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Hi Bernhard,
this sounds odd - wouldn't both maps be calculated from F/PHI by coot
itself? Why would Paul (Kevin?) make a difference there between phenix
and refmac5?
Curiously,
Tim
On 01/17/2013 10:23 AM, Bernhard Lohkamp wrote:
Hi Pedro,
this
Hi, Bernhard,
To clarify my previous e-mail, in both cases the maps are being
calculated from weighted coefficients from an MTZ file output by the program.
I tried calculating a weighted 2Fo-Fc map in CCP4i using the PHENIX
MTZ file and the end-result (red bars) was the same.
Pedro.
At
I see the same thing with Autobuster structures.
-Original Message-
From: Mailing list for users of COOT Crystallographic Software
[mailto:COOT@JISCMAIL.AC.UK] On Behalf Of Pedro M. Matias
Sent: Thursday, January 17, 2013 6:16 AM
To: COOT@JISCMAIL.AC.UK
Subject: Re: Problem with Coot
(hesitating to restart an old flame war)
There has been a long-standing argument about scaling of electron density maps,
with many people deprecating sigma-scaling, for two reasons
1) in 2Fo-Fc type maps, sigma = RMS density is a function among other things
of the solvent content (smaller with
Excuse me if I'm wrong but should't the correlation coefficient
between Fo and Fc (which is what the Density Fit analysis is looking
at) be independent of this issue, provided Fo and Fc are on the same
scale ? And since the map is calculated from weighted 2Fo-Fc
amplitudes and phases the
I'm sorry to re-hash this issue, but I just wanted to know what the
present general consensus is on linux flavors. I teach a
crystallography class every 2 years, and I have a small cluster of
computers running fedora, but the deal is that by the time I get around
to my class, fedora has
IMO, unless you just like upgrading your OS on a frequent basis and the
migraines that go with it, choose some sort of LTS (long-term-support)
release. Currently I'm using Ubuntu 12.04 LTS (good for 5 years), but
CentOS or Mint would be good choices, too, and that is what I considered
when I
I currently use a combination of RHEL 5 and CentOS 6 on the machines
which I manage. Steadily migrating to CentOS 6 as some of the libraries
needed for newer software are not easily available for RedHat 5.
If you are coming from a Fedora background, then Redhat/CentOS do have
the advantage of
Well, the problem seems to occur when Intensities are input to PHENIX
instead of structure factors. I repeated a run using Fobs, SigFobs as
input instead of IMEAN, SIGIMEAN and the Density Fit Analysis graph
looks normal.
At 16:57 17-01-2013, Nathaniel Echols wrote:
Actually, after some
Hi,
I'm a Fedora fan myself. I only recently needed to upgrade (i-e
reinstall) from FC8 to FC16 because the latest Coot wouldn't run on
FC8 anymore. I didn't upgrade to FC17 because NX (No Machine)
wouldn't work anymore. I guess that in terms of release stability
RHEL and Scientific Linux
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