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<DIV>Eran & others,</DIV>
<DIV>The commands that I used are: <SPAN style="FONT-SIZE: 11pt; LINE-HEIGHT: 115%; FONT-FAMILY: 'Calibri','sans-serif'; mso-fareast-font-family: Calibri; mso-bidi-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: EN-US; mso-bidi-language: AR-SA">Select :c, :n; isosurface minset 1000 pocket cavity 1.2. I am doing everything in Proteopedia.</SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 11pt; LINE-HEIGHT: 115%; FONT-FAMILY: 'Calibri','sans-serif'; mso-fareast-font-family: Calibri; mso-bidi-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: EN-US; mso-bidi-language: AR-SA"></SPAN> </DIV>
<DIV><SPAN style="FONT-SIZE: 11pt; LINE-HEIGHT: 115%; FONT-FAMILY: 'Calibri','sans-serif'; mso-fareast-font-family: Calibri; mso-bidi-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: EN-US; mso-bidi-language: AR-SA">Here is a message that Angel sent to me after he did some testing.</SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 11pt; LINE-HEIGHT: 115%; FONT-FAMILY: 'Calibri','sans-serif'; mso-fareast-font-family: Calibri; mso-bidi-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: EN-US; mso-bidi-language: AR-SA"></SPAN> </DIV>
<DIV><SPAN style="FONT-SIZE: 11pt; LINE-HEIGHT: 115%; FONT-FAMILY: 'Calibri','sans-serif'; mso-fareast-font-family: Calibri; mso-bidi-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: EN-US; mso-bidi-language: AR-SA">"I've run your script and the error says<BR>script compiler ERROR: } expected</SPAN></DIV>
<DIV> </DIV>
<DIV><SPAN style="FONT-SIZE: 11pt; LINE-HEIGHT: 115%; FONT-FAMILY: 'Calibri','sans-serif'; mso-fareast-font-family: Calibri; mso-bidi-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: EN-US; mso-bidi-language: AR-SA">but I'm not sure about the the use of the colon, n:m syntax. In any case, since it's a state <BR>produced by Jmol, I think it's a bug. You should report it to jmol-developers<BR>Though I guess what Bob will tell you... upgrade!</SPAN></DIV>
<DIV> </DIV>
<DIV><SPAN style="FONT-SIZE: 11pt; LINE-HEIGHT: 115%; FONT-FAMILY: 'Calibri','sans-serif'; mso-fareast-font-family: Calibri; mso-bidi-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: EN-US; mso-bidi-language: AR-SA">If I load the pdb file and try the offending line in 11.6.13, there is no error"<BR></SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 11pt; LINE-HEIGHT: 115%; FONT-FAMILY: 'Calibri','sans-serif'; mso-fareast-font-family: Calibri; mso-bidi-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: EN-US; mso-bidi-language: AR-SA">It appears that upgrading Jmol will help.</SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 11pt; LINE-HEIGHT: 115%; FONT-FAMILY: 'Calibri','sans-serif'; mso-fareast-font-family: Calibri; mso-bidi-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: EN-US; mso-bidi-language: AR-SA"></SPAN> </DIV>
<DIV><SPAN style="FONT-SIZE: 11pt; LINE-HEIGHT: 115%; FONT-FAMILY: 'Calibri','sans-serif'; mso-fareast-font-family: Calibri; mso-bidi-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: EN-US; mso-bidi-language: AR-SA">Karl</DIV></SPAN>
<DIV><BR><BR>>>> Eran Hodis <eran.hodis@weizmann.ac.il> 1/16/2009 7:28 PM >>><BR>Hi Karl and Angel,<BR><BR>What is the command, Karl, that you issued in order to make and display the surface in the SAT (Proteopedia's Scene Authoring Tools)?<BR><BR>The generated state script that you referenced has the following line:<BR> "calculate surfaceDistance WITHIN ({6073:9161 23278:26366 35260:35345 35430:35515}) ;"<BR><BR>which I cannot successfully execute on its own. I get the same error as you:<BR>"script compiler ERROR: } expected"<BR><BR>Karl I assume the answer to Angel's question is that you used only the Jmol applets on the Proteopedia website? If so, we currently run 11.5.51, although we should update it when we have a chance.<BR><BR>Best,<BR>Eran<BR><BR>-----Original Message-----<BR>>From Karl Oberholser <oberhols@messiah.edu><BR>Sent Fri 1/16/2009 5:51 PM<BR>To proteopedialist-for-users@bioinformatics.org<BR>Subject [Proteo
pedia] Script compiler error<BR><BR>Hi All,<BR><BR>I am attempting to compute a surface using the Jmol cavity command. I can<BR>make and display the surface in SAT, but when I test the green link no<BR>surface is made, and I obtain the following error:<BR>script compiler ERROR: } expected<BR>----line 199 command 22 of<BR>/wiki/scripts/Complex_III_of_Electron_Transport_Chain/Surface_qn/2.spt:<BR> calculate surfaceDistance WITHIN ({6073:9161 23278:26366<BR>35260:35345 35430:35515}) ; <<<<<BR>----line 1 command 2 of file null:<BR> script >><BR>"/wiki/scripts/Complex_III_of_Electron_Transport_Chain/Surface_qn/2.spt" <<<BR>I do not know what to make of this! Any help would be appreciated.<BR><BR>Karl<BR><BR><BR><BR>Karl M. Oberholser <BR>Professor Chemistry<BR>Chemistry & Biochemistry Dept. <BR>Messiah College <BR>Grantham
, PA US <BR>Molecular Science Lab:<BR><A href="http://www.messiah.edu/molscilab/">http://www.messiah.edu/molscilab/</A> <BR>Proteopedia user page: <BR><A href="http://proteopedia.org/wiki/index.php/User:Karl_Oberholser">http://proteopedia.org/wiki/index.php/User:Karl_Oberholser</A> <BR> <BR>-------------- next part --------------<BR>An HTML attachment was scrubbed...<BR>URL: <<A href="http://www.bioinformatics.org/pipermail/proteopedialist">http://www.bioinformatics.org/pipermail/proteopedialist</A>-for-users/attachments/20090116/8abbd0e2/attachment.html><BR>_______________________________________________<BR>Proteopedialist-for-users mailing list<BR>Proteopedialist-for-users@bioinformatics.org<BR><A href="http://www.bioinformatics.org/mailman/listinfo/proteopedialist">http://www.bioinformatics.org/mailman/listinfo/proteopedialist</A>-for-users<BR><BR>
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