<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=""><div class="">Dear Oleg,</div><div class=""><br class=""></div>I would not say that the PDB was not handling the mmCIF file at all.<div class="">In fact the file is « accepted » but not well processed. I do have glycans chains in the enzyme I am working with and they appear in the processing such as part of the polypeptide chain but they should not.</div><div class="">Maybe a specific issue with glycol processing ?</div><div class=""><br class=""></div><div class="">I've used the PDB file from Phenix for deposit and added the TER record after the polypeptide chain and before the glycosylation and this solve this issue (but no more a mmCIF file).</div><div class=""><br class=""></div><div class="">I will try the last nightly and have a test with another structure I am working on.</div><div class=""><br class=""></div><div class="">Best regards</div><div class=""><br class=""></div><div class="">Xavier</div><div class=""><div><br class=""><blockquote type="cite" class=""><div class="">Le 19 déc. 2018 à 21:12, Oleg Sobolev <<a href="mailto:osobolev@lbl.gov" class="">osobolev@lbl.gov</a>> a écrit :</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Dear Xavier,<div class=""><br class=""></div><div class="">Unfortunately, we were not able to figure out the reason PDB not handling Phenix mmCIFs. What is exact error message you are getting? Since the 1.14 release we changed some output to be more compliant with PDB mmCIF, so there is a chance it will work with the latest nightly. Please keep us updated.</div><div class=""><br class=""></div><div class="">Best regards,</div><div class="">Oleg Sobolev.</div></div><br class=""><div class="gmail_quote"><div dir="ltr" class="">On Tue, Dec 18, 2018 at 10:23 PM Xavier Brazzolotto <<a href="mailto:xavier.brazzolotto@chemdef.fr" class="">xavier.brazzolotto@chemdef.fr</a>> wrote:<br class=""></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="overflow-wrap: break-word;" class="">Dear Oleg,<div class=""><br class=""></div><div class="">I had the same issue lately (mmCIF not handled by PDB deposition system using Phenix 1.14.3260).</div><div class="">Is this issue has been resolved in a recent nightly ?<br class=""><div class=""><br class=""></div><div class="">Many thanks</div><div class=""><br class=""></div><div class="">Xavier</div><div class=""><br class=""><blockquote type="cite" class=""><div class="">Le 29 nov. 2018 à 20:20, Oleg Sobolev <<a href="mailto:osobolev@lbl.gov" target="_blank" class="">osobolev@lbl.gov</a>> a écrit :</div><br class="gmail-m_2435528438548355430Apple-interchange-newline"><div class=""><div dir="ltr" class="">Dear Dominik,<div class=""><br class=""></div><div class="">Thank you for letting us know!</div><div class=""><br class=""></div><div class="">Would it be possible to send me (off-list) the 1.13 and 1.14 cif files for investigation along with the pdb file used for conversion. Also PDB deposition message would be helpful (if available). All files will be kept confidential.</div><div class=""><br class=""></div><div class="">Best regards,</div><div class="">Oleg Sobolev.</div></div><br class=""><div class="gmail_quote"><div dir="ltr" class="">On Thu, Nov 29, 2018 at 2:17 AM Dominik Oberthuer <<a href="mailto:dominik.oberthuer@desy.de" target="_blank" class="">dominik.oberthuer@desy.de</a>> wrote:<br class=""></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Dear all,<br class="">
<br class="">
I recently found that phenix.refine in version 1.14-3260 generates <br class="">
coordinate mmCIFs that the PDB deposition system can't handle.<br class="">
<br class="">
After struggling with this for some time I used an installation of <br class="">
Phenix 1.13-2998 I still have on my MacBook and used the <br class="">
mmCIF/PDB-conversion tool from this version and had no more trouble with <br class="">
uploading the mmCIF to the PDB.<br class="">
<br class="">
Maybe it is worthwhile to check which changes from 1.13 to 1.14 might <br class="">
have caused these issues.<br class="">
<br class="">
Thanks!<br class="">
<br class="">
Dominik<br class="">
<br class="">
-- <br class="">
Dr. Dominik Oberthür<br class="">
<br class="">
CFEL - Center for Free-Electron Laser Science - DESY<br class="">
Coherent Imaging Division<br class="">
<br class="">
Notkestrasse 85<br class="">
22607 Hamburg<br class="">
Germany<br class="">
<br class="">
phone: +49 (0)40 8998 6394<br class="">
<a href="mailto:dominik.oberthuer@cfel.de" target="_blank" class="">dominik.oberthuer@cfel.de</a><br class="">
<br class="">
_______________________________________________<br class="">
phenixbb mailing list<br class="">
<a href="mailto:phenixbb@phenix-online.org" target="_blank" class="">phenixbb@phenix-online.org</a><br class="">
<a href="http://phenix-online.org/mailman/listinfo/phenixbb" rel="noreferrer" target="_blank" class="">http://phenix-online.org/mailman/listinfo/phenixbb</a><br class="">
Unsubscribe: <a href="mailto:phenixbb-leave@phenix-online.org" target="_blank" class="">phenixbb-leave@phenix-online.org</a></blockquote></div>
_______________________________________________<br class="">phenixbb mailing list<br class=""><a href="mailto:phenixbb@phenix-online.org" target="_blank" class="">phenixbb@phenix-online.org</a><br class=""><a href="http://phenix-online.org/mailman/listinfo/phenixbb" target="_blank" class="">http://phenix-online.org/mailman/listinfo/phenixbb</a><br class="">Unsubscribe: <a href="mailto:phenixbb-leave@phenix-online.org" target="_blank" class="">phenixbb-leave@phenix-online.org</a></div></blockquote></div><br class=""><div class="">
<div style="letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;" class=""><div style="letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;" class=""><div style="letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;" class=""><div style="letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;" class=""><div style="text-align:start;text-indent:0px" class=""><div style="text-align:start;text-indent:0px" class=""><div style="text-align:start;text-indent:0px" class=""><div style="text-align:start;text-indent:0px" class=""><div style="letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px;" class="">Xavier Brazzolotto, PhD</div><div style="letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px;" class=""><a href="mailto:xavier.brazzolotto@chemdef.fr" target="_blank" class="">xavier.brazzolotto@chemdef.fr</a></div><div style="letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px;" class=""><div class=""><div class=""><br class=""></div><div class=""><b class=""><i class="">Département de Toxicologie </i><i class="">et Risques Chimiques</i></b></div><div class=""><b class=""><i class="">Unité Neurotoxiques</i></b></div><div class=""><i class=""><b class="">Institut de Recherche Biomédicale des Armées</b></i></div><div class=""><i class=""><b class="">1 Place du Général Valérie André, BP 73</b></i></div><div class=""><i class=""><b class="">91223 Brétigny sur Orge</b></i></div><div class=""><i class=""><b class="">France</b></i></div></div><div class=""><br class=""></div><div class="">Phone<span class="gmail-m_2435528438548355430Apple-tab-span" style="white-space:pre-wrap"> </span>+33 (0) <span style="text-align:-webkit-auto" class="">1 78 65 14 00</span></div><div class=""><span style="text-align:-webkit-auto" class="">Alt Phone<span class="gmail-m_2435528438548355430Apple-tab-span" style="white-space:pre-wrap"> </span></span><span style="text-align:-webkit-auto" class="">+33 (0) 4 57 42 87 19</span></div><div class="">Cell<span class="gmail-m_2435528438548355430Apple-tab-span" style="white-space:pre-wrap"> </span>+33 (0) 6 58 36 39 09</div></div><div style="letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px;" class=""><br class=""></div><div style="letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px;" class=""><i style="font-family:Calibri,sans-serif;font-size:14px" class="">The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender.</i></div><div style="letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px;" class=""><i style="font-family:Calibri,sans-serif;font-size:14px" class=""><br class=""></i></div><div class=""><i style="letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; font-family: Calibri, sans-serif; font-size: 14px;" class="">This is not an official email address of the French Ministry of the Armed Forces. It does not allow diffusion of protected informations and does not </i><font face="Calibri, sans-serif" class=""><span style="font-size:14px" class=""><i class="">necessarily complies to the ministry cyber security policy.</i></span></font></div></div></div></div></div></div></div></div></div>
</div>
<br class=""></div></div></blockquote></div>
</div></blockquote></div><br class=""><div class="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="text-align: start; text-indent: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="text-align: start; text-indent: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="text-align: start; text-indent: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="text-align: start; text-indent: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">Xavier Brazzolotto, PhD</div><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><a href="mailto:xavier.brazzolotto@chemdef.fr" class="">xavier.brazzolotto@chemdef.fr</a></div><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><div style="orphans: 2; widows: 2;" class=""><div class=""><br class=""></div><div class=""><b class=""><i class="">Département de Toxicologie </i><i class="">et Risques Chimiques</i></b></div><div class=""><b class=""><i class="">Unité Neurotoxiques</i></b></div><div class=""><i class=""><b class="">Institut de Recherche Biomédicale des Armées</b></i></div><div class=""><i class=""><b class="">1 Place du Général Valérie André, BP 73</b></i></div><div class=""><i class=""><b class="">91223 Brétigny sur Orge</b></i></div><div class=""><i class=""><b class="">France</b></i></div></div><div style="orphans: 2; widows: 2;" class=""><br class=""></div><div style="orphans: 2; widows: 2;" class="">Phone<span class="Apple-tab-span" style="white-space: pre;"> </span>+33 (0) <span style="text-align: -webkit-auto;" class="">1 78 65 14 00</span></div><div style="orphans: 2; widows: 2;" class=""><span style="text-align: -webkit-auto;" class="">Alt Phone<span class="Apple-tab-span" style="white-space: pre;"> </span></span><span style="text-align: -webkit-auto;" class="">+33 (0) 4 57 42 87 19</span></div><div style="orphans: 2; widows: 2;" class="">Cell<span class="Apple-tab-span" style="white-space: pre;"> </span>+33 (0) 6 58 36 39 09</div></div><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br class=""></div><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><i style="font-family: Calibri, sans-serif; font-size: 14px; orphans: 2; widows: 2;" class="">The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender.</i></div><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><i style="font-family: Calibri, sans-serif; font-size: 14px; orphans: 2; widows: 2;" class=""><br class=""></i></div><div class=""><i style="color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; font-family: Calibri, sans-serif; font-size: 14px; orphans: 2; widows: 2;" class="">This is not an official email address of the French Ministry of the Armed Forces. It does not allow diffusion of protected informations and does not </i><font face="Calibri, sans-serif" class=""><span style="font-size: 14px;" class=""><i class="">necessarily complies to the ministry cyber security policy.</i></span></font></div></div></div></div></div></div></div></div></div>
</div>
<br class=""></div></body></html>