<div class="__aliyun_email_body_block"><div  style="clear:both;"><span  style="font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;color:#000000;">Hi Greg,</span></div><div  style="clear:both;"><span  style="font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;color:#000000;">     Thank you for your suggestions and instructions. </span></div><div  style="clear:both;"><span  style="font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;color:#000000;">     I have tried your method,and yes, <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;"> ‘Mask map with region(s) to prevent large drifts' for the Fit-to-segment can avoid large shift of the antibody molecule. However, I can not get the resonable fitting with the options you suggested yet. I have uploadeded the antibody (Ab, 4-8_H3-0175.pdb) and the antigen (Ag, S.pdb) to the link:</span></span></div><div  style="clear:both;"><span  style="font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;color:#000000;"><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;">                       https://drive.google.com/drive/folders/16ELIDsUxiNwRGp9ely2SRn-zjAdHCudH?usp=sharing</span></span></div><div  style="clear:both;"><br ></div><div  style="clear:both;">    After fitting the Ag to the map for the Ag-Ab complex (emd_22156.map), I then selected the target region(s) for the Ab and use 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-segment tool to fit it with the options <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;">‘Align principal axes’ and <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;"> ‘Mask map with region(s) to prevent large drifts', and got the complex fit-to-segment_1.pdb. I also tried the option "<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;">‘Rotational search’" and got the complex <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;"> </span><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-segment_2.pdb. Unfortunately, in both of the two complex structure, there are obvious structural clash bewteen the Ag and the Ab. The </span></span></span></span></span> fit-to-segment_1.pdb and <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;"> </span><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-segment_2.pdb can also be found at the above link. Then I tried to adjust the size the target area by "ungroup" and "group" functions in the "Segment Map" tool to exclude the area occupied by the Ag in the target region, and get 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;">emd_22156_regrouped.seg (which can be found at the above link). Howeve, when I fitted the Ab to target region this resegmented map, the Ab positions are wrong ( the CDRs face is not facing the Ag). </span></span></div><div  style="clear:both;"><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;"><br ></span></div><div  style="clear:both;"><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;">    Do you have other suggestions for correct fitting of the Ab molecule?</span></div><div  style="clear:both;"><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;"><br ></span></div><div  style="clear:both;"><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;">Best regards,</span></div><div  style="clear:both;"><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;">Yeping</span></div><div  style="clear:both;"><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;">    </span></div><div  style="clear:both;"><br ></div><div  style="clear:both;"><br ></div><div  style="clear:both;">------------------------------------------------------------------</div><blockquote  style="margin-right:.0px;margin-top:.0px;margin-bottom:.0px;"><div  style="clear:both;"><span  style="font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;color:#000000;">From:Greg Pintilie <gregdp@gmail.com></span></div><div  style="clear:both;"><span  style="font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;color:#000000;">Sent At:2020 Aug. 19 (Wed.) 20:13</span></div><div  style="clear:both;"><span  style="font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;color:#000000;">To:孙业平 <sunyeping@aliyun.com></span></div><div  style="clear:both;"><span  style="font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;color:#000000;">Cc:chimera-users <chimera-users@cgl.ucsf.edu></span></div><div  style="clear:both;"><span  style="font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;color:#000000;">Subject:Re: [Chimera-users] Cannot dock molecule to targeted region?</span></div><div  style="clear:both;"><span  style="font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;color:#000000;"><br ></span></div><div  class=""><br  class=""></div>Hi Yeping,<div  class=""><br  class=""></div><div  class="">It seems that the part of the map you are fitting to has lower values, and the Fit-To-Segments procedure is moving the model (your antibody) towards higher values. To prevent this, there is an option in the Fit To Segments dialog ‘Mask map with region(s) to prevent large drifts’. If you enable this option you should not see the model move outside the region. You may have to press the Options button at the bottom of the dialog first to reveal this option if you don’t see it. Also make sure to try ‘Rotational search’ if the default/faster ‘Align principal axes’ doesn’t seem to find the right fit.</div><div  class=""><br  class=""></div><div  class="">There is also the ‘fitmap’ command in Chimera which does a more global search, perhaps the Chimera team may have some advice on it in this scenario, but I think you have the right idea with segmenting first and then doing the fit - it’s a bit more work but you can target the search better with it.</div><div  class=""><a  class="" href="https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/fitmap.html" target="_blank">https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/fitmap.html</a></div><div  class=""><br  class=""></div><div  class="">Greg</div><div  class=""><br  class=""><div ><br  class=""><div  class="">On Aug 19, 2020, at 1:53 AM, 孙业平 <<a  class="" href="mailto:sunyeping@aliyun.com" target="_blank">sunyeping@aliyun.com</a>> wrote:</div><br  class="Apple-interchange-newline"><div  class=""><div  class="" style="clear:both;"><span  class=" __aliyun_node_has_color" style="font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;">Dear all,</span></div><div  class="" style="clear:both;"><span  class=" __aliyun_node_has_color" style="font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;"><br  class=""></span></div><div  class="" style="clear:both;"><span  class=" __aliyun_node_has_color" style="font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;">    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  class="" style="clear:both;"><span  class=" __aliyun_node_has_color" style="font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;">                 <a  class="" href="https://drive.google.com/drive/folders/16ELIDsUxiNwRGp9ely2SRn-zjAdHCudH?usp=sharing" target="_blank">https://drive.google.com/drive/folders/16ELIDsUxiNwRGp9ely2SRn-zjAdHCudH?usp=sharing</a>.</span></div><div  class="" style="clear:both;"><span  class=" __aliyun_node_has_color" style="font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;">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  class="" style="clear:both;"><span  class=" __aliyun_node_has_color" style="font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;">    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  class=" __aliyun_node_has_bgcolor" style="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;float:none;display:inline;">"Fit to segments" action</span>.</span></div><div  class="" style="clear:both;"><span  class=" __aliyun_node_has_color" style="font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;">    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  class="" style="clear:both;"><span  class=" __aliyun_node_has_color" style="font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;"><br  class=""></span></div><div  class="" style="clear:both;"><span  class=" __aliyun_node_has_color" style="font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;">Best regards,</span></div><div  class="" style="clear:both;"><span  class=" __aliyun_node_has_color" style="font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;">Yeping Sun</span></div>_______________________________________________<br  class="">Chimera-users mailing list: <a  class="" href="mailto:Chimera-users@cgl.ucsf.edu" target="_blank">Chimera-users@cgl.ucsf.edu</a><br  class="">Manage subscription: <a  class="" href="https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" target="_blank">https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br  class=""></div></div><br  class=""></div></blockquote><div ><br ></div></div>