<html><body><div style="color:#000; background-color:#fff; font-family:HelveticaNeue-Light, Helvetica Neue Light, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:16px"><div>hi,</div><div dir="ltr">no it was the TER cards, it works now.</div><div dir="ltr">i thought i had already tried that.<br></div><div id="yui_3_16_0_1_1432137981352_1150174">sorry to bother you.<br><span></span></div><div id="yui_3_16_0_1_1432137981352_1150175"><span>thanks</span></div><div id="yui_3_16_0_1_1432137981352_1150200"><span>jpd</span></div><br> <div id="yui_3_16_0_1_1432137981352_1150165" style="font-family: HelveticaNeue-Light, Helvetica Neue Light, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 16px;"> <div id="yui_3_16_0_1_1432137981352_1150164" style="font-family: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 16px;"> <div id="yui_3_16_0_1_1432137981352_1150163" dir="ltr"> <hr id="yui_3_16_0_1_1432137981352_1150173" size="1"> <font id="yui_3_16_0_1_1432137981352_1150172" face="Arial" size="2"> <b><span style="font-weight:bold;">From:</span></b> Oleg Sobolev <osobolev@lbl.gov><br> <b><span style="font-weight: bold;">To:</span></b> Nigel Moriarty <nwmoriarty@lbl.gov> <br><b><span style="font-weight: bold;">Cc:</span></b> jp d <yoyoq@yahoo.com>; PHENIX User Mailing List <phenixbb@phenix-online.org> <br> <b><span style="font-weight: bold;">Sent:</span></b> Thursday, May 28, 2015 2:34 PM<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [phenixbb] reference model restraints by segid<br> </font> </div> <div id="yui_3_16_0_1_1432137981352_1150207" class="y_msg_container"><br><div id="yiv0152877915"><div id="yui_3_16_0_1_1432137981352_1150210"><div id="yui_3_16_0_1_1432137981352_1150209" dir="ltr">Hi,<div id="yui_3_16_0_1_1432137981352_1150211"><br clear="none"></div><div id="yui_3_16_0_1_1432137981352_1150208">If removing of TER indices won't work in dev-2056, I will be happy to investigate and find a way to make it work for everybody. To do so I will need the inputs you are using (i.e. models and parameter files)</div><div><br clear="none"></div><div>Best regards,</div><div id="yui_3_16_0_1_1432137981352_1150212">Oleg Sobolev.</div></div><div id="yui_3_16_0_1_1432137981352_1150213" class="yiv0152877915gmail_extra"><br clear="none"><div id="yui_3_16_0_1_1432137981352_1150216" class="yiv0152877915gmail_quote">On Thu, May 28, 2015 at 2:10 PM, Nigel Moriarty <span dir="ltr"><<a rel="nofollow" shape="rect" ymailto="mailto:nwmoriarty@lbl.gov" target="_blank" href="mailto:nwmoriarty@lbl.gov">nwmoriarty@lbl.gov</a>></span> wrote:<br clear="none"><blockquote id="yui_3_16_0_1_1432137981352_1150215" class="yiv0152877915gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div id="yui_3_16_0_1_1432137981352_1150214" dir="ltr">The error says it doesn't like the TER cards. Remove them all and retry.</div><div id="yui_3_16_0_1_1432137981352_1150217" class="yiv0152877915gmail_extra"><br clear="all"><div><div><div dir="ltr">Cheers<div><br clear="none"></div><div>Nigel<div><br clear="none"></div><div>---</div><div>Nigel W. Moriarty<br clear="none">Building 64R0246B, Physical Biosciences Division<br clear="none">Lawrence Berkeley National Laboratory<br clear="none">Berkeley, CA 94720-8235<br clear="none">Phone : <a href="" rel="nofollow" shape="rect">510-486-5709</a> Email : NWMoriarty@LBL.gov<br clear="none">Fax : <a href="" rel="nofollow" shape="rect">510-486-5909</a> Web : <a rel="nofollow" shape="rect" target="_blank" href="http://cci.lbl.gov/">CCI.LBL.gov</a></div></div></div></div></div>
<br clear="none"><div class="yiv0152877915gmail_quote"><div><div class="yiv0152877915h5">On Thu, May 28, 2015 at 1:29 PM, jp d <span dir="ltr"><<a rel="nofollow" shape="rect" ymailto="mailto:yoyoq@yahoo.com" target="_blank" href="mailto:yoyoq@yahoo.com">yoyoq@yahoo.com</a>></span> wrote:<br clear="none"></div></div><blockquote class="yiv0152877915gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div><div class="yiv0152877915h5"><div><div style="color:#000;background-color:#fff;font-family:HelveticaNeue-Light, Helvetica Neue Light, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:16px;"><div><div><div style="color:#000;background-color:#fff;font-family:HelveticaNeue-Light, Helvetica Neue Light, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:16px;"><div>Hi,</div><div>I am having trouble getting phenix to used segid's in reference model restraints when<br clear="none"></div><div dir="ltr">my reference and target pdbs both don't use chain ID's.</div><div dir="ltr">phenix quits with this message:</div><div dir="ltr"><br clear="none"></div><div dir="ltr">*** Adding Reference Model Restraints ***<br clear="none">Sorry: chain ' ' in /home/path/removed/agnref2.pdb contains one or more errant TER cards.<br clear="none">Please remove and try again.<br clear="none"><br clear="none"></div><div dir="ltr">my definition file looks like this:</div><div dir="ltr">refinement {<br clear="none"> main {<br clear="none"> reference_model_restraints = True<br clear="none"> }<br clear="none"> reference_model {<br clear="none"> file = two.pdb<br clear="none"> }<br clear="none">}<br clear="none"> <br clear="none">refinement.reference_model.reference_group {<br clear="none"> reference = segid A16S<br clear="none"> selection = segid A16S<br clear="none">}<br clear="none"></div><div dir="ltr"><div dir="ltr">(above about 50 more times)</div><div><br clear="none"></div></div><div dir="ltr">this was on versions 1.9-1692 , dev-2016 and dev-2056<br clear="none"></div><div dir="ltr"><br clear="none"></div><div dir="ltr"><div>any suggestions ?</div><div>thanks</div><div>jpd<br clear="none"></div><div><br clear="none"></div></div><div dir="ltr"><br clear="none"> </div></div></div></div></div></div><br clear="none"></div></div>_______________________________________________<br clear="none">
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