>
> > 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
> <[log in to unmask] <mailto:[log in to unmask]>> 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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