[phenixbb] difference map
faisaldbg at gmail.com
Wed Feb 9 22:50:30 PST 2011
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
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
On Thu, Feb 10, 2011 at 2:50 PM, <det102 at uoxray.uoregon.edu> wrote:
> 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
>> phenixbb mailing list
>> phenixbb at phenix-online.org
> phenixbb mailing list
> phenixbb at phenix-online.org
LABORATORY OF STRUCTURAL BIOINFORMATICS
KOREA UNIVERSITY, SEOUL
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