<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="">Yeah, those files and the instructions no longer match the plugin. For instance, the instructions say to open the Amide_I.cfg file using the menu entry File->Import -> .cfg file. Well, there is no such menu entry. I think you’re going to have to try to figure out the interface by trial and error. Sorry!<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><br class="Apple-interchange-newline">
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<br class=""><div><blockquote type="cite" class=""><div class="">On Jul 9, 2017, at 10:45 AM, Roger Hawksworth <<a href="mailto:r_hawksworth@hotmail.co.uk" class="">r_hawksworth@hotmail.co.uk</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div id="divtagdefaultwrapper" dir="ltr" style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; font-size: 12pt; font-family: Calibri, Helvetica, sans-serif;" class=""><div style="margin-top: 0px; margin-bottom: 0px;" class="">Hi Elaine,</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">thank you for the info and suggestions.</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">I managed to find a separate source for the cfg files but they still seem to be in some "funny" format. If interested see at</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><a class="OWAAutoLink" id="LPlnk146133" href="http://sda.iu.edu/nlopredict/index.shtml" previewremoved="true">http://sda.iu.edu/nlopredict/index.shtml</a></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">Best Wishes,</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""> Roger H<br class=""><br class=""></div><div style="" class=""><div class=""><hr tabindex="-1" style="width: 637px; display: inline-block;" class=""><div id="x_divRplyFwdMsg" dir="ltr" class=""><font face="Calibri, sans-serif" style="font-size: 11pt;" class=""><b class="">From:</b><span class="Apple-converted-space"> </span>Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>><br class=""><b class="">Sent:</b><span class="Apple-converted-space"> </span>08 July 2017 15:08<br class=""><b class="">To:</b><span class="Apple-converted-space"> </span>Roger Hawksworth<br class=""><b class="">Cc:</b><span class="Apple-converted-space"> </span><a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a><br class=""><b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [Chimera-users] Problem using Chimera with NLOpredict</font><div class=""> </div></div></div><font size="2" class=""><span style="font-size: 10pt;" class=""><div class="PlainText">Hi Roger,<br class="">So (to repeat what was in your Word document):<br class=""><br class="">Sounds like Chimera in general is working, but then there is an error in the NLOPredict plugin when you follow the example on the NLOPredict site and open one of the data files provided at that site,<span class="Apple-converted-space"> </span><br class=""><<a id="LPlnk618687" href="http://nlopredict.sourceforge.net/" previewremoved="true" class="">http://nlopredict.sourceforge.net/</a>><p style="margin-top: 0px; margin-bottom: 0px;" class=""></p><div id="LPBorder_GT_14996219562660.5374522094411938" style="width: 650px; text-indent: 0px; overflow: auto; margin-bottom: 20px; display: inline-block;" class=""><table id="LPContainer_14996219562540.3081898533845129" role="presentation" cellspacing="0" style="width: 585px; overflow: auto; padding-top: 20px; padding-bottom: 20px; margin-top: 20px; border-top-color: rgb(200, 200, 200); border-bottom-color: rgb(200, 200, 200); border-top-width: 1px; border-bottom-width: 1px; border-top-style: dotted; border-bottom-style: dotted; position: relative; background-color: rgb(255, 255, 255);" class=""><tbody class=""><tr valign="top" style="border-spacing: 0px;" class=""><td id="TextCell_14996219562560.13165275046087854" colspan="2" style="padding: 0px; vertical-align: top; display: table-cell; position: relative;" class=""><div id="LPRemovePreviewContainer_14996219562560.40262196849386095" style="float: right;" class=""></div><div id="LPTitle_14996219562560.8985164432657573" style="top: 0px; color: rgb(0, 120, 215); line-height: 21px; font-family: wf_segoe-ui_light, 'Segoe UI Light', 'Segoe WP Light', 'Segoe UI', 'Segoe WP', Tahoma, Arial, sans-serif; font-size: 21px; font-weight: 400;" class=""><a id="LPUrlAnchor_14996219562590.9682486254408316" href="http://nlopredict.sourceforge.net/" target="_blank" style="text-decoration: none;" class="">NLOPredict - Nonlinear Optical Prediction</a></div><div id="LPMetadata_14996219562600.0048371113574496305" style="margin: 10px 0px 16px; color: rgb(102, 102, 102); line-height: 14px; font-family: wf_segoe-ui_normal, 'Segoe UI', 'Segoe WP', Tahoma, Arial, sans-serif; font-size: 14px; font-weight: 400;" class=""><a href="http://nlopredict.sourceforge.net/" class="">nlopredict.sourceforge.net</a></div><div id="LPDescription_14996219562630.17275536750506115" style="color: rgb(102, 102, 102); line-height: 20px; overflow: hidden; font-family: wf_segoe-ui_normal, 'Segoe UI', 'Segoe WP', Tahoma, Arial, sans-serif; font-size: 14px; font-weight: 400; display: block; max-height: 100px;" class="">NLOPredict. NLOPredict is a nonlinear optical prediction and data analysis tool. Currently, it is implemented as a plugin for the UCSF CHIMERA molecular modeling system.</div></td></tr></tbody></table></div><p style="margin-top: 0px; margin-bottom: 0px;" class=""></p><br class=""><br class=""><br class="">We do not develop or distribute that plugin, and my knowledge of it is limited. Other than your contacting the NLOPredict developers about this problem, my only other idea is that maybe something has changed in Chimera and that the plugin may work better with an older version. <span class="Apple-converted-space"> </span><br class=""><br class="">I don’t see anything on their website about which version of Chimera is recommended, but NLOPredict was developed several years ago, so instead of version 1.11.2 you might try going back a couple versions and seeing what happens. However, it may be more efficient to contact the NLOPredict developers and just ask what version of Chimera they recommend.<br class=""><br class="">Chimera release notes (dates of different versions):<<a id="LPlnk97903" href="http://www.cgl.ucsf.edu/chimera/docs/relnotes.html" previewremoved="true" class="">http://www.cgl.ucsf.edu/chimera/docs/relnotes.html</a>><p style="margin-top: 0px; margin-bottom: 0px;" class=""></p><div id="LPBorder_GT_14996220123800.8354983178608497" style="width: 650px; text-indent: 0px; overflow: auto; margin-bottom: 20px; display: inline-block;" class=""><table id="LPContainer_14996220123670.9318035895189801" role="presentation" cellspacing="0" style="width: 585px; overflow: auto; padding-top: 20px; padding-bottom: 20px; margin-top: 20px; border-top-color: rgb(200, 200, 200); border-bottom-color: rgb(200, 200, 200); border-top-width: 1px; border-bottom-width: 1px; border-top-style: dotted; border-bottom-style: dotted; position: relative; background-color: rgb(255, 255, 255);" class=""><tbody class=""><tr valign="top" style="border-spacing: 0px;" class=""><td id="TextCell_14996220123690.7753220620076041" colspan="2" style="padding: 0px; vertical-align: top; display: table-cell; position: relative;" class=""><div id="LPRemovePreviewContainer_14996220123690.9617644245130066" style="float: right;" class=""></div><div id="LPTitle_14996220123690.7436408334333024" style="top: 0px; color: rgb(0, 120, 215); line-height: 21px; font-family: wf_segoe-ui_light, 'Segoe UI Light', 'Segoe WP Light', 'Segoe UI', 'Segoe WP', Tahoma, Arial, sans-serif; font-size: 21px; font-weight: 400;" class=""><a id="LPUrlAnchor_14996220123720.7959500996854623" href="http://www.cgl.ucsf.edu/chimera/docs/relnotes.html" target="_blank" style="text-decoration: none;" class="">UCSF Chimera Release Notes</a></div><div id="LPMetadata_14996220123730.9540460621282542" style="margin: 10px 0px 16px; color: rgb(102, 102, 102); line-height: 14px; font-family: wf_segoe-ui_normal, 'Segoe UI', 'Segoe WP', Tahoma, Arial, sans-serif; font-size: 14px; font-weight: 400;" class=""><a href="http://www.cgl.ucsf.edu/" class="">www.cgl.ucsf.edu</a></div><div id="LPDescription_14996220123770.2346633544766793" style="color: rgb(102, 102, 102); line-height: 20px; overflow: hidden; font-family: wf_segoe-ui_normal, 'Segoe UI', 'Segoe WP', Tahoma, Arial, sans-serif; font-size: 14px; font-weight: 400; display: block; max-height: 100px;" class="">Chimera Release Notes. All releases with the same version number have the same feature set across all supported platforms. There will be some visual ...</div></td></tr></tbody></table></div><p style="margin-top: 0px; margin-bottom: 0px;" class=""></p><br class=""><br class="">Chimera download old versions:<br class=""><<a id="LPlnk564646" href="http://www.cgl.ucsf.edu/chimera/olddownload.html" previewremoved="true" class="">http://www.cgl.ucsf.edu/chimera/olddownload.html</a>><p style="margin-top: 0px; margin-bottom: 0px;" class=""></p><div id="LPBorder_GT_14996220124330.9514017975092321" style="width: 650px; text-indent: 0px; overflow: auto; margin-bottom: 20px; display: inline-block;" class=""><table id="LPContainer_14996220124210.4175280137999834" role="presentation" cellspacing="0" style="width: 585px; overflow: auto; padding-top: 20px; padding-bottom: 20px; margin-top: 20px; border-top-color: rgb(200, 200, 200); border-bottom-color: rgb(200, 200, 200); border-top-width: 1px; border-bottom-width: 1px; border-top-style: dotted; border-bottom-style: dotted; position: relative; background-color: rgb(255, 255, 255);" class=""><tbody class=""><tr valign="top" style="border-spacing: 0px;" class=""><td id="TextCell_14996220124230.11039544895373493" colspan="2" style="padding: 0px; vertical-align: top; display: table-cell; position: relative;" class=""><div id="LPRemovePreviewContainer_14996220124240.9768686715793553" style="float: right;" class=""></div><div id="LPTitle_14996220124240.8777000106286927" style="top: 0px; color: rgb(0, 120, 215); line-height: 21px; font-family: wf_segoe-ui_light, 'Segoe UI Light', 'Segoe WP Light', 'Segoe UI', 'Segoe WP', Tahoma, Arial, sans-serif; font-size: 21px; font-weight: 400;" class=""><a id="LPUrlAnchor_14996220124270.8201964284994809" href="http://www.cgl.ucsf.edu/chimera/olddownload.html" target="_blank" style="text-decoration: none;" class="">Download UCSF Chimera</a></div><div id="LPMetadata_14996220124280.9823067424234967" style="margin: 10px 0px 16px; color: rgb(102, 102, 102); line-height: 14px; font-family: wf_segoe-ui_normal, 'Segoe UI', 'Segoe WP', Tahoma, Arial, sans-serif; font-size: 14px; font-weight: 400;" class=""><a href="http://www.cgl.ucsf.edu/" class="">www.cgl.ucsf.edu</a></div><div id="LPDescription_14996220124300.21151195743280632" style="color: rgb(102, 102, 102); line-height: 20px; overflow: hidden; font-family: wf_segoe-ui_normal, 'Segoe UI', 'Segoe WP', Tahoma, Arial, sans-serif; font-size: 14px; font-weight: 400; display: block; max-height: 100px;" class="">Platform Installer, Size, and Checksum Date Notes; Mac OS X: chimera-1.11.1-mac.dmg Size: 104050363 bytes MD5: d9c1c7576a3f42c49b871a818257580b: Sep 22, 2016</div></td></tr></tbody></table></div><p style="margin-top: 0px; margin-bottom: 0px;" class=""></p><br class=""><br class=""><br class="">Before all that, probably should try downloading that cfg file afresh to make sure that it just didn’t get into some weird state before you tried to open it. The cfg files at the NLOPredict website seem to binary, or some format that is not easily viewed, so I can’t really tell anything from looking at them.<br class=""><br class="">I hope this helps,<br class="">Elaine<br class="">-----<br class="">Elaine C. Meng, Ph.D. <span class="Apple-converted-space"> </span><br class="">UCSF Chimera(X) team<br class="">Department of Pharmaceutical Chemistry<br class="">University of California, San Francisco<br class=""><br class="">> On Jul 8, 2017, at 3:46 AM, Roger Hawksworth <<a href="mailto:r_hawksworth@hotmail.co.uk" class="">r_hawksworth@hotmail.co.uk</a>> wrote:<br class="">><span class="Apple-converted-space"> </span><br class="">> Hi,<br class="">> Please see attached Word .docx file which is also contained within the attached .zip file.<br class="">><span class="Apple-converted-space"> </span><br class="">> Today, 08th July 2017, is the first time that I have used Chimera. Perhaps the .cfg file I tried to use is somehow "corrupt"?<br class="">> Best Wishes,<br class="">> Roger H<br class="">><span class="Apple-converted-space"> </span><br class=""><br class=""></div></span></font></div></div><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">_______________________________________________</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">Chimera-users mailing list:<span class="Apple-converted-space"> </span></span><a href="mailto:Chimera-users@cgl.ucsf.edu" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">Chimera-users@cgl.ucsf.edu</a><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">Manage subscription:<span class="Apple-converted-space"> </span></span><a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""></div></blockquote></div><br class=""></div></body></html>