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<span style="font-family:tahoma,sans-serif"><font><span style="background-color:rgb(255,255,255)"><span style="color:rgb(33,33,33);background-image:none;background-repeat:repeat">Hi all, <br>I am working with a protein dimer-ligand structure (resolution: 2.8</span></span><span style="background-color:rgb(255,255,255)"><span style="color:rgb(33,33,33);background-image:none;background-repeat:repeat">Å) and am going to make a figure showing the </span></span><span style="background-color:rgb(255,255,255)"><span style="color:rgb(33,33,33);background-image:none;background-repeat:repeat">bound ligand superimposed with the electron density (Fo-Fc) map obtained after
omit refinement</span></span>. <br></font></span></div><span style="font-family:tahoma,sans-serif"><font>What I did is to make the ligand-free structure model and then use Phenix.refine using the following parameters plus simulated annealing (torsion angle) or (Cartesian): <br></font></span></div><font color="black"><span style="background-color:white" dir="ltr"><span style="font-weight:normal;font-variant:normal;text-transform:none"><div style="margin-top:0px;margin-bottom:0px">Default: XYZ coordinates + Real-space+ Individual B factors + Occupancies.</div>
<div style="margin-top:0px;margin-bottom:0px">Also click: Optimize X-ray/stereochemistry weight + Optimize X-ray/ADP weight + Secondary structure restraints + NCS. <br><br></div><div style="margin-top:0px;margin-bottom:0px">Contoured at 2<span class="">σ</span>, the Fo-Fc map generated show green density for most part of the ligand, but for several atoms in the middle of the ligand, the green density is missing... <font color="black"><span style="background-color:white" dir="ltr"><span style="font-weight:normal;font-variant:normal;text-transform:none">It's like this:
some atoms have green density and the next few no green density and then
a couple few has green density and then a couple more no green
denisty....</span></span></font> The missing green density usually means that part is disordered in the structure, right? I am not sure why the density is missing for some atoms in the middle of the ligand. It would makes more sense if the missing green density is at the end of the ligand...<br><br></div><div style="margin-top:0px;margin-bottom:0px">Does anyone happen to have any clue about what it means for the green density missing in my case? <br><br></div><div style="margin-top:0px;margin-bottom:0px">Also, I am not sure whether I did the omit refinement right:<br></div><div style="margin-top:0px;margin-bottom:0px">(1). For simulated annealing, it has two options, one is Cartesian and the other is Torsion angle, and it's said that torsion angle is more suitable of low resolution data. Is there any difference about which one to choose in my case?<br>(2). Is it Okay to run the omit refinement in the presence of the following parameters as I did: <br><font color="black"><span style="background-color:white" dir="ltr"><span style="font-weight:normal;font-variant:normal;text-transform:none">Optimize X-ray/stereochemistry weight + Optimize X-ray/ADP weight + Secondary structure restraints + NCS.<br><br></span></span></font></div><div style="margin-top:0px;margin-bottom:0px"><font color="black"><span style="background-color:white" dir="ltr"><span style="font-weight:normal;font-variant:normal;text-transform:none">Thank you so much!<br><br>Best, <br>Wei <br></span></span></font></div><div style="margin-top:0px;margin-bottom:0px"><font color="black"><span style="background-color:white" dir="ltr"><span style="font-weight:normal;font-variant:normal;text-transform:none"><br></span></span></font></div></span></span></font></div>