<html><head>
<meta http-equiv="Content-Type" content="text/html; charset=Windows-1252">
<style type="text/css" style="display:none;"> P {margin-top:0;margin-bottom:0;} </style>
</head><body dir="ltr">
<div class="elementToProof"><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">Hello Elaine,</span></div>
<div class="elementToProof"><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);"><br>
</span></div>
<div class="elementToProof"><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);" class="ContentPasted1">It's nice to hear from you. I guess I input the sequence in a correct
way as I tried to input the sequence the same way as in this video <a href="https://www.youtube.com/watch?v=6lXeCPuTePs" id="LPlnkOWALinkPreview">https://www.youtube.com/watch?v=6lXeCPuTePs</a> </span></div>
<div class="_Entity _EType_OWALinkPreview _EId_OWALinkPreview _EReadonly_1">
<div id="LPBorder_BVTaHR0cHM6Ly93d3cueW91dHViZS5jb20vd2F0Y2g:dj02bFhlQ1B1VGVQcw.." class="LPBorder464147" style="width: 100%; margin-top: 16px; margin-bottom: 16px; position: relative; max-width: 800px; min-width: 424px;">
<table id="LPContainer464147" role="presentation" style="padding: 12px 36px 12px 12px; width: 100%; border-width: 1px; border-style: solid; border-color: rgb(200, 200, 200); border-radius: 2px;">
<tbody>
<tr valign="top" style="border-spacing: 0px;">
<td>
<div id="LPImageContainer464147" style="position: relative; margin-right: 12px; height: 180px; overflow: hidden; width: 240px;">
<a target="_blank" id="LPImageAnchor464147" href="https://www.youtube.com/watch?v=6lXeCPuTePs"><img id="LPThumbnailImageId464147" alt="" height="180" width="240" style="display: block;" src="https://www.bing.com/th?id=OVP.95Ygyv4AXQTgCS0WB9iXtgHgFo&pid=Api"></a></div>
</td>
<td style="width: 100%;">
<div id="LPTitle464147" style="font-size: 21px; font-weight: 300; margin-right: 8px; font-family: wf_segoe-ui_light, "Segoe UI Light", "Segoe WP Light", "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif; margin-bottom: 12px;">
<a target="_blank" id="LPUrlAnchor464147" href="https://www.youtube.com/watch?v=6lXeCPuTePs" style="text-decoration: none; color: var(--themePrimary);">Running AlphaFold to Predict Protein Complexes from ChimeraX</a></div>
<div id="LPDescription464147" style="font-size: 14px; max-height: 100px; color: rgb(102, 102, 102); font-family: wf_segoe-ui_normal, "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif; margin-bottom: 12px; margin-right: 8px; overflow: hidden;">
How to predict the structure of a photoreaction center complex of 3 proteins from ChimeraX using AlphaFold-Multimer. Requires a ChimeraX daily build newer than December 2, 2021 or version 1.4. It is not in ChimeraX version 1.3. Web page describing steps https://www.rbvi.ucsf.edu/chimerax/data/alphafold-dec2021/af_multimer.html</div>
<div id="LPMetadata464147" style="font-size: 14px; font-weight: 400; color: rgb(166, 166, 166); font-family: wf_segoe-ui_normal, "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif;">
www.youtube.com</div>
</td>
</tr>
</tbody>
</table>
</div>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);" class="elementToProof">
Below is a screenshot of interface. I would like to do a protein-protein interaction predication.</div>
<div class="elementToProof"><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);"><img style="max-width:100%" class="FluidPluginCopy ContentPasted0 w-879 h-469" size="35103" contenttype="image/png" data-outlook-trace="F:1|T:1" src="cid:c426f420-36c5-4d71-afa5-349318422ae5"><br>
</span></div>
<div class="elementToProof"><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">Best,</span></div>
<div class="elementToProof"><br>
</div>
<div class="elementToProof" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
Junyi</div>
<div id="appendonsend"></div>
<hr style="display:inline-block;width:98%" tabindex="-1">
<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Elaine Meng <meng@cgl.ucsf.edu><br>
<b>Sent:</b> Thursday, January 19, 2023 11:34 AM<br>
<b>To:</b> Liang, Junyi <LIANGJ3@ccf.org><br>
<b>Cc:</b> chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> [EXT] Re: [chimerax-users] missing or invalid sequences</font>
<div> </div>
</div>
<div>CAUTION CYBER RISK: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender, expected to receive this content and trust that it’s safe. If you determine that the email isn’t from a
trusted source, you can delete the email, submit it via the BlueFish button in Outlook for investigation or forward the email as an attachment to phishtanktriage@ccf.org if you don’t have the Bluefish button or are on a mobile device.<br>
<br>
Without the details of what you did, I can only guess that somehow you did not enter the sequences correctly. They should be plain text, with only a comma between sequences of different proteins.<br>
<br>
see AlphaFold predict help:<br>
<<a href="https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#predict">https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#predict</a>><br>
<br>
To say anything more informative, we would need to see exactly what you pasted into the sequence area, and what options you chose in the input dialog.<br>
<br>
I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D. <br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
<br>
> On Jan 19, 2023, at 7:27 AM, Liang, Junyi via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:<br>
> <br>
> I would like to predicate interaction between two proteins, and tried chimerax version 1.5 after noticing a youtube video
<a href="https://www.youtube.com/watch?v=6lXeCPuTePs">
https://www.youtube.com/watch?v=6lXeCPuTePs</a>.<br>
> <br>
> Running AlphaFold to Predict Protein Complexes from ChimeraX<br>
> How to predict the structure of a photoreaction center complex of 3 proteins from ChimeraX using AlphaFold-Multimer. Requires a ChimeraX daily build newer than December 2, 2021 or version 1.4. It is not in ChimeraX version 1.3. Web page describing steps
<a href="https://www.rbvi.ucsf.edu/chimerax/data/alphafold-dec2021/af_multimer.html">
https://www.rbvi.ucsf.edu/chimerax/data/alphafold-dec2021/af_multimer.html</a><br>
> <a href="http://www.youtube.com">
www.youtube.com</a><br>
> I input the two protein sequences in same way as shown in the video and hit predict. But your software says "missing or invalid sequences". How come?<br>
> <br>
</div>
<br><p class="MsoNormal"><font size="5" color="green"><span style="font-size:18.0pt;color:green"></span></font><font size="2" color="navy" face="Calibri"><span style="font-size:10.0pt;font-family:Calibri;color:navy"> </span></font><font size="1" color="green" face="Arial"><span style="font-size:7.0pt;font-family:Arial;color:green">Please consider the environment before printing this e-mail</span></font></p>Cleveland Clinic is currently ranked as one of the nation’s top hospitals by <i>U.S. News & World Report</i> (2022-2023). Visit us online at <a href="http://www.clevelandclinic.org" target="_blank">http://www.clevelandclinic.org</a> for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.</body></html>