On 31/07/2020 20:33, James Holton wrote:
But, if you real really want to do real real-space, then I suppose
coot is doing that? I'm actually not sure.
If by "real-space refinement" you mean the same thing as described by
Bob Diamond [1], then no, the sum of the squared difference
Dear Thierry,
- Le 31 Juil 20, à 21:58, Fischmann, Thierry
<22f7fda0a875-dmarc-requ...@jiscmail.ac.uk> a écrit :
> Jim wrote:
> “ technically, not in Phenix either. The real-space refinement in Phenix
> simply
> picks peaks in the density and then pulls nearby atoms toward them. .
The isolde suggestion already made is an excellent one. The hardest part of
that is getting the right version of chimeraX working. But, once you've done
that its pretty straightforward.
Hopefully not for too much longer. All going well, ISOLDE 1.0 (to work
in ChimeraX 1.0) should be out
Jim wrote:
"technically, not in Phenix either. The real-space refinement in Phenix simply
picks peaks in the density and then pulls nearby atoms toward them. . Like a
black hole gobbling up nearby planets (snip)"
Do you have a reference to support this assertion?
"It took me a while to realize
Not in CCP4, no. And, technically, not in Phenix either. The real-space
refinement in Phenix simply picks peaks in the density and then pulls
nearby atoms toward them. Like a black hole gobbling up nearby planets.
It took me a while to realize that! If you manage to turn off geometry
Auftrag von Tom Burnley -
> UKRI STFC
> Gesendet: Mittwoch, 29. Juli 2020 18:51
> An: CCP4BB@JISCMAIL.AC.UK
> Betreff: Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] real real-space-refinement
>
> EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk
>
>
>
> Hi Herman
] Re: [ccp4bb] real real-space-refinement
EXTERNAL : Real sender is tom.burn...@stfc.ac.uk
Hi Herman,
Just a couple of tips for Refmac...
1) increase number of cycles - we find some cases require a lot of cycles, more
than you may be used from MX refinement.
2) optimise weight
: [ccp4bb] real
real-space-refinement
Hi everybody,
Thank you very much for the many tips! I discovered that in Coot by clicking on
the N- and C-terminus of a protein chain, one can indeed run a real-space
refinement on the complete chain and the same is true for a rigid body fit.
However, subsequent
etin board Im Auftrag von Tom Burnley -
UKRI STFC
Gesendet: Mittwoch, 29. Juli 2020 18:51
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] real real-space-refinement
EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk
Hi Herman,
There is lots of information o
and
> C-terminus for real-space refinement to see what happens. I would prefer to
> have some script to do it.
> Best, Herman
>
> Von: Eleanor Dodson
> Gesendet: Mittwoch, 29. Juli 2020 17:23
> An: Schreuder, Herman /DE
> Cc: CCP4BB@JISCMAIL.AC.UK
> Betreff: [EXTE
Would the stepped refinement protocol in Coot do what you want? It does a
real space refinement for every residue automatically.
Cheers
Christian
On Wed, Jul 29, 2020 at 5:20 PM Schreuder, Herman /DE <
herman.schreu...@sanofi.com> wrote:
> Dear BB,
>
>
>
> I would like to do a real
(and
runs Refmac via CCP4).
All the best,
Tom
From: CCP4 bulletin board on behalf of Boaz Shaanan
Sent: 29 July 2020 16:31:46
To: ccp4bb
Subject: Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] real real-space-refinement
Hi,
Try searching ccp-em.
Boaz
Boaz Shaanan
UK
Betreff: [EXTERNAL] Re: [ccp4bb] real real-space-refinement
EXTERNAL : Real sender is
eleanor.dod...@york.ac.uk
Wont coot do that?
Eleanor
On Wed, 29 Jul 2020 at 16:20, Schreuder, Herman /DE <herman.schreu...@sanofi.com> wrote:
Dear BB,
I would like to do a real real-
Gesendet: Mittwoch, 29. Juli 2020 17:23
An: Schreuder, Herman /DE
Cc: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] Re: [ccp4bb] real real-space-refinement
EXTERNAL : Real sender is
eleanor.dod...@york.ac.uk<mailto:eleanor.dod...@york.ac.uk>
Wont coot do that?
Eleanor
On Wed, 29 Jul 2020 at
Wont coot do that?
Eleanor
On Wed, 29 Jul 2020 at 16:20, Schreuder, Herman /DE <
herman.schreu...@sanofi.com> wrote:
> Dear BB,
>
>
>
> I would like to do a real real-space-refinement of a protein against a
> cryo-EM map; not the mtz-based Refmac approach. A quick internet search
> produced a
Dear BB,
I would like to do a real real-space-refinement of a protein against a cryo-EM
map; not the mtz-based Refmac approach. A quick internet search produced a lot
of Phenix hits, but little ccp4 hits. Does somebody know how to do this using
ccp4 programs, or has someone a Coot script to do
16 matches
Mail list logo
