Whatever you do it is good practice to do your first run of refinement as
Review Restraints"
Under the Monitoring folder set the level to many (default medium)
and set the sigma cut off for chirals to 3.00 say to get a god list
Then run the job and you will get a list of violations of restraints
If your chirality ideal is -2 and the calculated value is +2 then think
whether you have built the ligand wrongly or whetherthe sign is wrongly
defined.
Eleanor
PS - you will also find the bad clashes ..
Garib Murshudov wrote:
Chiralities in refmac dictionaries are local just like in smile
strings. You can of course put atoms by their priorities then
you will have correspondence to R/S assignments. However you do not
have to do it.
In many case I find it useful to put chirality 'both' and then refine
against this dictionary. This way you can handle severla stereoisomers
(configurations) with the same dictionary.
Regards
Garib
On 20 Mar 2007, at 00:49, Vu Thai wrote:
thanks for the link. I had already seen it and was using it to assign my
chirality. I guess I should clarify my question. In sketcher, does one
input the highest priority neighbor first, then the second, and
finally the
third? The sketcher GUI has three columns list: B/3, F/4, & 1/5. Do
these
columns have any significance?
Vu
On Mon, 19 Mar 2007 15:35:43 -0700, Dale Tronrud
<[EMAIL PROTECTED]>
wrote:
Garib has documentation on his website that I presume matches what is
required by sketcher. It can be found at
http://www.ysbl.york.ac.uk/~garib/refmac/docs/theory/chiral.html
(I did a Google of "ccp4 chiral" to find it.)
Dale Tronrud
Vu Thai wrote:
Hi All,
I was wondering how to properly define the stereochemistry for a
new ligand
in sketcher. In the sketcher interface there are three columns
after the
stereochem sign option. I would assume that the order in which you
enter
the chiral neighbors would effect the sign that you choose for your
stereochemistry. Does any one know how sketcher reads these three
columns
to determine the stereochemsitry?
Thanks in advance for your help.
Cheers,
Vu
