<div>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.</div>
<div>The unit cell parameters are quite same.</div>
<div> </div>
<div>For native: a=120.557 b=196.262 c=109.339 , alpha =90, beta=114.231 and gamma=90</div>
<div>ligand complexed data= a=119.952 b=196.084 c=109.206 , alpha =90, beta=114.116 and gamma=90</div>
<div> </div>
<div>My 2Fo-Fc map as well as Fo-Fc is quite significant and i modeled the ligand uisng that.</div>
<div> </div>
<div>Regards</div>
<div>Intekhab Alam<br><br></div>
<div class="gmail_quote">On Thu, Feb 10, 2011 at 2:50 PM, <span dir="ltr"><<a href="mailto:det102@uoxray.uoregon.edu">det102@uoxray.uoregon.edu</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote"><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
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<div class="h5"><br><br>On 2/9/2011 7:33 PM, intekhab alam wrote:<br></div></div>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">
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<div class="h5"><br>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.<br>
--<br>INTEKHAB ALAM<br>LABORATORY OF STRUCTURAL BIOINFORMATICS<br>KOREA UNIVERSITY, SEOUL<br><br><br><br></div></div>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>INTEKHAB ALAM<br>LABORATORY OF STRUCTURAL BIOINFORMATICS<br>KOREA UNIVERSITY, SEOUL<br>