[phenixbb] difference map
Thomas C. Terwilliger
terwilliger at lanl.gov
Thu Feb 10 10:00:37 PST 2011
I had a look at your data, thanks for providing it to Pavel. Here is what
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
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,
>> 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
>> uisng that.
>> 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
>>>> density at sigma level 5. I calculated an omit map that clearly showed
>>>> presence of my ligand at the specific position. Is there anything wrong
>>>> my calculation. What alternate ways are there to improve my difference
>>>> 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
>> INTEKHAB ALAM
>> LABORATORY OF STRUCTURAL BIOINFORMATICS
>> KOREA UNIVERSITY, SEOUL
>> phenixbb mailing list
>> phenixbb at phenix-online.org
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