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Greetings Eric,</div>
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Thank you for the prompt response. Unfortunately, I cannot open my XYZ file on Chimera. The attached file is my XYZ, and I would like to know if you are able to look it over. I investigated the source you provided for a standard XYZ format but perhaps you can
give me more insight into why my XYZ file will not open.</div>
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Additionally, can you further explain how I would create the simulation/movie created from OCRA? </div>
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I look forward to hearing from you soon. Have a great day!</div>
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Best regards,</div>
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Rade Jibawi Rivera</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Eric Pettersen <pett@cgl.ucsf.edu><br>
<b>Sent:</b> Tuesday, March 9, 2021 1:51 PM<br>
<b>To:</b> Rade Jibawi Rivera <rj687@mynsu.nova.edu><br>
<b>Cc:</b> chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: [Chimera-users] ORCA XYZ FILES</font>
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<div>Hi Rade,
<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>If ORCA writes XYZ files in "standard" XYZ format as described here: <a href="https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fen.wikipedia.org%2Fwiki%2FXYZ_file_format&data=04%7C01%7Crj687%40mynsu.nova.edu%7Cf065e9bd1b934322e67c08d8e32c541f%7C2c2b2d312e3e4df1b571fb37c042ff1b%7C1%7C0%7C637509127252002486%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=CIEiVvDHOeetBP%2F4HNRMYhSdtZ9s6Vg2W%2Fr5aHNo5aU%3D&reserved=0" originalsrc="https://en.wikipedia.org/wiki/XYZ_file_format" shash="R5ZVfnycyjM9QrRpH86QHC6uSwQGIGPbwUNtKVJOlc9WFD+tr4s+PtL2f+zfdeyMIQhYnP4uqmFoKN2xypzr7/nqSEnwl9FRgCwceLA0J7KNTNHiuHP5WdedXrY+mfCdSO9WPqFvBlhWfv0A54/MkT2RrBvHIsf/RBGwKQj+Dpw=" class="">https://en.wikipedia.org/wiki/XYZ_file_format</a> then
Chimera should be able to read them as a trajectory (as described here: <a href="https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.cgl.ucsf.edu%2Fchimera%2Fcurrent%2Fdocs%2FContributedSoftware%2Fmovie%2Fframemovie.html&data=04%7C01%7Crj687%40mynsu.nova.edu%7Cf065e9bd1b934322e67c08d8e32c541f%7C2c2b2d312e3e4df1b571fb37c042ff1b%7C1%7C0%7C637509127252002486%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=b63SIzxDGLoOkb1oGcso5MU5X7ZajV0A5Oc5eqp3cUs%3D&reserved=0" originalsrc="https://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/movie/framemovie.html" shash="el5RL3dA3E9Q50C7wj9gIMyf7pLR6nynCxwJA0HucO+XIAYlrUlRMJNMPFJN2TD2M3Ii8597YgmP64uS88lV7udzGco0Z8YOWDD5zlBX+K6hf5YURUZoCBMzAXatVx+nx9yb8+yWfsZ0Dbnh1txHkCP93C0xk8cMp3fjrOMDS9I=" class="">https://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/movie/framemovie.html</a>).</div>
<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>When you say "bond interactions", do you mean that bonds break and form over the course of the trajectory? Chimera
<i class="">can</i><span class="" style="font-style:normal"> handle that, but it requires some arcane magic to turn that on -- I can describe the necessary steps if you need that capability.</span></div>
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<div class="">--Eric</div>
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<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>Eric Pettersen</div>
<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>UCSF Computer Graphics Lab</div>
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<div class="">On Mar 8, 2021, at 1:25 PM, Rade Jibawi Rivera <<a href="mailto:rj687@mynsu.nova.edu" class="">rj687@mynsu.nova.edu</a>> wrote:</div>
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<span class="" style="margin:0px; font-size:12pt; background-color:rgb(255,255,255)">Hello,</span>
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I am a student from Nova Southeastern University, and I am conducting research where I am interested in utilizing your software "Chimera" for visualization of molecular dynamics. My concern is if your software will be able to create a movie of bond interactions
with multiple time frames using ORCA XYZ output files. I would greatly appreciate it if you can give in some input. I hope to hear from you. Thank you for your time and consideration.</div>
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Best regards,</div>
<span class="" style="margin:0px; font-size:12pt; background-color:rgb(255,255,255)">Rade Jibawi Rivera</span><br class="">
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