[phenixbb] difference map

[intekhab alam]

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, <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
>>
>>
>>
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-- 
INTEKHAB ALAM
LABORATORY OF STRUCTURAL BIOINFORMATICS
KOREA UNIVERSITY, SEOUL
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