<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Gleb,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>You should be reporting these via Help->Report A Bug rather than sending them to the entire chimera-users list. Please resubmit this using Report A Bug.</div><div class=""><br class=""></div><div class="">—Eric</div><div class=""><br class=""><div class="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>Eric Pettersen</div><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>UCSF Computer Graphics Lab</div><div class=""><br class=""></div></div>
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<br class=""><div><blockquote type="cite" class=""><div class="">On Jun 29, 2016, at 4:19 AM, James Starlight <<a href="mailto:jmsstarlight@gmail.com" class="">jmsstarlight@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="">So the question is now related only to force-field optimization of the<br class="">ensemble via Chimera. Assuming that I have several pdb snapshots<br class="">consisted of protein in deffrent conformation (taken from the gromos<br class="">force field after md done in gromacs) with the ions put to the binding<br class="">pockets- now I need to make quick optimization of this ensemble. In my<br class="">case just for the minimization using latest Amber ff aplied on those<br class="">ensemble Chimera produced error related to assigning of the hydrogens<br class="">(probably due to the mismatching between previous ff and amber however<br class="">the same error in case if I remove all hydrogens prior to<br class="">optimisation):<br class=""><br class=""> Args: ()<br class="">Traceback (innermost last):<br class=""> File "/opt/UCSF/Chimera64-1.11rc/lib/python2.7/site-packages/Pmw/Pmw_1_3_3/lib/PmwBase.py",<br class="">line 1747, in __call__<br class=""> return apply(self.func, args)<br class=""> File "/opt/UCSF/Chimera64-1.11rc/share/chimera/baseDialog.py", line<br class="">449, in command<br class=""> getattr(s, buttonFuncName(txt))()<br class=""> File "/opt/UCSF/Chimera64-1.11rc/share/chimera/baseDialog.py", line 704, in OK<br class=""> self.Apply()<br class=""> File "/opt/UCSF/Chimera64-1.11rc/share/AddH/gui.py", line 302, in Apply<br class=""> initiateAddHyd(self.molList.getvalue(), addFunc=method, okCB=self.cb, **kw)<br class=""> File "/opt/UCSF/Chimera64-1.11rc/share/AddH/unknownsGUI.py", line<br class="">274, in initiateAddHyd<br class=""> addFunc(models, **kw)<br class=""> File "/opt/UCSF/Chimera64-1.11rc/share/AddH/__init__.py", line 543,<br class="">in hbondAddHydrogens<br class=""> inIsolation=inIsolation, **protSchemes)<br class=""> File "/opt/UCSF/Chimera64-1.11rc/share/AddH/__init__.py", line 554,<br class="">in hbondAddHydrogens<br class=""> idatmType, hisNs, coordinations, inIsolation)<br class=""> File "/opt/UCSF/Chimera64-1.11rc/share/AddH/hbond.py", line 237, in<br class="">addHydrogens<br class=""> hbonds = findHBonds(mlist, distSlop=recDistSlop, angleSlop=recAngleSlop)<br class=""> File "/opt/UCSF/Chimera64-1.11rc/share/FindHBond/base.py", line 574,<br class="">in findHBonds<br class=""> (donorAtom, donorHyds) + args):<br class="">TypeError: accPhiPsi() takes exactly 8 arguments (10 given)<br class=""><br class="">TypeError: accPhiPsi() takes exactly 8 arguments (10 given)<br class=""><br class=""> File "/opt/UCSF/Chimera64-1.11rc/share/FindHBond/base.py", line 574,<br class="">in findHBonds<br class=""> (donorAtom, donorHyds) + args):<br class=""><br class="">Any alternative suggestions?<br class=""><br class="">Gleb<br class=""><br class=""><br class="">2016-06-28 16:01 GMT+02:00 James Starlight <<a href="mailto:jmsstarlight@gmail.com" class="">jmsstarlight@gmail.com</a>>:<br class=""><blockquote type="cite" class="">Dear Pymol Users!<br class=""><br class="">Within the Pymol session I have 2 loaded superimposed objects:<br class="">1) one experimental pdb consisted of protein with co-factors (ligand<br class="">and metals);<br class="">2) ensemble of 20 MD snapshots of the same protein (superimposed on<br class="">each others) without any cofactors;<br class=""><br class="">For my particular task I need<br class="">1) to copy the selection (which include metals and ligand atoms) from<br class="">the reference structure to each model of the MD ensemble (via Pymol),<br class="">2) make quick geometrical optimization of side-chains (I guess it<br class="">better to do it using Chimera) within the active side of each model<br class="">from MD ensemble<br class="">3) perform post-processing - analysis of the distances between<br class="">cofactors and optimized side-chains of each MD conformers to obtain<br class="">statistical distribution of averaged distances (I guess it better to<br class="">do it via some MD software like Gromacs).<br class=""><br class="">I will be very thankful for any suggestions for practical realization<br class="">of those steps!<br class=""><br class=""><br class=""><br class="">James<br class=""></blockquote>_______________________________________________<br class="">Chimera-users mailing list: <a href="mailto:Chimera-users@cgl.ucsf.edu" class="">Chimera-users@cgl.ucsf.edu</a><br class="">Manage subscription: <a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br class=""></div></div></blockquote></div><br class=""></div></body></html>