A simple way to validate real space density fit is to look at it under
validate--->density fit anlysis in COOT.
I think even the GUI of phenix.refine at the end of a run the results give a
list of all residues that are under the user-definied RSCCoeficient.
With those two tools you should be able
Hi all,
Unfortunately, I am no longer able to support or maintain (let alone develop
or port to new OS versions) any of my old USF programs. For this reason, Mark
Harris (http://xray.bmc.uu.se/markh/email.html) has made a distribution kit
with source code (yes, Fortran77...) and compilation sc
On Friday, September 02, 2011 08:56:03 am Jerry McCully wrote:
>
> Dear ALL;
>
>I am sorry for this "HKL2000 scalepack" question.
>
>To confirm the scape group using Pointless, I processed the images
> using HKL2000
>but kept the original index using "No merg
> You have those tools at hand, but you need to script them or type whatever
> you like.
> The RSR fit e.g. can be found in MAPMAN with the command RS_fit-real-space
> blabla
> All plots generated on the EDS server site should have a USF tool which
> produces some numbers which you then convert via
Dear ALL;
I am sorry for this "HKL2000 scalepack" question.
To confirm the scape group using Pointless, I processed the images
using HKL2000 but kept the original index using "No merge original index".
Now Pointless gave the right space group, and I want to mer
> it will be before we all travel to work with jetpacks or flying cars
http://www.popularmechanics.com/science/4247253
" Thunderbolt Aerosystems, based in California, plans to start selling its
ThunderPack TP-R2G2 rocket belt to customers this summer."
http://www.popularmechanics.com/technology/
Dear Jacob,
... or you could use the "anomalous residual map" in SHARP, the first
program to offer this kind of calculation 15 years ago or so: see
La Fortelle, E. de & Bricogne, G. (1997). Methods Enzymol. 276, 472–494.
and/or the SHARP manual at
http://www.globalphasing.com/s
Hi all,
Simple question, is there a way I can upload my own data into the EDS
server? I see only place for it to take from data already published in the
PDB.
First of all, if you deposit at PDBe, EDS will be run on your deposition and
you can access the results after annotation. Second, RCSB
It is quite possible that the S- and Cl- signal is being lost under that
from the Se sites. Could be:
1) simply noise that would swamp the S-SAD signal anyway
2) you just aren't contouring your map low enough ("sigma" is not on an
absolute scale)
3) trigonometry. Remember, with SAD you are no
Dear all,
I am using coot 0.6.2 on MacBook. It was working nicely when I was
using previous version. With this new coot I am problem as I can not
do anything except visualisation. If I try to build or refine always
show the message "refinement setup failure, Failed to find
restraints" or "mis
Dear Jacob,
The signal for weak anomalous sites can be stronger in Phaser SAD LLG maps than
in model-phased anomalous difference Fouriers, especially if the substructure
already contains the stronger sites, so that you're just looking for what is
still left to be explained in the SAD data. You
Did you try density modification starting with the sad phases with phase
extension to 2.7 A followed by auto-tracing? The model should be better than
the one built from the 3.7 A sad map.
Sent from Jack's iPad
On Sep 1, 2011, at 11:24 PM, "Kianoush Sadre-Bazzaz"
mailto:ksad...@yahoo.com>> w
Dear all,
I am using coot 0.6.2 on MacBook. It was working nicely when I was using
previous version. With this new coot I am problem as I can not do anything
except visualisation. If I try to build or refine always show the message
"refinement setup failure, Failed to find restraints" or "miss
Yes I would like to use it as part of validation ie to see RSCC maps and other
validation based on density. If EDS cannot do this, is there another program
that does something similar? I am aware of overlapmap in ccp4 but it is not as
thorough.
From: Tim Gruen
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Boaz,
On 09/02/2011 01:19 PM, Boaz Shaanan wrote:
> Hi,
>
> I could be missing something, but why would you want to do this? Once (or
Obviously because one would like to see the analyses before submitting
the structure to the PDB, as part of t
Dear all
Simple question, is there a way I can upload my own data into the EDS server? I
see only place for it to take from data already published in the PDB.
Apologies for non ccp4 based question
Careina
Some important reason for using 64bit is due to the following.
The "effective" precision of a float (32bit) is about 5 dp
The "effective" precision of a double/real*8 (64 bit) is about 10 dp
The number of dp is only approximate since we are encoding this using
binary.
The max/min value of a f
This is the first announcement of an X-ray protein crystallography
course in Oulu, Finland, from January, 30 till February 3, 2012.
Further details of the outline of the program are given on the
WWW-site, as listed below. The topic of the course focuses on data
collection, data processing,
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