> d if you do so, be sure to tell us which versions of refmac and coot
you are using
I use Win Coot-0.7-pre-1 (version 4039), and Refmac5 from CCP4i.
It seems you are using an 'old' CCP4 (you dont specify the version,
6.1.3?) with an old(er) dictionary. WinCoot currently uses its own (up
to date) dictionary (*). To use the same dictionary as refmac within
CCP4i you can edit your runwincoot.bat file and delete the line which says:
set COOT_REFMAC_LIB_DIR=%COOT_SHARE%\coot\lib
Then it will pick up the CCP4 dictionaries.
B
(*) Maybe WinCoot should not by default override the location of
dictionaries, but for various reasons it wasnt. Maybe I should change
this tomorrow...
The red bar on NAD in Coot is likely due to the defference
dictionaries between coot and refmac.
How could I tell Coot to use the restrains from Refmac?
I have one of log files from Refmac5 attached (named as 189_refmac5).
The NAD was refined by coot, and the coordinates were then refined by
Refmac5. The NAD was back to what it was after the refmac.
Thank you for advices.
Uma
On Mon, Apr 30, 2012 at 5:00 AM, Paul Emsley
<paul.ems...@bioch.ox.ac.uk <mailto:paul.ems...@bioch.ox.ac.uk>> wrote:
Dear Eleanor, Ros,
On 29/04/12 11:32, Eleanor Dodson wrote:
I think you will find the dictionaries for coot and refmac are
different..
REFMAC default dictionary will $CLIBD/monomers/n/NAD.cif
Who knows where coot finds its dictionaries ...
Coot uses the environment variable
COOT_REFMAC_LIB_DIR
if that is not set, it uses
COOT_MONOMER_LIB_DIR
if that is not set, it uses
CLIBD_MON
if that it not set, it uses
CCP4_LIB
if that is not set, it uses
COOT_PREFIX/share/coot/lib
which means that Coot typically picks up the standard CCP4
library, but allows you to over-ride that for special cases, or if
you are using Phenix.
So it is good advice to check for a start that Coot and Refmac are
using the same restraints. When Coot reads in the mmCIF
dictionary, it writes that information to the console.
1) check the REFMAC restraints in that dictionary are sensible -
spec, are the planes and chiral centres as you would expect
It is my experience that Refmac restraints used in Coot tend to
flatten furanoses and pyrrolidines.
2) read the REFMAC dictionary into coot and see what happens.. do
you still have the problem.
3) check the REFMAC log file for what it thinks are outliers
after the COOT refinement - I reset the geometric monitoring
parameters - see on the GUI - to list things with errors of 5
Sigma say ( I think the default is 10 Sigma)
Yes, agreed.
4) If there are difference complain..
And if you do so, be sure to tell us which versions of refmac and
coot you are using - we find that sort of thing important when
debugging. Also, in this case, it might be useful to know about
the restraints weights, presumably the default seeing as you don't
mention it?
BTW, I rarely if ever use Regularize Zone if there electron
density to fit.
If you hover over the red bar in the geometry analysis in Coot, it
tells you the most deviant geometrical feature. Is this
consistent with the analysis from Refmac?
Regards,
Paul.
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