeepMind - Google?). It seems that they have already
published some code. Well, exciting times.
Cheers,
Isabel
Isabel Garcia-SaezPhD
Institut de Biologie Structurale
Viral Infection and Cancer Group (VIC)-Cell Division Team
71, Avenue des Martyrs
CS 10090
38044 Grenoble Cedex 9
France
Tel.: 00 33 (0) 457 42 86 15
e-mail: isabel.gar...@ibs.fr <mailto:isabel.gar...@ibs.fr>
FAX: 00 33 (0) 476 50 18 90
http://www.ibs.fr/
------------------------------------------------------------------------
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1>
------------------------------------------------------------------------
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1>
------------------------------------------------------------------------
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1>
########################################################################
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list
hosted by www.jiscmail.ac.uk, terms & conditions are available at
https://www.jiscmail.ac.uk/policyandsecurity/
