<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">
<!--StartFragment--> <div class="MsoNormal"><font class="Apple-style-span" color="#FF0000"><span class="Apple-style-span" style="color: rgb(0, 0, 0); ">Thanks for the reply. I think I didn't explain myself properly, of course I want to do bss, but we have noticed that previous versions of phenix (1.24 I think) did bss once per macro cycle and now with the newer versions, we get the same plus a final bbs cycle at the end of the whole process -shown in red- Is that final cycle introduced by default in the newer versions?</span></font></div><div class="MsoNormal">Thanks again.</div><div class="MsoNormal"><br></div><div class="MsoNormal">Cesar.</div><div class="MsoNormal"><font class="Apple-style-span" color="#FF0000"><br></font></div><div class="MsoNormal"><font class="Apple-style-span" color="#FF0000"><br></font></div><div class="MsoNormal"><font class="Apple-style-span" color="#FF0000"><br></font></div><div class="MsoNormal"><span style="color:red">REMARK<span style="mso-spacerun: yes">��� </span>3_bss:<span style="mso-spacerun: yes">�� </span>1.222<span style="mso-spacerun: yes">� </span>0.008<span style="mso-spacerun: yes">� </span>0.075 19.562<span style="mso-spacerun: yes">� </span>0.005<span style="mso-spacerun: yes">� </span>4.107<span style="mso-spacerun: yes">�� </span>1.2876e-01<o:p></o:p></span></div> <div class="MsoNormal">REMARK<span style="mso-spacerun: yes">��� </span>3_xyz:<span style="mso-spacerun: yes">�� </span>1.021<span style="mso-spacerun: yes">� </span>0.005<span style="mso-spacerun: yes">� </span>0.063 19.049<span style="mso-spacerun: yes">� </span>0.004<span style="mso-spacerun: yes">� </span>4.111<span style="mso-spacerun: yes">�� </span>1.0306e-01<o:p></o:p></div> <div class="MsoNormal">REMARK<span style="mso-spacerun: yes">��� </span>3_adp:<span style="mso-spacerun: yes">�� </span>1.021<span style="mso-spacerun: yes">� </span>0.005<span style="mso-spacerun: yes">� </span>0.063 19.049<span style="mso-spacerun: yes">� </span>0.004<span style="mso-spacerun: yes">� </span>4.111<span style="mso-spacerun: yes">�� </span>1.0306e-01<o:p></o:p></div> <span style="font-size:12.0pt;font-family:Times;color:red;mso-ansi-language: EN-US">REMARK<span style="mso-spacerun: yes">��� </span>3_bss:<span style="mso-spacerun: yes">�� </span>1.021<span style="mso-spacerun: yes">� </span>0.005<span style="mso-spacerun: yes">� </span>0.063 19.049<span style="mso-spacerun: yes">� </span>0.004<span style="mso-spacerun: yes">� </span>4.111<span style="mso-spacerun: yes">�� </span>1.0306e-01</span><!--EndFragment-->� <div><br><div><div>On Dec 3, 2008, at 9:00 PM, <a href="mailto:phenixbb-request@phenix-online.org">phenixbb-request@phenix-online.org</a> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Send phenixbb mailing list submissions to</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-tab-span" style="white-space:pre"> </span><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">To subscribe or unsubscribe via the World Wide Web, visit</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-tab-span" style="white-space:pre"> </span><a href="http://www.phenix-online.org/mailman/listinfo/phenixbb">http://www.phenix-online.org/mailman/listinfo/phenixbb</a></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">or, via email, send a message with subject or body 'help' to</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-tab-span" style="white-space:pre"> </span><a href="mailto:phenixbb-request@phenix-online.org">phenixbb-request@phenix-online.org</a></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">You can reach the person managing the list at</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-tab-span" style="white-space:pre"> </span><a href="mailto:phenixbb-owner@phenix-online.org">phenixbb-owner@phenix-online.org</a></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">When replying, please edit your Subject line so it is more specific</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">than "Re: Contents of phenixbb digest..."</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Today's Topics:</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-converted-space">�� </span>1. Bulk solvent (<a href="mailto:csantiag@cnb.csic.es">csantiag@cnb.csic.es</a>)</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-converted-space">�� </span>2. Re: Bulk solvent (junfeng liu)</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-converted-space">�� </span>3. Re: Bulk solvent (Pavel Afonine)</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-converted-space">�� </span>4. Re: Bulk solvent (Pavel Afonine)</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-converted-space">�� </span>5. Re: Question regarding phenix.elbow (Nigel W Moriarty)</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">----------------------------------------------------------------------</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Message: 1</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Date: Wed, 3 Dec 2008 10:15:30 +0100 (CET)</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">From: <a href="mailto:csantiag@cnb.csic.es">csantiag@cnb.csic.es</a></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Subject: [phenixbb] Bulk solvent</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">To: <a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Message-ID:</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-tab-span" style="white-space:pre"> </span><<a href="mailto:49732.150.244.83.180.1228295730.squirrel@webmail.cnb.csic.es">49732.150.244.83.180.1228295730.squirrel@webmail.cnb.csic.es</a>></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Content-Type: text/plain;charset=iso-8859-1</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Hi all,</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I'm refining a protein and after running phenix.refine I always get a bulk</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">solvent refinement cycle at the end of the process. Is there any way to</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">get rid of the last step?</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">------------------------------------------------------------------------</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">REMARK<span class="Apple-converted-space">� </span>stage <span class="Apple-converted-space">� � � </span>angl <span class="Apple-converted-space">� </span>bond <span class="Apple-converted-space">� </span>chir <span class="Apple-converted-space">� </span>dihe <span class="Apple-converted-space">� </span>plan <span class="Apple-converted-space">� </span>repu<span class="Apple-converted-space">� </span>geom_target</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">REMARK<span class="Apple-converted-space">� � </span>0<span class="Apple-converted-space">� � </span>: <span class="Apple-converted-space">� </span>1.007<span class="Apple-converted-space">� </span>0.027<span class="Apple-converted-space">� </span>0.237 18.975<span class="Apple-converted-space">� </span>0.004<span class="Apple-converted-space">� </span>4.107 <span class="Apple-converted-space">� </span>2.7953e-01</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">REMARK<span class="Apple-converted-space">� � </span>1_bss: <span class="Apple-converted-space">� </span>1.007<span class="Apple-converted-space">� </span>0.027<span class="Apple-converted-space">� </span>0.237 18.975<span class="Apple-converted-space">� </span>0.004<span class="Apple-converted-space">� </span>4.107 <span class="Apple-converted-space">� </span>2.7953e-01</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">REMARK<span class="Apple-converted-space">� � </span>1_xyz: <span class="Apple-converted-space">� </span>1.844<span class="Apple-converted-space">� </span>0.015<span class="Apple-converted-space">� </span>0.087 19.502<span class="Apple-converted-space">� </span>0.005<span class="Apple-converted-space">� </span>4.106 <span class="Apple-converted-space">� </span>1.9824e-01</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">REMARK<span class="Apple-converted-space">� � </span>1_adp: <span class="Apple-converted-space">� </span>1.844<span class="Apple-converted-space">� </span>0.015<span class="Apple-converted-space">� </span>0.087 19.502<span class="Apple-converted-space">� </span>0.005<span class="Apple-converted-space">� </span>4.106 <span class="Apple-converted-space">� </span>1.9824e-01</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">REMARK<span class="Apple-converted-space">� � </span>2_bss: <span class="Apple-converted-space">� </span>1.844<span class="Apple-converted-space">� </span>0.015<span class="Apple-converted-space">� </span>0.087 19.502<span class="Apple-converted-space">� </span>0.005<span class="Apple-converted-space">� </span>4.106 <span class="Apple-converted-space">� </span>1.9824e-01</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">REMARK<span class="Apple-converted-space">� � </span>2_xyz: <span class="Apple-converted-space">� </span>1.222<span class="Apple-converted-space">� </span>0.008<span class="Apple-converted-space">� </span>0.075 19.562<span class="Apple-converted-space">� </span>0.005<span class="Apple-converted-space">� </span>4.107 <span class="Apple-converted-space">� </span>1.2876e-01</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">REMARK<span class="Apple-converted-space">� � </span>2_adp: <span class="Apple-converted-space">� </span>1.222<span class="Apple-converted-space">� </span>0.008<span class="Apple-converted-space">� </span>0.075 19.562<span class="Apple-converted-space">� </span>0.005<span class="Apple-converted-space">� </span>4.107 <span class="Apple-converted-space">� </span>1.2876e-01</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">REMARK<span class="Apple-converted-space">� � </span>3_bss: <span class="Apple-converted-space">� </span>1.222<span class="Apple-converted-space">� </span>0.008<span class="Apple-converted-space">� </span>0.075 19.562<span class="Apple-converted-space">� </span>0.005<span class="Apple-converted-space">� </span>4.107 <span class="Apple-converted-space">� </span>1.2876e-01</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">REMARK<span class="Apple-converted-space">� � </span>3_xyz: <span class="Apple-converted-space">� </span>1.021<span class="Apple-converted-space">� </span>0.005<span class="Apple-converted-space">� </span>0.063 19.049<span class="Apple-converted-space">� </span>0.004<span class="Apple-converted-space">� </span>4.111 <span class="Apple-converted-space">� </span>1.0306e-01</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">REMARK<span class="Apple-converted-space">� � </span>3_adp: <span class="Apple-converted-space">� </span>1.021<span class="Apple-converted-space">� </span>0.005<span class="Apple-converted-space">� </span>0.063 19.049<span class="Apple-converted-space">� </span>0.004<span class="Apple-converted-space">� </span>4.111 <span class="Apple-converted-space">� </span>1.0306e-01</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">REMARK<span class="Apple-converted-space">� � </span>3_bss: <span class="Apple-converted-space">� </span>1.021<span class="Apple-converted-space">� </span>0.005<span class="Apple-converted-space">� </span>0.063 19.049<span class="Apple-converted-space">� </span>0.004<span class="Apple-converted-space">� </span>4.111 <span class="Apple-converted-space">� </span>1.0306e-01</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">REMARK</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">------------------------------------------------------------------------</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">C?sar Santiago</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Dept of Macromolecules Structure</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Centro Nacional de Biotecnolog?a, CSIC</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Campus Cantoblanco</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">28049 Madrid</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Spain</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><a href="mailto:csantiag@cnb.csic.es">csantiag@cnb.csic.es</a></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">------------------------------</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Message: 2</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Date: Wed, 03 Dec 2008 09:36:30 +0000</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">From: junfeng liu <<a href="mailto:jliu@nimr.mrc.ac.uk">jliu@nimr.mrc.ac.uk</a>></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Subject: Re: [phenixbb] Bulk solvent</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">To: PHENIX user mailing list <<a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Message-ID: <<a href="mailto:4936531E.5030505@nimr.mrc.ac.uk">4936531E.5030505@nimr.mrc.ac.uk</a>></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Content-Type: text/plain; charset=ISO-8859-1; format=flowed</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Add</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">bulk_solvent_and_scale=False<span class="Apple-converted-space">�</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">when you run it again.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><a href="mailto:csantiag@cnb.csic.es">csantiag@cnb.csic.es</a> wrote:</div> <blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Hi all,</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I'm refining a protein and after running phenix.refine I always get a bulk</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">solvent refinement cycle at the end of the process. Is there any way to</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">get rid of the last step?</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">------------------------------------------------------------------------</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">REMARK<span class="Apple-converted-space">� </span>stage <span class="Apple-converted-space">� � � </span>angl <span class="Apple-converted-space">� </span>bond <span class="Apple-converted-space">� </span>chir <span class="Apple-converted-space">� </span>dihe <span class="Apple-converted-space">� </span>plan <span class="Apple-converted-space">� </span>repu<span class="Apple-converted-space">� </span>geom_target</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">REMARK<span class="Apple-converted-space">� � </span>0<span class="Apple-converted-space">� � </span>: <span class="Apple-converted-space">� </span>1.007<span class="Apple-converted-space">� </span>0.027<span class="Apple-converted-space">� </span>0.237 18.975<span class="Apple-converted-space">� </span>0.004<span class="Apple-converted-space">� </span>4.107 <span class="Apple-converted-space">� </span>2.7953e-01</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">REMARK<span class="Apple-converted-space">� � </span>1_bss: <span class="Apple-converted-space">� </span>1.007<span class="Apple-converted-space">� </span>0.027<span class="Apple-converted-space">� </span>0.237 18.975<span class="Apple-converted-space">� </span>0.004<span class="Apple-converted-space">� </span>4.107 <span class="Apple-converted-space">� </span>2.7953e-01</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">REMARK<span class="Apple-converted-space">� � </span>1_xyz: <span class="Apple-converted-space">� </span>1.844<span class="Apple-converted-space">� </span>0.015<span class="Apple-converted-space">� </span>0.087 19.502<span class="Apple-converted-space">� </span>0.005<span class="Apple-converted-space">� </span>4.106 <span class="Apple-converted-space">� </span>1.9824e-01</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">REMARK<span class="Apple-converted-space">� � </span>1_adp: <span class="Apple-converted-space">� </span>1.844<span class="Apple-converted-space">� </span>0.015<span class="Apple-converted-space">� </span>0.087 19.502<span class="Apple-converted-space">� </span>0.005<span class="Apple-converted-space">� </span>4.106 <span class="Apple-converted-space">� </span>1.9824e-01</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">REMARK<span class="Apple-converted-space">� � </span>2_bss: <span class="Apple-converted-space">� </span>1.844<span class="Apple-converted-space">� </span>0.015<span class="Apple-converted-space">� </span>0.087 19.502<span class="Apple-converted-space">� </span>0.005<span class="Apple-converted-space">� </span>4.106 <span class="Apple-converted-space">� </span>1.9824e-01</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">REMARK<span class="Apple-converted-space">� � </span>2_xyz: <span class="Apple-converted-space">� </span>1.222<span class="Apple-converted-space">� </span>0.008<span class="Apple-converted-space">� </span>0.075 19.562<span class="Apple-converted-space">� </span>0.005<span class="Apple-converted-space">� </span>4.107 <span class="Apple-converted-space">� </span>1.2876e-01</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">REMARK<span class="Apple-converted-space">� � </span>2_adp: <span class="Apple-converted-space">� </span>1.222<span class="Apple-converted-space">� </span>0.008<span class="Apple-converted-space">� </span>0.075 19.562<span class="Apple-converted-space">� </span>0.005<span class="Apple-converted-space">� </span>4.107 <span class="Apple-converted-space">� </span>1.2876e-01</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">REMARK<span class="Apple-converted-space">� � </span>3_bss: <span class="Apple-converted-space">� </span>1.222<span class="Apple-converted-space">� </span>0.008<span class="Apple-converted-space">� </span>0.075 19.562<span class="Apple-converted-space">� </span>0.005<span class="Apple-converted-space">� </span>4.107 <span class="Apple-converted-space">� </span>1.2876e-01</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">REMARK<span class="Apple-converted-space">� � </span>3_xyz: <span class="Apple-converted-space">� </span>1.021<span class="Apple-converted-space">� </span>0.005<span class="Apple-converted-space">� </span>0.063 19.049<span class="Apple-converted-space">� </span>0.004<span class="Apple-converted-space">� </span>4.111 <span class="Apple-converted-space">� </span>1.0306e-01</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">REMARK<span class="Apple-converted-space">� � </span>3_adp: <span class="Apple-converted-space">� </span>1.021<span class="Apple-converted-space">� </span>0.005<span class="Apple-converted-space">� </span>0.063 19.049<span class="Apple-converted-space">� </span>0.004<span class="Apple-converted-space">� </span>4.111 <span class="Apple-converted-space">� </span>1.0306e-01</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">REMARK<span class="Apple-converted-space">� � </span>3_bss: <span class="Apple-converted-space">� </span>1.021<span class="Apple-converted-space">� </span>0.005<span class="Apple-converted-space">� </span>0.063 19.049<span class="Apple-converted-space">� </span>0.004<span class="Apple-converted-space">� </span>4.111 <span class="Apple-converted-space">� </span>1.0306e-01</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">REMARK</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">------------------------------------------------------------------------</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">C?sar Santiago</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Dept of Macromolecules Structure</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Centro Nacional de Biotecnolog?a, CSIC</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Campus Cantoblanco</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">28049 Madrid</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Spain</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><a href="mailto:csantiag@cnb.csic.es">csantiag@cnb.csic.es</a></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">_______________________________________________</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">phenixbb mailing list</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><a href="http://www.phenix-online.org/mailman/listinfo/phenixbb">http://www.phenix-online.org/mailman/listinfo/phenixbb</a></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div> </blockquote><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">------------------------------</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Message: 3</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Date: Wed, 03 Dec 2008 08:09:57 -0800</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">From: Pavel Afonine <<a href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a>></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Subject: Re: [phenixbb] Bulk solvent</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">To: PHENIX user mailing list <<a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Cc: <a href="mailto:csantiag@cnb.csic.es">csantiag@cnb.csic.es</a></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Message-ID: <<a href="mailto:4936AF55.8010508@lbl.gov">4936AF55.8010508@lbl.gov</a>></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Content-Type: text/plain; charset=ISO-8859-1; format=flowed</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Hi C?sar,</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">this step is important. Bulk solvent modeling is based on mask<span class="Apple-converted-space">�</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">calculation and since during refinement of coordinates the atoms shift<span class="Apple-converted-space">�</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">the mask gets invalidated. This is why we do a final bulk solvent<span class="Apple-converted-space">�</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">correction step at the very last step of refinement just before the<span class="Apple-converted-space">�</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">final statistics is reported. So I'm puzzled about why you want to turn<span class="Apple-converted-space">�</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">it off. If it causes any problem, it's much better to find out the<span class="Apple-converted-space">�</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">primary reason for it rather than turn bulk solvent correction. Could<span class="Apple-converted-space">�</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">you please give more details?</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">If you do "main.bulk_solvent_and_scale=false" phenix.refine will not do<span class="Apple-converted-space">�</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">bulk solvent correction and anisotropic scaling at all which is bad.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Pavel.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">On 12/3/2008 1:15 AM, <a href="mailto:csantiag@cnb.csic.es">csantiag@cnb.csic.es</a> wrote:</div> <blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Hi all,</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I'm refining a protein and after running phenix.refine I always get a bulk</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">solvent refinement cycle at the end of the process. Is there any way to</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">get rid of the last step?</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">------------------------------------------------------------------------</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">REMARK<span class="Apple-converted-space">� </span>stage <span class="Apple-converted-space">� � � </span>angl <span class="Apple-converted-space">� </span>bond <span class="Apple-converted-space">� </span>chir <span class="Apple-converted-space">� </span>dihe <span class="Apple-converted-space">� </span>plan <span class="Apple-converted-space">� </span>repu<span class="Apple-converted-space">� </span>geom_target</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">REMARK<span class="Apple-converted-space">� � </span>0<span class="Apple-converted-space">� � </span>: <span class="Apple-converted-space">� </span>1.007<span class="Apple-converted-space">� </span>0.027<span class="Apple-converted-space">� </span>0.237 18.975<span class="Apple-converted-space">� </span>0.004<span class="Apple-converted-space">� </span>4.107 <span class="Apple-converted-space">� </span>2.7953e-01</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">REMARK<span class="Apple-converted-space">� � </span>1_bss: <span class="Apple-converted-space">� </span>1.007<span class="Apple-converted-space">� </span>0.027<span class="Apple-converted-space">� </span>0.237 18.975<span class="Apple-converted-space">� </span>0.004<span class="Apple-converted-space">� </span>4.107 <span class="Apple-converted-space">� </span>2.7953e-01</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">REMARK<span class="Apple-converted-space">� � </span>1_xyz: <span class="Apple-converted-space">� </span>1.844<span class="Apple-converted-space">� </span>0.015<span class="Apple-converted-space">� </span>0.087 19.502<span class="Apple-converted-space">� </span>0.005<span class="Apple-converted-space">� </span>4.106 <span class="Apple-converted-space">� </span>1.9824e-01</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">REMARK<span class="Apple-converted-space">� � </span>1_adp: <span class="Apple-converted-space">� </span>1.844<span class="Apple-converted-space">� </span>0.015<span class="Apple-converted-space">� </span>0.087 19.502<span class="Apple-converted-space">� </span>0.005<span class="Apple-converted-space">� </span>4.106 <span class="Apple-converted-space">� </span>1.9824e-01</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">REMARK<span class="Apple-converted-space">� � </span>2_bss: <span class="Apple-converted-space">� </span>1.844<span class="Apple-converted-space">� </span>0.015<span class="Apple-converted-space">� </span>0.087 19.502<span class="Apple-converted-space">� </span>0.005<span class="Apple-converted-space">� </span>4.106 <span class="Apple-converted-space">� </span>1.9824e-01</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">REMARK<span class="Apple-converted-space">� � </span>2_xyz: <span class="Apple-converted-space">� </span>1.222<span class="Apple-converted-space">� </span>0.008<span class="Apple-converted-space">� </span>0.075 19.562<span class="Apple-converted-space">� </span>0.005<span class="Apple-converted-space">� </span>4.107 <span class="Apple-converted-space">� </span>1.2876e-01</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">REMARK<span class="Apple-converted-space">� � </span>2_adp: <span class="Apple-converted-space">� </span>1.222<span class="Apple-converted-space">� </span>0.008<span class="Apple-converted-space">� </span>0.075 19.562<span class="Apple-converted-space">� </span>0.005<span class="Apple-converted-space">� </span>4.107 <span class="Apple-converted-space">� </span>1.2876e-01</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">REMARK<span class="Apple-converted-space">� � </span>3_bss: <span class="Apple-converted-space">� </span>1.222<span class="Apple-converted-space">� </span>0.008<span class="Apple-converted-space">� </span>0.075 19.562<span class="Apple-converted-space">� </span>0.005<span class="Apple-converted-space">� </span>4.107 <span class="Apple-converted-space">� </span>1.2876e-01</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">REMARK<span class="Apple-converted-space">� � </span>3_xyz: <span class="Apple-converted-space">� </span>1.021<span class="Apple-converted-space">� </span>0.005<span class="Apple-converted-space">� </span>0.063 19.049<span class="Apple-converted-space">� </span>0.004<span class="Apple-converted-space">� </span>4.111 <span class="Apple-converted-space">� </span>1.0306e-01</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">REMARK<span class="Apple-converted-space">� � </span>3_adp: <span class="Apple-converted-space">� </span>1.021<span class="Apple-converted-space">� </span>0.005<span class="Apple-converted-space">� </span>0.063 19.049<span class="Apple-converted-space">� </span>0.004<span class="Apple-converted-space">� </span>4.111 <span class="Apple-converted-space">� </span>1.0306e-01</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">REMARK<span class="Apple-converted-space">� � </span>3_bss: <span class="Apple-converted-space">� </span>1.021<span class="Apple-converted-space">� </span>0.005<span class="Apple-converted-space">� </span>0.063 19.049<span class="Apple-converted-space">� </span>0.004<span class="Apple-converted-space">� </span>4.111 <span class="Apple-converted-space">� </span>1.0306e-01</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">REMARK</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">------------------------------------------------------------------------</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">C?sar Santiago</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Dept of Macromolecules Structure</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Centro Nacional de Biotecnolog?a, CSIC</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Campus Cantoblanco</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">28049 Madrid</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Spain</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><a href="mailto:csantiag@cnb.csic.es">csantiag@cnb.csic.es</a></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">_______________________________________________</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">phenixbb mailing list</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><a href="http://www.phenix-online.org/mailman/listinfo/phenixbb">http://www.phenix-online.org/mailman/listinfo/phenixbb</a></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div> </blockquote><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">------------------------------</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Message: 4</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Date: Wed, 03 Dec 2008 08:13:21 -0800</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">From: Pavel Afonine <<a href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a>></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Subject: Re: [phenixbb] Bulk solvent</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">To: PHENIX user mailing list <<a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Message-ID: <<a href="mailto:4936B021.7010401@lbl.gov">4936B021.7010401@lbl.gov</a>></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Content-Type: text/plain; charset="iso-8859-1"</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Yes, this will turn bulk solvent correction and anisotropic scaling off<span class="Apple-converted-space">�</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">completely. In some cases it may result in R-factors increase by ~5% or<span class="Apple-converted-space">�</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">similar. So it may only make sense in exotic cases or if you do<span class="Apple-converted-space">�</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">numerical experiments (simulated data etc..).</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Pavel.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">On 12/3/2008 1:36 AM, junfeng liu wrote:</div> <blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Add</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">bulk_solvent_and_scale=False<span class="Apple-converted-space">�</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">when you run it again.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><a href="mailto:csantiag@cnb.csic.es">csantiag@cnb.csic.es</a> wrote:</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div> <blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Hi all,</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I'm refining a protein and after running phenix.refine I always get a bulk</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">solvent refinement cycle at the end of the process. Is there any way to</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">get rid of the last step?</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">------------------------------------------------------------------------</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">REMARK<span class="Apple-converted-space">� </span>stage <span class="Apple-converted-space">� � � </span>angl <span class="Apple-converted-space">� </span>bond <span class="Apple-converted-space">� </span>chir <span class="Apple-converted-space">� </span>dihe <span class="Apple-converted-space">� </span>plan <span class="Apple-converted-space">� </span>repu<span class="Apple-converted-space">� </span>geom_target</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">REMARK<span class="Apple-converted-space">� � </span>0<span class="Apple-converted-space">� � </span>: <span class="Apple-converted-space">� </span>1.007<span class="Apple-converted-space">� </span>0.027<span class="Apple-converted-space">� </span>0.237 18.975<span class="Apple-converted-space">� </span>0.004<span class="Apple-converted-space">� </span>4.107 <span class="Apple-converted-space">� </span>2.7953e-01</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">REMARK<span class="Apple-converted-space">� � </span>1_bss: <span class="Apple-converted-space">� </span>1.007<span class="Apple-converted-space">� </span>0.027<span class="Apple-converted-space">� </span>0.237 18.975<span class="Apple-converted-space">� </span>0.004<span class="Apple-converted-space">� </span>4.107 <span class="Apple-converted-space">� </span>2.7953e-01</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">REMARK<span class="Apple-converted-space">� � </span>1_xyz: <span class="Apple-converted-space">� </span>1.844<span class="Apple-converted-space">� </span>0.015<span class="Apple-converted-space">� </span>0.087 19.502<span class="Apple-converted-space">� </span>0.005<span class="Apple-converted-space">� </span>4.106 <span class="Apple-converted-space">� </span>1.9824e-01</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">REMARK<span class="Apple-converted-space">� � </span>1_adp: <span class="Apple-converted-space">� </span>1.844<span class="Apple-converted-space">� </span>0.015<span class="Apple-converted-space">� </span>0.087 19.502<span class="Apple-converted-space">� </span>0.005<span class="Apple-converted-space">� </span>4.106 <span class="Apple-converted-space">� </span>1.9824e-01</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">REMARK<span class="Apple-converted-space">� � </span>2_bss: <span class="Apple-converted-space">� </span>1.844<span class="Apple-converted-space">� </span>0.015<span class="Apple-converted-space">� </span>0.087 19.502<span class="Apple-converted-space">� </span>0.005<span class="Apple-converted-space">� </span>4.106 <span class="Apple-converted-space">� </span>1.9824e-01</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">REMARK<span class="Apple-converted-space">� � </span>2_xyz: <span class="Apple-converted-space">� </span>1.222<span class="Apple-converted-space">� </span>0.008<span class="Apple-converted-space">� </span>0.075 19.562<span class="Apple-converted-space">� </span>0.005<span class="Apple-converted-space">� </span>4.107 <span class="Apple-converted-space">� </span>1.2876e-01</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">REMARK<span class="Apple-converted-space">� � </span>2_adp: <span class="Apple-converted-space">� </span>1.222<span class="Apple-converted-space">� </span>0.008<span class="Apple-converted-space">� </span>0.075 19.562<span class="Apple-converted-space">� </span>0.005<span class="Apple-converted-space">� </span>4.107 <span class="Apple-converted-space">� </span>1.2876e-01</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">REMARK<span class="Apple-converted-space">� � </span>3_bss: <span class="Apple-converted-space">� </span>1.222<span class="Apple-converted-space">� </span>0.008<span class="Apple-converted-space">� </span>0.075 19.562<span class="Apple-converted-space">� </span>0.005<span class="Apple-converted-space">� </span>4.107 <span class="Apple-converted-space">� </span>1.2876e-01</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">REMARK<span class="Apple-converted-space">� � </span>3_xyz: <span class="Apple-converted-space">� </span>1.021<span class="Apple-converted-space">� </span>0.005<span class="Apple-converted-space">� </span>0.063 19.049<span class="Apple-converted-space">� </span>0.004<span class="Apple-converted-space">� </span>4.111 <span class="Apple-converted-space">� </span>1.0306e-01</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">REMARK<span class="Apple-converted-space">� � </span>3_adp: <span class="Apple-converted-space">� </span>1.021<span class="Apple-converted-space">� </span>0.005<span class="Apple-converted-space">� </span>0.063 19.049<span class="Apple-converted-space">� </span>0.004<span class="Apple-converted-space">� </span>4.111 <span class="Apple-converted-space">� </span>1.0306e-01</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">REMARK<span class="Apple-converted-space">� � </span>3_bss: <span class="Apple-converted-space">� </span>1.021<span class="Apple-converted-space">� </span>0.005<span class="Apple-converted-space">� </span>0.063 19.049<span class="Apple-converted-space">� </span>0.004<span class="Apple-converted-space">� </span>4.111 <span class="Apple-converted-space">� </span>1.0306e-01</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">REMARK</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">------------------------------------------------------------------------</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">C?sar Santiago</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Dept of Macromolecules Structure</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Centro Nacional de Biotecnolog?a, CSIC</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Campus Cantoblanco</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">28049 Madrid</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Spain</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><a href="mailto:csantiag@cnb.csic.es">csantiag@cnb.csic.es</a></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">_______________________________________________</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">phenixbb mailing list</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><a href="http://www.phenix-online.org/mailman/listinfo/phenixbb">http://www.phenix-online.org/mailman/listinfo/phenixbb</a></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div> </blockquote><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">_______________________________________________</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">phenixbb mailing list</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><a href="http://www.phenix-online.org/mailman/listinfo/phenixbb">http://www.phenix-online.org/mailman/listinfo/phenixbb</a></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div> </blockquote><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">-------------- next part --------------</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">An HTML attachment was scrubbed...</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">URL: <a href="http://www.phenix-online.org/pipermail/phenixbb/attachments/20081203/46389290/attachment-0001.htm">http://www.phenix-online.org/pipermail/phenixbb/attachments/20081203/46389290/attachment-0001.htm</a></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">------------------------------</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Message: 5</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Date: Wed, 03 Dec 2008 11:32:05 -0800</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">From: Nigel W Moriarty <<a href="mailto:NWMoriarty@lbl.gov">NWMoriarty@lbl.gov</a>></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Subject: Re: [phenixbb] Question regarding phenix.elbow</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">To: PHENIX user mailing list <<a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Message-ID: <<a href="mailto:4936DEB5.5030000@lbl.gov">4936DEB5.5030000@lbl.gov</a>></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Content-Type: text/plain; charset=ISO-8859-1; format=flowed</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">YoungJin</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I have fixed this error and its will be in the next release.<span class="Apple-converted-space">� </span>Did you<span class="Apple-converted-space">�</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">try ReadySet! as Pavel suggested?<span class="Apple-converted-space">� </span>I can provide a restraints so you can<span class="Apple-converted-space">�</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">continue your refinement if you desire.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Thanks</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Nigel</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">On 12/1/08 6:53 AM, Young-Jin Cho wrote:</div> <blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Hi</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I would like to know how I can add H atoms to my ligand, ADP in the protein complex.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I was trying to add H atoms to one of my ligand, ADP.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">When I types "phenix.elbow --final-geometry=test10bcoot_h_refine_001.pdb --residue=ADP --output=model_h",</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">it went on but failed with the following error message:</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Traceback (most recent call last):</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-converted-space">� </span>File "/home2/yjcho/phenix-1.3-final/elbow/elbow/command_line/builder.py", line 1201, in <module></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-converted-space">� � </span>run()</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-converted-space">� </span>File "/home2/yjcho/phenix-1.3-final/elbow/elbow/command_line/builder.py", line 1108, in run</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-converted-space">� � </span>molecule = post_process(molecule, options)</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-converted-space">� </span>File "/home2/yjcho/phenix-1.3-final/elbow/elbow/command_line/builder.py", line 577, in post_process</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-converted-space">� � </span>options,</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-converted-space">� </span>File "/home2/yjcho/phenix-1.3-final/elbow/elbow/utilities/optimisation_manager.py", line 331, in optimisation_manager</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-converted-space">� � </span>pre_opt))</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-converted-space">� </span>File "/home2/yjcho/phenix-1.3-final/elbow/elbow/chemistry/IOMixins.py", line 857, in WritePDB</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-converted-space">� � </span>original_order=original_order,</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-converted-space">� </span>File "/home2/yjcho/phenix-1.3-final/elbow/elbow/chemistry/IOMixins.py", line 965, in WritePDB2String</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-converted-space">� � </span>self.AdjustHydrogenNames()</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-converted-space">� </span>File "/home2/yjcho/phenix-1.3-final/elbow/elbow/chemistry/IOMixins.py", line 940, in AdjustHydrogenNames</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-converted-space">� � </span>if test_name[3]==" ": test_name[3]="0"</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">TypeError: 'str' object does not support item assignment</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">FYI. ADP is names as ADP as a residue name in the pdb file but has different chain names.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">By the way, I should mention that I used phenix.reduce first for adding H atoms but it was not able to add sugar H's in ADP molecule albeit other residues were fine.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Thanks in advance for your help.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Best,</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">YoungJin</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">_______________________________________________</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">phenixbb mailing list</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><a href="http://www.phenix-online.org/mailman/listinfo/phenixbb">http://www.phenix-online.org/mailman/listinfo/phenixbb</a></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div> </blockquote><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">--<span class="Apple-converted-space">�</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Nigel W. Moriarty</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Building 64R0246B, Physical Biosciences Division</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Lawrence Berkeley National Laboratory</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Berkeley, CA 94720-8235</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Phone : 510-486-5709</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Fax <span class="Apple-converted-space">� </span>: 510-486-5909</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Email : <a href="mailto:NWMoriarty@LBL.gov">NWMoriarty@LBL.gov</a></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Web <span class="Apple-converted-space">� </span>: CCI.LBL.gov</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">------------------------------</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">_______________________________________________</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">phenixbb mailing list</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><a href="http://www.phenix-online.org/mailman/listinfo/phenixbb">http://www.phenix-online.org/mailman/listinfo/phenixbb</a></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">End of phenixbb Digest, Vol 37, Issue 3</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">***************************************</div> </blockquote></div><br></div></body></html>