<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>We can reproduce the problem you’re having (only occurs on Linux) and are working on a solution. Until we fix it, you have three options:</div><div class=""><br class=""></div><div class="">1) Use a non-Linux machine</div><div class="">2) Since PubChem 11163 is simply a diglycine, use the “peptide” option in Build Structure with the sequence “GG”. This will differ slightly from the PubChem structure in that the PubChem one will be protonated as neutral, whereas the Build Structure one (if you later add hydrogens) will be protonated for biological pH.</div><div class="">3) Assuming you installed Chimera in the default location on your Linux box, run it as “SSL_CERT_DIR=/etc/ssl/certs ~/.local/UCSF-Chimera64-<VERSION>/bin/chimera”. You will have to look in your ~/.local directory and replace <VERSION> with the Chimera version number you see there. Then you should be able to use a PubChem fetch successfully.</div><div class=""><br class=""></div><div class="">—Eric</div><div class=""><br class=""></div><div class=""><br class=""><div class="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>Eric Pettersen</div><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>UCSF Computer Graphics Lab</div><div class=""><br class=""></div></div>
</div>
<br class=""><div><blockquote type="cite" class=""><div class="">On Aug 20, 2017, at 11:03 AM, Dilip H N <<a href="mailto:cy16f01.dilip@nitk.edu.in" class="">cy16f01.dilip@nitk.edu.in</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><img width="0" height="0" class="mailtrack-img" alt="" src="https://mailtrack.io/trace/mail/48e83897ede6640ade45690300da8eec39864daa.png?u=1287386" style="display: flex;"><span style="font-size: 12.8px;" class="">Hello,</span><div style="font-size: 12.8px;" class="">I have installed chimera in ubuntu 14.04..</div><div style="font-size: 12.8px;" class="">I am finding difficult to get the .pdb format for diglyicne peptide (and further to create the topology and run the simulation in gromacs)... </div><div style="font-size: 12.8px;" class="">1] If in Build Structure i select PubChem CID and type 11163 (Diglycine PubChem CID) i am getting error as:-</div><div style="font-size: 12.8px;" class="">Error fetching 11163:[Errno socket error] [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssi.c:590)<br clear="all" class=""><div class="">2] I even tried through File - Fetch by ID - Pubchem and typed 1163 (Diglycine PubChem CID).. but in vain..i am getting the same error..</div><div class=""><br class=""></div><div class="">So can anybody kindly help....i am a novice here..</div><div class="">Any suggestions are highly appreciated..</div><div class=""><br class=""></div><div class="">Thank you... </div></div><br class=""><br class=""><br class=""><div style="display: inline;" class=""><div class="mt-signature" style="padding-right: 5px;"><a href="https://mailtrack.io/" class="mt-signature-logo" style="text-decoration: none;"><img src="https://s3-eu-west-1.amazonaws.com/mailtrack-crx/icon-signature.png" height="14" class=""><span class="Apple-converted-space"> </span></a><span style="color: rgb(153, 153, 153);" class="">Sent with<span class="Apple-converted-space"> </span></span><a href="https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.dilip@nitk.edu.in&idSignature=22" class="mt-install">Mailtrack</a></div></div></div><div class="gmail_extra" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><br class=""><div class="gmail_quote">On Sun, Aug 20, 2017 at 11:15 PM, Dilip H N<span class="Apple-converted-space"> </span><span dir="ltr" class=""><<a href="mailto:cy16f01.dilip@nitk.edu.in" target="_blank" class="">cy16f01.dilip@nitk.edu.in</a>></span><span class="Apple-converted-space"> </span>wrote:<br class=""><blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-style: solid; border-left-color: rgb(204, 204, 204); padding-left: 1ex;"><div dir="ltr" class=""><img width="0" height="0" class="m_-7742111250559486655mailtrack-img" alt="" src="data:image/gif;base64,R0lGODlhAQABAIAAAAAAAP///yH5BAEAAAAALAAAAAABAAEAAAIBRAA7" style="display: flex;">Hello,<div class="">I have install chimers in ubuntu 14.04..</div><div class="">I am finding difficult to get the .pdb format for diglyicne peptide... </div><div class="">1] If in Build Structure i select PubChem CID and type 11163 (Diglycine PubChem CID) i am getting error as:-</div><div class="">Error fetching 11163:[Errno socket error] [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssi.c:590)<br clear="all" class=""><div class="">2] I even tried through File - Fetch by ID - Pubchem and typed 1163 (Diglycine PubChem CID).. but in vain..i am getting the same error..</div><div class=""><br class=""></div><div class="">So can anybody kindly help....i am a novice here..</div><div class=""><br class=""></div><div class="">Thank you...</div><span class="HOEnZb"><font color="#888888" class="">--<span class="Apple-converted-space"> </span><br class=""><div class="m_-7742111250559486655gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class="">With Best Regards,<div class=""><br class=""></div><div class="">DILIP.H.N<div class="">Ph.D Student</div></div></div></div></div></div></div></div></div><br class=""><br class=""><br class=""><div style="display: inline;" class=""><div class="m_-7742111250559486655mt-signature" style="padding-right: 5px;"><a href="https://mailtrack.io/" class="m_-7742111250559486655mt-signature-logo" target="_blank" style="text-decoration: none;"><img src="https://s3-eu-west-1.amazonaws.com/mailtrack-crx/icon-signature.png" height="14" class=""><span class="Apple-converted-space"> </span></a><span style="color: rgb(153, 153, 153);" class="">Sent with<span class="Apple-converted-space"> </span></span><a href="https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.dilip@nitk.edu.in&idSignature=22" class="m_-7742111250559486655mt-install" target="_blank">Mailtrack</a></div></div></font></span></div></div></blockquote></div><br class=""><br clear="all" class=""><div class=""><br class=""></div>--<span class="Apple-converted-space"> </span><br class=""><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class="">With Best Regards,<div class=""><br class=""></div><div class="">DILIP.H.N<div class="">Ph.D Student</div></div></div></div></div></div></div></div></div></div><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">_______________________________________________</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">Chimera-users mailing list:<span class="Apple-converted-space"> </span></span><a href="mailto:Chimera-users@cgl.ucsf.edu" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">Chimera-users@cgl.ucsf.edu</a><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">Manage subscription:<span class="Apple-converted-space"> </span></span><a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a></div></blockquote></div><br class=""></div></body></html>