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<div dir="ltr" data-setdir="false">Hi Elaine,</div><div dir="ltr" data-setdir="false"><br></div><div dir="ltr" data-setdir="false">Thank you so much for explaining all this!</div><div dir="ltr" data-setdir="false"><br></div><div dir="ltr" data-setdir="false">I will try it immediately.</div><div dir="ltr" data-setdir="false"><br></div><div dir="ltr" data-setdir="false"><br></div><div dir="ltr" data-setdir="false">Thanks a lot for your time and help,</div><div dir="ltr" data-setdir="false">Chara</div><div><br></div>
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On Thursday, January 6, 2022, 08:00:38 PM GMT+1, Elaine Meng <meng@cgl.ucsf.edu> wrote:
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<div><div dir="ltr">Hi Chara,<br clear="none">In the Build Structure tool (menu: Tools... Structure Editing... Build Structure) <br clear="none"><<a shape="rect" href="https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html" target="_blank">https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html</a>><br clear="none"><br clear="none">....you can:<br clear="none"><br clear="none">- use the Start Structure section to build a peptide de novo. You can choose the sequence and all of the individual backbone angles, so it can be whatever conformation you want (alpha-helix, etc.)<br clear="none"><br clear="none"><<a shape="rect" href="https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#start" target="_blank">https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#start</a>><br clear="none"><br clear="none">- use the Join Models section to put different peptides together pairwise. So you could get some peptides from de novo building as explained above, and/or you could open known PDB structures and delete the parts you don't want, to use sections of those known structures.<br clear="none"><br clear="none"><<a shape="rect" href="https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#join" target="_blank">https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#join</a>> <br clear="none"><br clear="none">E.g. if you build 1 de novo peptide as model #0, then open a PDB structure as model #1 and delete the sections you don't want, then you can use the Join Models section of the Build Structure tool to join #0 and #1 to make a new single-chain model. Then if you had another peptide in a different model, you could use Join Models again to make yet another model that has all three pieces bonded together.<br clear="none"><br clear="none">You may also be interested in the other sections of Build Structure for modifying your structure.<br clear="none"><br clear="none">One more possibility:<br clear="none">If you already have most of the protein and you just want to build more residues on one end or the other, you can do it using the "addaa" command:<br clear="none"><<a shape="rect" href="https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addaa.html" target="_blank">https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addaa.html</a>><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"><br clear="none"><div class="yqt1409736453" id="yqtfd25753"><br clear="none">> On Jan 6, 2022, at 6:12 AM, Chara Spanou via Chimera-users <<a shape="rect" ymailto="mailto:chimera-users@cgl.ucsf.edu" href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a>> wrote:<br clear="none">> <br clear="none">> Hello chimera-users,<br clear="none">> <br clear="none">> I would like to introduce a-helices into my protein structure ab initio.<br clear="none">> <br clear="none">> Is it possible to do this with chimera?<br clear="none">> <br clear="none">> Another option that I have is to take a-helical pieces of sequence from a different model<br clear="none">> <br clear="none">> and introduce these into the desired model.<br clear="none">> <br clear="none">> Would that be more feasible?<br clear="none">> <br clear="none">> There is a chance I also need to introduce loops and turns ab initio to best localize the<br clear="none">> <br clear="none">> introduced a-helices within my protein structure.<br clear="none">> <br clear="none">> Can you please indicate how can a chimera user build all this ab initio?<br clear="none">> <br clear="none">> <br clear="none">> Thank you in advance for your time and help,<br clear="none">> <br clear="none">> Chara Spanou<br clear="none">> PhD student<br clear="none">> University of Cologne<br clear="none"><br clear="none"></div></div></div>
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