<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="">Dear Guenter,<div class=""><br class=""></div><div class="">I also tried to run pipedream with the same options Guenter had used, except -nofreeref instead of -hklref, plus -remediate -sidechainrebuild and -runpepflip </div><div class=""><br class=""></div><div class="">The run finished without any error messages. hydrogenate.log shows that the ccp4 program reduce was used.</div><div class=""><br class=""></div><div class="">By inspecting report.tsv, it seems that reduce is defined by BDG_TOOLS_MOLPOBITY_ROOT but the executable is from the ccp4 path?</div><div class=""><br class=""></div><div class="">Is it possible that one has also to setup molprobity (I did) in order to call reduce correctly?</div><div class=""><br class=""></div><div class="">My system is CentOS 7, CCP4 7.1.011, buster snapshot 20210224. molprobity was installed according to the method provided by the BUSTER installation guide.</div><div class=""><br class=""></div><div class="">Hope that helps,</div><div class=""><br class=""></div><div class="">Wei-Chun</div><div class=""><br class=""></div><div class=""><div 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 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 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 style="orphans: auto; text-align: start; text-indent: 0px; widows: auto; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="orphans: auto; text-align: start; text-indent: 0px; widows: auto; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="orphans: auto; text-align: start; text-indent: 0px; widows: auto; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="orphans: auto; text-align: start; text-indent: 0px; widows: auto; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="orphans: auto; text-align: start; text-indent: 0px; widows: auto; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="background-color: rgb(255, 255, 255);" class=""><div style="color: rgb(136, 136, 136); font-family: 'Proxima Nova Soft'; font-size: 13px; letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class="">—</div><div style="color: rgb(136, 136, 136); font-family: 'Proxima Nova Soft'; font-size: 13px; letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px; min-height: 15px;" class=""><br class=""></div><div style="color: rgb(136, 136, 136); font-family: 'Proxima Nova Soft'; font-size: 13px; letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class="">Dr. rer. nat. Wei-Chun Kao</div><div style="margin: 0px;" class=""><div style="margin: 0px;" class=""><font color="#888888" face="Proxima Nova Soft" size="2" class=""><a href="mailto:wei-chun.kao@biochemie.uni-freiburg.de" class="">wei-chun.kao@biochemie.uni-freiburg.de</a></font></div></div><div style="color: rgb(18, 85, 204); font-family: 'Proxima Nova Soft'; font-size: 13px; letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class=""><span style="color: rgb(136, 136, 136);" class="">TEL: <span style="color: rgb(18, 85, 204);" class=""><a href="tel:%2B49-761-203-5277" class="">+49-761-203-5277</a></span></span></div><div style="color: rgb(18, 85, 204); font-family: 'Proxima Nova Soft'; font-size: 13px; letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class=""><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px;" class=""><div style="color: rgb(18, 85, 204); font-family: 'Proxima Nova Soft'; font-size: 13px; margin: 0px;" class=""><span style="color: rgb(145, 145, 145); font-size: small;" class=""><a href="http://orcid.org/0000-0001-8687-6334" class="">orcid.org/0000-0001-8687-6334</a><span class="Apple-tab-span" style="white-space: pre;"> </span></span></div></div></div><div style="color: rgb(136, 136, 136); font-family: 'Proxima Nova Soft'; font-size: 13px; letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px; min-height: 15px;" class=""><br class=""></div><div style="color: rgb(136, 136, 136); font-family: 'Proxima Nova Soft'; font-size: 13px; letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class="">Institute for Biochemistry and Molecular Biology</div><div style="color: rgb(136, 136, 136); font-family: 'Proxima Nova Soft'; font-size: 13px; letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class="">AG Carola Hunte</div><div style="color: rgb(136, 136, 136); font-family: 'Proxima Nova Soft'; font-size: 13px; letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class="">Albert-Ludwigs-Universitaet Freiburg</div><div style="color: rgb(136, 136, 136); font-family: 'Proxima Nova Soft'; font-size: 13px; letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class="">Stefan-Meier-Str. 17</div><div style="color: rgb(136, 136, 136); font-family: 'Proxima Nova Soft'; font-size: 13px; letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class="">D-79104 Freiburg im Breisgau</div><div style="color: rgb(136, 136, 136); font-family: 'Proxima Nova Soft'; font-size: 13px; letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class="">Germany</div></div></div></div></div></div></div></div></div></div>
</div>
<div><br class=""><blockquote type="cite" class=""><div class="">On 24. Feb 2021, at 21:10, Guenter Fritz <<a href="mailto:guenter.fritz.phenix.ccp4@gmail.com" class="">guenter.fritz.phenix.ccp4@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
<meta http-equiv="content-type" content="text/html; charset=UTF-8" class="">
<div class=""><p class="">Dear Buster developers,</p><p class="">I was trying to run pipedream, but get the notice that reduce is
not in the path, although it is. <br class="">
</p><p class="">Below is my input and the output. Any hintwhat I am doing wrong
is welcome.<br class="">
</p><p class="">System is Centos 8, CCP4 is 7.1, latest release of buster from
today. <br class="">
</p><p class="">Many thanks and best regards,</p><p class="">Guenter<br class="">
</p><p class=""><font face="Courier New, Courier, monospace" class="">[guenter@epikur
pipedream_test]$ pipedream -hklin paefs_215.mtz -hklref
paefs_215.mtz -xyzin paefs_215.pdb -rhofit grade-XXX.cif
-nthreads 6 -d paefs_215_results <br class="">
.......<br class="">
</font></p><p class=""><font face="Courier New, Courier, monospace" class="">Command run:
pipedream -hklin paefs_215.mtz -hklref paefs_215.mtz -xyzin
paefs_215.pdb -rhofit grade-XXX.cif -nthreads 6 -d
paefs_215_results<br class="">
For details see paefs_215_results/summary.out<br class="">
<br class="">
ERROR: Unable to run hydrogenate - 'reduce' (in CCP4
distribution) not found on path!</font></p><p class=""><font face="Courier New, Courier, monospace" class="">[guenter@epikur
pipedream_test]$ which reduce <br class="">
/opt/software/CCP4/7.1/ccp4-7.1/bin/reduce</font><br class="">
<br class="">
<br class="">
</p>
</div>
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