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>In most cas
Cheers,
Robbie
Sent from my Windows 10 phone
From: Andrew Leslie
Sent: 17 August 2017 17:29
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb
mes Holton
MAD Scientist
On 8/17/2017 8:40 AM, Robbie Joosten wrote:
In most cases resetting the B-factors would be enough to perturb the
model.
Cheers,
Robbie
Sent from my Windows 10 phone
*From: *Andrew Leslie <mailto:and...@mrc-lmb.cam.ac.uk>
*Sent: *17 August 2017 17:29
*To: *CCP4BB@JIS
Frank, Given that experimental electron density maps resulting from structure
factors with a figure of merit of 0.5 are still interpretable, I don't think
that "wiggling" the phases will be so bad. Fom of 0.5 corresponds to a phase
error of 60 degrees, which is a pretty big shift.
Interesting
Hi Andrew,
as far as I understand, PDBSET only affects the coordinates. The WIGL command
in SHELXL also add noise to the ADPs, which has a dramatic effect on the
resulting R1-value. See Figure S5 A vs. S5 B in doi: 10.1073/pnas.1502136112
At least one should reset the B-values in refmac, I gues
On the same question, asked some time ago, Eleanor (or James?) pointed
out that the this perturbation changes the phases only of the higher
resolution reflections.
I believe the implied conclusion was that "resetting" a structure does
not have the same effect on all phases as randomising them
Dear all,
Many thanks for all of your suggestions - it seems that I was looking with the
wrong search terms (perturb => shake) and there are indeed many tools out there
for performing this.
Problem solved :-)
Best wishes Graeme
> On 17 Aug 2017, at 18:18, Victor Lamzin wrote:
>
> Dear Graem
Dear Graeme,
You can also type the following on a command line, optional commands are
given in square parentheses.
Victor
$warpbin/arp_warp
mode shakemodel allatoms
files ccp4 xyzin FILENAME.pdb xyzout FILENAME.pdb
symmetry SPACEGROUP
shakemodel [ bexclude B1 ] [ breset B1 B2 ] [ randomise X
Dear Graeme,
The WIGL instruction in SHELXL does exactly that, and has some useful
options.
http://shelx.uni-ac.gwdg.de/SHELX/shelxl_html.php#WIGL
Best wishes, George
On 08/17/2017 05:17 PM, Graeme Winter wrote:
Dear All,
Is there a protocol out there to gently perturb atomic positions so
b] "reset" a structure before re-refinement
Hi Graeme,
You can do this with PDBSET, keyword NOISE
Cheers,
Andrew
> On 17 Aug 2017, at 16:17, Graeme Winter wrote:
>
> Dear All,
>
> Is there a protocol out there to gently perturb atomic positions so that
> re-run
Hi Graeme,
You can do this with PDBSET, keyword NOISE
Cheers,
Andrew
> On 17 Aug 2017, at 16:17, Graeme Winter wrote:
>
> Dear All,
>
> Is there a protocol out there to gently perturb atomic positions so that
> re-running refinement can essentially put them back without bias from the
> ori
Dear All,
Is there a protocol out there to gently perturb atomic positions so that
re-running refinement can essentially put them back without bias from the
original refinement? In particular, if trying to perform the Karplus and
Diederichs paired refinement protocol, I do not want to run the l
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