Hi Intekhab,

I had a look at your data, thanks for providing it to Pavel.  Here is what
I see:

1. taking your starting model, removing the RIB ligand, and refining
against the native.sca and ligand.sca data gives models that have good
R/Rfree in each case (0.19/0.23 and 0.18/0.23), but differ by about 0.5A
rms.  The models have coordinated shifts relative to each other in which
many atoms move together.

2. The largest positive density in your Fo-Fc map for the ligand.sca
refinement is at the position of your ligand. The density is not great,
and doesn't cover the entire ligand.

3. The Fo(ligand)-Fo(native) map phased with your starting model shows
some density on parts of the ligand, and is considerably less clear than
the Fo-Fc map above, as you pointed out.

4. The Fo-Fc map with native.sca shows a little density on part of the
ligand.

I would suggest that the Fo(ligand)-Fo(native) map is probably a
relatively inaccurate picture of the ligand because it is a composite of
all changes between native and ligand-bound structures.  The Fo-Fc map
based on ligand.sca refinement is probably your best picture of the
ligand.  The fact that this Fo-Fc map is not very clear despite the
reasonable resolution (2.5 A) and good R/Rfree suggests that the ligand is
not always in exactly the same orientation or location.

All the best,
Tom T

>> 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@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
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb@phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>>

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