<html><head></head><body><div class="ydpa796e90ayahoo-style-wrap" style="font-family:verdana, helvetica, sans-serif;font-size:16px;"><div><div>Hi Elaine,</div><div><br></div><div>Thanks for the useful tips. </div><div><br></div><div>I encountered another problem when I tried to save the session.</div><div>The pop out shows : cannot save surfaces without associated structure. Surface will not be saved".</div><div><br></div><div>What can i do to resolve this? I have surfaces in the model.</div><div><br></div><div>Thank you</div><div><br></div><div class="ydpa796e90asignature"><span style="font-size:medium;font-family:verdana, helvetica, sans-serif;"><font face="times new roman, new york, times, serif">Best Regards,<br>Chan Soo Khim<br></font><br></span></div></div>
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On Friday, March 29, 2019, 12:16:43 AM GMT+8, Elaine Meng <meng@cgl.ucsf.edu> wrote:
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<div><div dir="ltr">Hi Chan Soo Khim,<br clear="none">The Modeller tools in Chimera (comparative modeling or adding missing loops) only model one protein chain at a time.<br clear="none"><<a shape="rect" href="http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html" target="_blank">http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html</a>><br clear="none"><br clear="none">You could “manually” put the model of the protein chain together with the RNA from the original structure:<br clear="none"><br clear="none">(1) open the original structure, delete everything except the RNA (e.g. command: delete ~nucleic acid )<br clear="none"><<a shape="rect" href="http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#deletion" target="_blank">http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#deletion</a>><br clear="none"><br clear="none">(2) open the protein model with loops<br clear="none"><br clear="none">(3) combine those two models into a new third model (e.g. command: combine #0,1 name mycomplex model #5 )<br clear="none"><<a shape="rect" href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html" target="_blank">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html</a>><br clear="none"><br clear="none">However, there might be poor contacts or overlapping atoms between the protein and the RNA since the protein modeling step ignores the RNA. Typically you would model multiple different loop conformations and look at them all together with the RNA (from the original structure) to decide which ones to keep in your model.<br clear="none"><br clear="none">I hope this helps,<br clear="none">Elaine<br clear="none">-----<br clear="none">Elaine C. Meng, Ph.D.<br clear="none">UCSF Chimera(X) team<br clear="none">Department of Pharmaceutical Chemistry<br clear="none">University of California, San Francisco<br clear="none"><div class="yqt1250546699" id="yqtfd36388"><br clear="none">> On Mar 27, 2019, at 11:46 PM, soo khim <<a shape="rect" ymailto="mailto:sookhim89@yahoo.com" href="mailto:sookhim89@yahoo.com">sookhim89@yahoo.com</a>> wrote:<br clear="none">> <br clear="none">> Hi chimera,<br clear="none">> I have a RNA-protein complex pdb file. After modeled the missing loops in the protein and saved the pdb file for remodel protein structure, the RNA is missing in the new pdb file. How should i save the remodel protein model together with its RNA?<br clear="none">> Thank you<br clear="none">> Best Regards,<br clear="none">> Chan Soo Khim<br clear="none"></div></div></div>
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