<div class="__aliyun_email_body_block"><div  style="clear:both;"><span  style="font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;color:#000000;"><br ></span></div><div  style="clear:both;"><span  style="color:#111111;font-family:Arial,sans-serif;">Dear all,</span><br ></div><div  style="clear:both;"><div  class="nova-e-text nova-e-text--size-m nova-e-text--family-sans-serif nova-e-text--spacing-s nova-e-text--color-inherit redraft-text __aliyun_node_has_color __aliyun_node_has_bgcolor" style="border:.0px;text-transform:none;display:block;margin:.0px .0px 15.0px;padding:.0px;color:#111111;font-weight:400;font-family:Roboto,Arial,sans-serif;font-size:14.0px;line-height:1.3;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;text-align:left;text-indent:.0px;widows:2;background-color:#ffffff;text-decoration-style:initial;text-decoration-color:initial;"><p  class="MsoNormal __aliyun_node_has_bgcolor" style="margin:.0px;font-size:14.0px;font-family:等线;text-align:left;background:white;"><span  class=" __aliyun_node_has_color" style="font-family:Arial,sans-serif;color:#111111;"> </span></p><p  class="MsoNormal __aliyun_node_has_bgcolor" style="margin:.0px;font-size:14.0px;font-family:等线;text-align:left;background:white;"><span  class=" __aliyun_node_has_color" style="font-family:Arial,sans-serif;color:#111111;">I seem to read some posts in the chimera email-list that discuss split
combined mol2 files contains many compound into single mol2 files for virtual
screening, but now I cannot find them. </span></p><p  class="MsoNormal __aliyun_node_has_bgcolor" style="margin:.0px;font-size:14.0px;font-family:等线;text-align:left;background:white;"><span  class=" __aliyun_node_has_color" style="font-family:Arial,sans-serif;color:#111111;">I wish to do some virtual screening with autodock 4. I have split a sdf
file contains over a thousand compounds into single mol2 file with the linux
shell "csplit" command. However, I find lots of such mol2 files still
contain multiple ligands </span><span  class=" __aliyun_node_has_color" style="font-family:宋体;color:#111111;">（</span><span  class=" __aliyun_node_has_color" style="font-family:Arial,sans-serif;color:#111111;">LIG1, LIG2,
LIG3, etc.) whose coordinates mix together and so can not be split by shell
command "csplit". Please find three such examples at:</span></p><p  class="MsoNormal __aliyun_node_has_bgcolor" style="margin:.0px;font-size:14.0px;font-family:等线;text-align:left;background:white;"><span  class=" __aliyun_node_has_color" style="font-family:Arial,sans-serif;color:#111111;"><a  href="https://www.researchgate.net/deref/https%3A%2F%2Fdrive.google.com%2Fdrive%2Ffolders%2F1AiW00lbA4tRfLu-l47QfxWVn8PqnQ-5J%3Fusp%3Dsharing" target="_blank"><span  class=" __aliyun_node_has_color" style="color:blue;border:1.0px none windowtext;padding:.0px;">https://drive.google.com/drive/folders/1AiW00lbA4tRfLu-l47QfxWVn8PqnQ-5J?usp=sharing</span></a></span></p><p  class="MsoNormal __aliyun_node_has_bgcolor" style="margin:.0px;font-size:14.0px;font-family:等线;text-align:left;background:white;"><span  class=" __aliyun_node_has_color" style="font-family:Arial,sans-serif;color:#111111;">I can split the ligands in a mol2 file manually in Chimera GUI: first open
the mol2 file, then select the ligands and save them as pdb files respectively
to get separate pdb files for these ligands. After then reopen these pdb files
respectively and save them as mol2 file. However, to process a large amount of
mol2 files manually is impossible, so I need a command or script to do this. I
hope chimera can do this.</span></p><p  class="MsoNormal __aliyun_node_has_bgcolor" style="margin:.0px;font-size:14.0px;font-family:等线;text-align:left;background:white;"><span  class=" __aliyun_node_has_color" style="font-family:Arial,sans-serif;color:#111111;">Chimera has a command "split": </span></p><p  class="MsoNormal __aliyun_node_has_bgcolor" style="margin:.0px;font-size:14.0px;font-family:等线;text-align:left;background:white;"><span  class=" __aliyun_node_has_color" style="font-family:Arial,sans-serif;color:#111111;">   </span></p><p  class="MsoNormal __aliyun_node_has_bgcolor" style="margin:.0px;font-size:14.0px;font-family:等线;text-align:left;background:white;"><b ><span  class=" __aliyun_node_has_color" style="font-size:18.0px;font-family:微软雅黑,sans-serif;color:black;">split [ <i >model_number(s)</i> ]
[ chains ] [ ligands ] [ connected ]
[ atoms <a  href="https://mail.aliyun.com/alimail/frameatom_spec.html" target="_blank"><i ><span  class=" __aliyun_node_has_color" style="color:blue;">atom-spec</span></i></a> ]<i ><sub >n</sub></i></span></b></p><p  class="MsoNormal __aliyun_node_has_bgcolor" style="margin:.0px;font-size:14.0px;font-family:等线;text-align:left;background:white;"><span  class=" __aliyun_node_has_color" style="font-family:Arial,sans-serif;color:#111111;"> </span></p><p  class="MsoNormal __aliyun_node_has_bgcolor" style="margin:.0px;font-size:14.0px;font-family:等线;text-align:left;background:white;"><span  class=" __aliyun_node_has_color" style="font-family:Arial,sans-serif;color:#111111;">However, it doesn't seem to be suitable for my scenario. Does anyone know
whether chimera can split such mol2 files and how?</span></p><p  class="MsoNormal __aliyun_node_has_bgcolor" style="margin:.0px;font-size:14.0px;font-family:等线;text-align:left;background:white;"><span  class=" __aliyun_node_has_color" style="font-family:Arial,sans-serif;color:#111111;">I will appreciate any help of you. </span></p><p  class="MsoNormal" style="margin:.0px;text-align:justify;font-size:14.0px;font-family:等线;"> </p></div></div><div  style="clear:both;"><div  class="nova-e-text nova-e-text--size-m nova-e-text--family-sans-serif nova-e-text--spacing-s nova-e-text--color-inherit redraft-text __aliyun_node_has_color __aliyun_node_has_bgcolor" style="border:.0px;text-transform:none;display:block;margin:.0px;padding:.0px;color:#111111;font-weight:400;font-family:Roboto,Arial,sans-serif;font-size:14.0px;line-height:1.3;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;text-align:left;text-indent:.0px;widows:2;background-color:#ffffff;text-decoration-style:initial;text-decoration-color:initial;"></div><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 ><br ></div></div>