Dear Debajyoti,
The way I check the chirality is to compare the fitted compound with the
structural formula. In coot, I rotate the ligand such that it has the
same orientation as in the formula and check that the "out of plane"
group goes in the right direction. However, it happens quite often that
the chirality of the bound compound is not the chirality the chemist
thinks it has, or the chirality is not known. In that case, I refine
both enantiomers and look which one fits best. Things to look for are
distorted bond angles, poor fitting and small positive and negative
blobs of difference density (green and red blobs in coot with default
settings).
To change the chirality, you have to edit the cif dictionary which
contains the description of your compound. In the dictionaries I use you
have to change the _chem_comp_chir.volume.sign from positiv to negativ
or vice versa.
Good luck!
Herman
________________________________
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On
Behalf Of Debajyoti Dutta
Sent: Friday, January 27, 2012 8:25 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Ligand chirality error
Hi all,
How to check the presence of improper chirality of a fitted
ligand. Is there any way to get rid of such error.
All suggestions are welcome. Thanks in advance.
sincerely
Debajyoti
<http://sigads.rediff.com/RealMedia/ads/click_nx.ads/www.rediffmail.com/
signatureline.htm@Middle?>
Follow Rediff Deal ho jaye!
<http://track.rediff.com/click?url=___http://dealhojaye.rediff.com?sc_ci
d=rediffmailsignature___&cmp=signature&lnk=rediffmailsignature&newservic
e=deals> to get exciting offers in your city everyday.
