<div>Hi Tom </div>
<div> </div>
<div>Thanks for the your time as well as suggestions regarding my data set. Thanks to Pavel also for the help he extended. </div>
<div> </div>
<div>Regards</div>
<div>Intekhab Alam<br><br></div>
<div class="gmail_quote">On Fri, Feb 11, 2011 at 3:00 AM, Thomas C. Terwilliger <span dir="ltr"><<a href="mailto:terwilliger@lanl.gov">terwilliger@lanl.gov</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">Hi Intekhab,<br><br>I had a look at your data, thanks for providing it to Pavel. Here is what<br>I see:<br>
<br>1. taking your starting model, removing the RIB ligand, and refining<br>against the native.sca and ligand.sca data gives models that have good<br>R/Rfree in each case (0.19/0.23 and 0.18/0.23), but differ by about 0.5A<br>
rms. The models have coordinated shifts relative to each other in which<br>many atoms move together.<br><br>2. The largest positive density in your Fo-Fc map for the ligand.sca<br>refinement is at the position of your ligand. The density is not great,<br>
and doesn't cover the entire ligand.<br><br>3. The Fo(ligand)-Fo(native) map phased with your starting model shows<br>some density on parts of the ligand, and is considerably less clear than<br>the Fo-Fc map above, as you pointed out.<br>
<br>4. The Fo-Fc map with native.sca shows a little density on part of the<br>ligand.<br><br>I would suggest that the Fo(ligand)-Fo(native) map is probably a<br>relatively inaccurate picture of the ligand because it is a composite of<br>
all changes between native and ligand-bound structures. The Fo-Fc map<br>based on ligand.sca refinement is probably your best picture of the<br>ligand. The fact that this Fo-Fc map is not very clear despite the<br>reasonable resolution (2.5 A) and good R/Rfree suggests that the ligand is<br>
not always in exactly the same orientation or location.<br>
<div class="im"><br>All the best,<br>Tom T<br><br></div>
<div>
<div></div>
<div class="h5">>> I tried both ways Fapo-F ligand as well as Fligand-Fapo. You are right the<br>>> red density becomes negative when the F is reversed.<br>>> The unit cell parameters are quite same.<br>
>><br>>> For native: a=120.557 b=196.262 c=109.339 , alpha =90, beta=114.231 and<br>>> gamma=90<br>>> ligand complexed data= a=119.952 b=196.084 c=109.206 , alpha =90,<br>>> beta=114.116 and gamma=90<br>
>><br>>> My 2Fo-Fc map as well as Fo-Fc is quite significant and i modeled the<br>>> ligand<br>>> uisng that.<br>>><br>>> Regards<br>>> Intekhab Alam<br>>><br>>> On Thu, Feb 10, 2011 at 2:50 PM, <<a href="mailto:det102@uoxray.uoregon.edu">det102@uoxray.uoregon.edu</a>> wrote:<br>
>><br>>>><br>>>> This is a long shot, but it's possible that you calculated a<br>>>> Fapo-Fligand map instead of the other way 'round. Normally you<br>>>> would have a positive peak surrounded by a negative ripple (due<br>
>>> to series termination and other factors). If you get the F's<br>>>> reversed the negative ripple becomes positive and the ligand<br>>>> density becomes negative. What does you negative contour say?<br>
>>><br>>>> Dale Tronrud<br>>>><br>>>><br>>>> On 2/9/2011 7:33 PM, intekhab alam wrote:<br>>>><br>>>>><br>>>>> Hi i am trying to calculate a difference map ( ligand-native ) using<br>
>>>> isomorphous difference map program in phenix. I used the reflection<br>>>>> files of<br>>>>> ligand and native and phase information of ligand derived data. But the<br>>>>> difference map donot fits the ligand, and appears as a circular chunk<br>
>>>> of<br>>>>> density at sigma level 5. I calculated an omit map that clearly showed<br>>>>> the<br>>>>> presence of my ligand at the specific position. Is there anything wrong<br>
>>>> in<br>>>>> my calculation. What alternate ways are there to improve my difference<br>>>>> map.<br>>>>> --<br>>>>> INTEKHAB ALAM<br>>>>> LABORATORY OF STRUCTURAL BIOINFORMATICS<br>
>>>> KOREA UNIVERSITY, SEOUL<br>>>>><br>>>>><br>>>>><br>>>>> _______________________________________________<br>>>>> phenixbb mailing list<br>>>>> <a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>
>>>> <a href="http://phenix-online.org/mailman/listinfo/phenixbb" target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a><br>>>>><br>>>> _______________________________________________<br>
>>> phenixbb mailing list<br>>>> <a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>>>> <a href="http://phenix-online.org/mailman/listinfo/phenixbb" target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a><br>
>>><br>>><br>>><br>>><br>>> --<br>>> INTEKHAB ALAM<br>>> LABORATORY OF STRUCTURAL BIOINFORMATICS<br>>> KOREA UNIVERSITY, SEOUL<br>>> _______________________________________________<br>
>> phenixbb mailing list<br>>> <a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>>> <a href="http://phenix-online.org/mailman/listinfo/phenixbb" target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a><br>
>><br><br>_______________________________________________<br>phenixbb mailing list<br><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br><a href="http://phenix-online.org/mailman/listinfo/phenixbb" target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a><br>
</div></div></blockquote></div><br><br clear="all"><br>-- <br>INTEKHAB ALAM<br>LABORATORY OF STRUCTURAL BIOINFORMATICS<br>KOREA UNIVERSITY, SEOUL<br>