<div class="__aliyun_email_body_block"><div  style="clear:both;"><span  class=" __aliyun_node_has_color" style="font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;color:#000000;">Dear all,</span></div><div  style="clear:both;"><span  class=" __aliyun_node_has_color" style="font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;color:#000000;"><br ></span></div><div  style="clear:both;"><span  class=" __aliyun_node_has_color" style="font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;color:#000000;">    I am trying to fit an antibody molecule to the cryo-EM density map for an antigen-antibody complex. The related files can be found at the following link</span></div><div  style="clear:both;"><span  class=" __aliyun_node_has_color" style="font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;color:#000000;">                 https://drive.google.com/drive/folders/16ELIDsUxiNwRGp9ely2SRn-zjAdHCudH?usp=sharing.</span></div><div  style="clear:both;"><span  class=" __aliyun_node_has_color" style="font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;color:#000000;">I first segmented the map ("emd_22158.map") and get the segment map ("emd_22158.seg") in chimera. Then I selected the regions corresponding to the antibody and use the "Fit to segments" tool of chimera to fit the antibody molecule. The "image1.png" shows the inital antibody postion and the expected docking postion in the segmented complex density (indicated by the red arrow). However, the antibody molecule cannot be fitted into the selected target  region after this operation, but moved to the position shown in "image2.png (only the target regions are shown). </span></div><div  style="clear:both;"><span  class=" __aliyun_node_has_color" style="font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;color:#000000;">    I have tried to ungoup and regroup the target region to make its overall shape more simial to the antibody, and place the antibody into the region and ajust its orienation, but whatever I tried, the results are the same: the antibody will move to the position shown in "image2.png" after performing the <span  style="color:#000000;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;text-align:start;text-indent:.0px;text-transform:none;widows:2;background-color:#ffffff;text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline;">"Fit to segments" action</span>.</span></div><div  style="clear:both;"><span  class=" __aliyun_node_has_color" style="font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;color:#000000;">    I wonder whether it is impossible to dock the antibody to the expected position with chimera or there is anything wrong with my operation. Could you help me with this issue? I will appreciate any help from you.</span></div><div  style="clear:both;"><span  class=" __aliyun_node_has_color" style="font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;color:#000000;"><br ></span></div><div  style="clear:both;"><span  class=" __aliyun_node_has_color" style="font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;color:#000000;">Best regards,</span></div><div  style="clear:both;"><span  class=" __aliyun_node_has_color" style="font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;color:#000000;">Yeping Sun</span></div></div>