I tried both ways Fapo-F ligand as well as Fligand-Fapo. You are right the
red density becomes negative when the F is reversed.
The unit cell parameters are quite same.
For native: a=120.557 b=196.262 c=109.339 , alpha =90, beta=114.231 and
gamma=90
ligand complexed data= a=119.952 b=196.084 c=109.206 , alpha =90,
beta=114.116 and gamma=90
My 2Fo-Fc map as well as Fo-Fc is quite significant and i modeled the ligand
uisng that.
Regards
Intekhab Alam
On Thu, Feb 10, 2011 at 2:50 PM,
This is a long shot, but it's possible that you calculated a Fapo-Fligand map instead of the other way 'round. Normally you would have a positive peak surrounded by a negative ripple (due to series termination and other factors). If you get the F's reversed the negative ripple becomes positive and the ligand density becomes negative. What does you negative contour say?
Dale Tronrud
On 2/9/2011 7:33 PM, intekhab alam wrote:
Hi i am trying to calculate a difference map ( ligand-native ) using isomorphous difference map program in phenix. I used the reflection files of ligand and native and phase information of ligand derived data. But the difference map donot fits the ligand, and appears as a circular chunk of density at sigma level 5. I calculated an omit map that clearly showed the presence of my ligand at the specific position. Is there anything wrong in my calculation. What alternate ways are there to improve my difference map. -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL
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-- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL