<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Hernando,<div class=""><br class=""></div><div class=""> It is hard to explain how a 400 residue AlphaFold prediction downloads automatically, but a 1500 residue prediction hangs downloading. It only downloads once the job finishes. But that is a bit suspicious because I have never seen Google Colab succeed with 1500 residues. The GPUs it offers are just too old, even with Colab Pro (which is what I use) -- I only get GPUs with 16 GB memory that can handle about 1200 residues -- larger runs don't have enough GPU memory. Here are some test runs of AlphaFold prediction on Google Colab Nvidia P100 (16 GB) and on a desktop PC Nvidia RTX 3090 (24 GB) and on a server Nvidia A40 (48 GB). The A40 can handle over 3000 residues.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="https://www.rbvi.ucsf.edu/chimerax/data/alphafold-jan2022/afspeed.html" class="">https://www.rbvi.ucsf.edu/chimerax/data/alphafold-jan2022/afspeed.html</a></div><div class=""><br class=""></div><div class="">I think your download problem is a Google Colab issue. Unfortunately Google Colab is an erratic service, although the price (free) is right.</div><div class=""><br class=""></div><div class=""> Tom</div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Sep 4, 2022, at 6:51 AM, Hernando J Sosa <<a href="mailto:hernando.sosa@einsteinmed.edu" class="">hernando.sosa@einsteinmed.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta charset="UTF-8" class=""><div class="elementToProof" style="font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">Thanks Tom,<br class=""></div><div class="elementToProof" style="font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;"><br class=""></div><div class="elementToProof" style="font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">I've run successfully other predictions but of smaller sequences (~400 residues). This happened with a larger but not huge complex ( ~1500 residues total). I've tried others runs but they crashed with an error message saying that RAM was insufficient, even though the goggle account was upgraded to pro (not pro+). <span class="Apple-converted-space"> </span><br class=""></div><div class="elementToProof" style="font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;"><br class=""></div><div class="elementToProof" style="font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">I am using a windows 10 computer and it was not in screen saving mode, but I was using the multiple desktop feature. It is likely that when the run finished the desktop with chimera and the google colab window was not the one that was on display. Would this be an issue ??<br class=""></div><div class="elementToProof" style="font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;"><br class=""></div><div class="elementToProof" style="font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">Best</div><div class="elementToProof" style="font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;"><br class=""></div><div class="elementToProof" style="font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">Hernando<br class=""></div><div style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><br class=""></div><div id="Signature" class=""><div class=""><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><span style="margin: 0px; font-size: 15px; font-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; color: rgb(32, 31, 30); text-align: start; background-color: rgb(255, 255, 255);" class=""><font size="2" face="Arial" class=""><span style="margin: 0px;" class="">___________________________________<br class=""></span></font></span></div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><div style="margin: 0px; font-size: 15px; font-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; color: rgb(32, 31, 30); text-align: start; background-color: rgb(255, 255, 255);" class=""><font size="2" face="Arial" class=""><span style="margin: 0px; font-size: 9pt; font-family: Arial, Helvetica, sans-serif;" class="">Hernando Sosa</span><span style="margin: 0px;" class=""><span style="margin: 0px; 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font-size: 15px; font-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; color: rgb(32, 31, 30); text-align: start; background-color: rgb(255, 255, 255);" class=""><font size="2" face="Arial" class=""><span style="margin: 0px;" class=""><span style="margin: 0px;" class=""></span></span><span style="margin: 0px;" class=""><span style="margin: 0px; font-size: 9pt; font-family: Arial, Helvetica, sans-serif;" class="">emai: <span class=""> </span></span><span style="margin: 0px;" class=""><a href="mailto:hernando.sosa@einsteinmed.org" target="_blank" rel="noopener noreferrer" data-auth="NotApplicable" title="hernando.sosa@einsteinmed.org" data-linkindex="0" style="margin: 0px;" class=""><span style="margin: 0px; font-size: 9pt; font-family: Arial, Helvetica, sans-serif;" class="">hernando.sosa@einsteinmed.</span></a><span style="margin: 0px; font-size: 9pt; font-family: Arial, Helvetica, sans-serif;" class="">edu</span><br class=""></span></span></font></div><div style="margin: 0px; font-size: 15px; font-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; color: rgb(32, 31, 30); text-align: start; background-color: rgb(255, 255, 255);" class=""><span style="margin: 0px;" class=""><font size="2" face="Arial" class=""><span style="margin: 0px; font-size: 9pt; font-family: "Arial Black", Arial, sans-serif;" class="">___________________________________</span></font></span></div><br class=""></div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><br class=""></div></div></div></div><div id="appendonsend" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""></div><hr tabindex="-1" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; display: inline-block; width: 879.046875px;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class=""></span><div id="divRplyFwdMsg" dir="ltr" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><font face="Calibri, sans-serif" style="font-size: 11pt;" class=""><b class="">From:</b><span class="Apple-converted-space"> </span>Tom Goddard <<a href="mailto:goddard@sonic.net" class="">goddard@sonic.net</a>><br class=""><b class="">Sent:</b><span class="Apple-converted-space"> </span>Friday, September 2, 2022 5:17 PM<br class=""><b class="">To:</b><span class="Apple-converted-space"> </span>Hernando J Sosa <<a href="mailto:hernando.sosa@einsteinmed.edu" class="">hernando.sosa@einsteinmed.edu</a>><br class=""><b class="">Cc:</b><span class="Apple-converted-space"> </span><a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a><span class="Apple-converted-space"> </span><<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>><br class=""><b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [chimerax-users] AlphaFold</font><div class=""> </div></div><div class="" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; line-break: after-white-space;"><table border="4" cellpadding="3" cellspacing="3" style="background-color: rgb(254, 0, 0); border-collapse: collapse; border: 4px solid rgb(203, 203, 203); color: rgb(255, 204, 103); width: 893px; text-align: center;" class=""><tbody class=""><tr class=""><td class=""><i class="">CAUTION: This email comes from an external source; the attachments and/or links may compromise our secure environment. Do not open or click on suspicious emails. Please click on the “Phish Alert” button on the top right of the Outlook dashboard to report any suspicious emails.</i></td></tr></tbody></table><div class="">Hi Hernando,<div class=""><br class=""></div><div class=""> I have not seen that problem. Does that always happen when you run an AlphaFold prediction? What operating system are you on? Mac? I have seen Mac ask for permission to download from a web site the first time you download from that site. It may be that the browser in ChimeraX showing the Alphafold run does not know how to ask. But it doesn't make much sense because I do not observe this. Another idea -- if your machine is sleeping when the job finishes maybe Google Colab gives up trying to download the results to your machine. If it is sleeping you might want to set your machine not to sleep during the run. This can also be important to avoid Google Colab dropping your job entirely due to inactivity. I guess another possibility is that it could be a firewall problem where your network firewall blocks the download. Since the download seems to succeed for most users, there seems to be something specific about your computer setup that causes the problem.</div><div class=""><br class=""></div><div class=""> At any rate, to get the results you should be able to click on Files in the left column of the AlphaFold google colab panel and among the files you should see results.zip which is what ChimeraX downloads when the job finishes. There should be a vertical "..." if hover over that file that pops up a menu that allows you to download the file. Try that. ChimeraX is receiving the download and putting it in ~/Downloads/ChimeraX/AlphaFold/prediction_N. It may also hang if there is some issue that prevents the downloads. Possibly you could connect to Google Colab through a standard web browser and try downloading the results.zip file and maybe you would at least get an error that would help diagnose the problem.</div><div class=""><br class=""></div><div class=""><span class="x_Apple-tab-span" style="white-space: pre;"></span>Tom</div><div class=""><br class=""></div><div class=""><div class=""><br class=""><blockquote type="cite" class=""><div class="">On Sep 2, 2022, at 1:26 PM, Hernando J Sosa via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:</div><br class="x_Apple-interchange-newline"><div class=""><div class="x_elementToProof" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none;"><span class=""> </span>Dear Chimera/ChimeraX,<span class="x_Apple-converted-space"> </span><br class=""></div><div class="x_elementToProof" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none;"><br class=""></div><div class="x_elementToProof" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none;">I've been running Alphafold through UCSF ChimeraX and sometimes the procedure gets stuck indefinitely at the last step, downloading the results files (see screenshot). Is this a known issue? is there a workaround ?</div><div class="x_elementToProof" style="font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;"><br class=""></div><div class="x_elementToProof" style="font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">Thanks</div><div class="x_elementToProof" style="font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;"><br class=""></div><div class="x_elementToProof" style="font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">Hernando</div><div class="x_elementToProof" style="font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;"><br class=""></div><div class="x_elementToProof" style="font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;"><span id="x_cid:fec1a7e2-7922-44b8-b86e-eb2401cd211c" class=""><image.png></span><br class=""></div><span class="" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none; float: none; display: inline !important;">_______________________________________________</span><br class="" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none;"><span class="" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none; float: none; display: inline !important;">ChimeraX-users mailing list</span><br class="" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none;"><a href="mailto:ChimeraX-users@cgl.ucsf.edu" class="" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;">ChimeraX-users@cgl.ucsf.edu</a><br class="" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none;"><span class="" style="font-family: Helvetica; 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