From: Christian B. <bae...@ma...> - 2007-07-18 09:42:17
|
Hi, I have upgraded to Jmol 11.2.4 and now my script for the cavity drawings in zeolites does not work properly anymore. I load two models from an xyz file and select the models using something like this isosurface channel resolution 2.0 select (*/2) ignore (*/1) minset 1000 POCKET cavity 1.0 sasurface 0.2 I works fine if you draw the channels for model one, but for model 2 it seems to mix model 1 into it as well. It works also fine for both models for the "normal" isosurfaces. Has anything changed with select/ignore in the new version? I have tried several options but none seems to work I use Jmol.js Thanks for your help Christian |
From: Bob H. <ha...@st...> - 2007-07-23 12:04:14
|
It was a bug in the isosurface POCKET and CAVITY subcommands. Fixed for 11.2.5 and 11.3.5 Christian Baerlocher wrote: >Hi, > >I have upgraded to Jmol 11.2.4 and now my script for the cavity >drawings in zeolites does not work properly anymore. > >I load two models from an xyz file and select the models using >something like this > > > >I works fine if you draw the channels for model one, but for model 2 >it seems to mix model 1 into it as well. > >It works also fine for both models for the "normal" isosurfaces. > >Has anything changed with select/ignore in the new version? I have >tried several options but none seems to work > >I use Jmol.js > >Thanks for your help > >Christian > > > >------------------------------------------------------------------------- >This SF.net email is sponsored by DB2 Express >Download DB2 Express C - the FREE version of DB2 express and take >control of your XML. No limits. Just data. Click to get it now. >http://sourceforge.net/powerbar/db2/ >_______________________________________________ >Jmol-users mailing list >Jmo...@li... >https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 |
From: Christian B. <bae...@ma...> - 2007-07-23 15:43:28
|
Thanks Bob, I have just downloaded version 11.2.5 and tested it: Unfortunately, I still have the same problem.... It works fine the first time, but when load the second model, it draws the wrong range. When I go back to the first model: wrong again. (I hope I am not doing something silly!) Christian P.S. Should I send you a test file? On Jul 23, 2007, at 2:04 PM, Bob Hanson wrote: > It was a bug in the isosurface POCKET and CAVITY subcommands. Fixed > for > 11.2.5 and 11.3.5 > > > Christian Baerlocher wrote: > >> Hi, >> >> I have upgraded to Jmol 11.2.4 and now my script for the cavity >> drawings in zeolites does not work properly anymore. >> >> I load two models from an xyz file and select the models using >> something like this >> >> >> >> I works fine if you draw the channels for model one, but for model 2 >> it seems to mix model 1 into it as well. >> >> It works also fine for both models for the "normal" isosurfaces. >> >> Has anything changed with select/ignore in the new version? I have >> tried several options but none seems to work >> >> I use Jmol.js >> >> Thanks for your help >> >> Christian >> >> >> >> --------------------------------------------------------------------- >> ---- >> This SF.net email is sponsored by DB2 Express >> Download DB2 Express C - the FREE version of DB2 express and take >> control of your XML. No limits. Just data. Click to get it now. >> http://sourceforge.net/powerbar/db2/ >> _______________________________________________ >> Jmol-users mailing list >> Jmo...@li... >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> > > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > > > > ---------------------------------------------------------------------- > --- > This SF.net email is sponsored by: Splunk Inc. > Still grepping through log files to find problems? Stop. > Now Search log events and configuration files using AJAX and a > browser. > Download your FREE copy of Splunk now >> http://get.splunk.com/ > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users |
From: Bob H. <ha...@st...> - 2007-07-23 23:07:12
|
hmm. Yes, please send a test file to ha...@st... Christian Baerlocher wrote: >Thanks Bob, > >I have just downloaded version 11.2.5 and tested it: Unfortunately, >I still have the same problem.... >It works fine the first time, but when load the second model, it >draws the wrong range. When I go back to the first model: wrong again. > >(I hope I am not doing something silly!) > >Christian > >P.S. Should I send you a test file? > > >On Jul 23, 2007, at 2:04 PM, Bob Hanson wrote: > > > >>It was a bug in the isosurface POCKET and CAVITY subcommands. Fixed >>for >>11.2.5 and 11.3.5 >> >> >>Christian Baerlocher wrote: >> >> >> >>>Hi, >>> >>>I have upgraded to Jmol 11.2.4 and now my script for the cavity >>>drawings in zeolites does not work properly anymore. >>> >>>I load two models from an xyz file and select the models using >>>something like this >>> >>> >>> >>>I works fine if you draw the channels for model one, but for model 2 >>>it seems to mix model 1 into it as well. >>> >>>It works also fine for both models for the "normal" isosurfaces. >>> >>>Has anything changed with select/ignore in the new version? I have >>>tried several options but none seems to work >>> >>>I use Jmol.js >>> >>>Thanks for your help >>> >>>Christian >>> >>> >>> >>>--------------------------------------------------------------------- >>>---- >>>This SF.net email is sponsored by DB2 Express >>>Download DB2 Express C - the FREE version of DB2 express and take >>>control of your XML. No limits. Just data. Click to get it now. >>>http://sourceforge.net/powerbar/db2/ >>>_______________________________________________ >>>Jmol-users mailing list >>>Jmo...@li... >>>https://lists.sourceforge.net/lists/listinfo/jmol-users >>> >>> >>> >>> >>-- >>Robert M. Hanson >>Professor of Chemistry >>St. Olaf College >>Northfield, MN >>http://www.stolaf.edu/people/hansonr >> >> >>If nature does not answer first what we want, >>it is better to take what answer we get. >> >>-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 >> >> >> >>---------------------------------------------------------------------- >>--- >>This SF.net email is sponsored by: Splunk Inc. >>Still grepping through log files to find problems? Stop. >>Now Search log events and configuration files using AJAX and a >>browser. >>Download your FREE copy of Splunk now >> http://get.splunk.com/ >>_______________________________________________ >>Jmol-users mailing list >>Jmo...@li... >>https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> > > >------------------------------------------------------------------------- >This SF.net email is sponsored by: Splunk Inc. >Still grepping through log files to find problems? Stop. >Now Search log events and configuration files using AJAX and a browser. >Download your FREE copy of Splunk now >> http://get.splunk.com/ >_______________________________________________ >Jmol-users mailing list >Jmo...@li... >https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 |
From: Bob H. <ha...@st...> - 2007-07-24 13:50:28
|
OK, this should be fixed for 11.3.6 and 11.2.6. In addition, there were a few other related matters that I think now are fixed: version=11.2.6 # bug fix: inappropriate draw pick spinning for single point # bug fix: dots not available in multimodel mode # bug fix: multiple isosurface cavities incorrect in a multimodel environment # bug fix: isosurface cavity not filled completely Christian Baerlocher wrote: >Thanks Bob, > >I have just downloaded version 11.2.5 and tested it: Unfortunately, >I still have the same problem.... >It works fine the first time, but when load the second model, it >draws the wrong range. When I go back to the first model: wrong again. > >(I hope I am not doing something silly!) > >Christian > >P.S. Should I send you a test file? > > >On Jul 23, 2007, at 2:04 PM, Bob Hanson wrote: > > > >>It was a bug in the isosurface POCKET and CAVITY subcommands. Fixed >>for >>11.2.5 and 11.3.5 >> >> >>Christian Baerlocher wrote: >> >> >> >>>Hi, >>> >>>I have upgraded to Jmol 11.2.4 and now my script for the cavity >>>drawings in zeolites does not work properly anymore. >>> >>>I load two models from an xyz file and select the models using >>>something like this >>> >>> >>> >>>I works fine if you draw the channels for model one, but for model 2 >>>it seems to mix model 1 into it as well. >>> >>>It works also fine for both models for the "normal" isosurfaces. >>> >>>Has anything changed with select/ignore in the new version? I have >>>tried several options but none seems to work >>> >>>I use Jmol.js >>> >>>Thanks for your help >>> >>>Christian >>> >>> >>> >>>--------------------------------------------------------------------- >>>---- >>>This SF.net email is sponsored by DB2 Express >>>Download DB2 Express C - the FREE version of DB2 express and take >>>control of your XML. No limits. Just data. Click to get it now. >>>http://sourceforge.net/powerbar/db2/ >>>_______________________________________________ >>>Jmol-users mailing list >>>Jmo...@li... >>>https://lists.sourceforge.net/lists/listinfo/jmol-users >>> >>> >>> >>> >>-- >>Robert M. Hanson >>Professor of Chemistry >>St. Olaf College >>Northfield, MN >>http://www.stolaf.edu/people/hansonr >> >> >>If nature does not answer first what we want, >>it is better to take what answer we get. >> >>-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 >> >> >> >>---------------------------------------------------------------------- >>--- >>This SF.net email is sponsored by: Splunk Inc. >>Still grepping through log files to find problems? Stop. >>Now Search log events and configuration files using AJAX and a >>browser. >>Download your FREE copy of Splunk now >> http://get.splunk.com/ >>_______________________________________________ >>Jmol-users mailing list >>Jmo...@li... >>https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> > > >------------------------------------------------------------------------- >This SF.net email is sponsored by: Splunk Inc. >Still grepping through log files to find problems? Stop. >Now Search log events and configuration files using AJAX and a browser. >Download your FREE copy of Splunk now >> http://get.splunk.com/ >_______________________________________________ >Jmol-users mailing list >Jmo...@li... >https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 |
From: Christian B. <bae...@ma...> - 2007-07-25 07:12:45
|
Great, thanks a lot. I am particularly happy that you also fixed the bug you listed last. I am eagerly looking forward to download version 11.2.6 and test it. Christian On Jul 24, 2007, at 3:50 PM, Bob Hanson wrote: > OK, this should be fixed for 11.3.6 and 11.2.6. In addition, there > were > a few other related matters that I think now are fixed: > > version=11.2.6 > > # bug fix: inappropriate draw pick spinning for single point > # bug fix: dots not available in multimodel mode > # bug fix: multiple isosurface cavities incorrect in a multimodel > environment > # bug fix: isosurface cavity not filled completely > > > Christian Baerlocher wrote: > >> Thanks Bob, >> >> I have just downloaded version 11.2.5 and tested it: Unfortunately, >> I still have the same problem.... >> It works fine the first time, but when load the second model, it >> draws the wrong range. When I go back to the first model: wrong >> again. >> >> (I hope I am not doing something silly!) >> >> Christian >> >> P.S. Should I send you a test file? >> >> >> On Jul 23, 2007, at 2:04 PM, Bob Hanson wrote: >> >> >> >>> It was a bug in the isosurface POCKET and CAVITY subcommands. Fixed >>> for >>> 11.2.5 and 11.3.5 >>> >>> >>> Christian Baerlocher wrote: >>> >>> >>> >>>> Hi, >>>> >>>> I have upgraded to Jmol 11.2.4 and now my script for the cavity >>>> drawings in zeolites does not work properly anymore. >>>> >>>> I load two models from an xyz file and select the models using >>>> something like this >>>> >>>> >>>> >>>> I works fine if you draw the channels for model one, but for >>>> model 2 >>>> it seems to mix model 1 into it as well. >>>> >>>> It works also fine for both models for the "normal" isosurfaces. >>>> >>>> Has anything changed with select/ignore in the new version? I have >>>> tried several options but none seems to work >>>> >>>> I use Jmol.js >>>> >>>> Thanks for your help >>>> >>>> Christian >>>> >>>> >>>> >>>> ------------------------------------------------------------------- >>>> -- >>>> ---- >>>> This SF.net email is sponsored by DB2 Express >>>> Download DB2 Express C - the FREE version of DB2 express and take >>>> control of your XML. No limits. Just data. Click to get it now. >>>> http://sourceforge.net/powerbar/db2/ >>>> _______________________________________________ >>>> Jmol-users mailing list >>>> Jmo...@li... >>>> https://lists.sourceforge.net/lists/listinfo/jmol-users >>>> >>>> >>>> >>>> >>> -- >>> Robert M. Hanson >>> Professor of Chemistry >>> St. Olaf College >>> Northfield, MN >>> http://www.stolaf.edu/people/hansonr >>> >>> >>> If nature does not answer first what we want, >>> it is better to take what answer we get. >>> >>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 >>> >>> >>> >>> -------------------------------------------------------------------- >>> -- >>> --- >>> This SF.net email is sponsored by: Splunk Inc. >>> Still grepping through log files to find problems? Stop. >>> Now Search log events and configuration files using AJAX and a >>> browser. >>> Download your FREE copy of Splunk now >> http://get.splunk.com/ >>> _______________________________________________ >>> Jmol-users mailing list >>> Jmo...@li... >>> https://lists.sourceforge.net/lists/listinfo/jmol-users >>> >>> >> >> >> --------------------------------------------------------------------- >> ---- >> This SF.net email is sponsored by: Splunk Inc. >> Still grepping through log files to find problems? Stop. >> Now Search log events and configuration files using AJAX and a >> browser. >> Download your FREE copy of Splunk now >> http://get.splunk.com/ >> _______________________________________________ >> Jmol-users mailing list >> Jmo...@li... >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> > > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > > > > ---------------------------------------------------------------------- > --- > This SF.net email is sponsored by: Splunk Inc. > Still grepping through log files to find problems? Stop. > Now Search log events and configuration files using AJAX and a > browser. > Download your FREE copy of Splunk now >> http://get.splunk.com/ > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users |
From: Christian B. <bae...@ma...> - 2007-07-25 14:47:22
|
Works perfect, Thanks a lot! I can now draw much nicer surfaces with well defined edges. Just super! Christian On Jul 24, 2007, at 3:50 PM, Bob Hanson wrote: > OK, this should be fixed for 11.3.6 and 11.2.6. In addition, there > were > a few other related matters that I think now are fixed: > > version=11.2.6 > > # bug fix: inappropriate draw pick spinning for single point > # bug fix: dots not available in multimodel mode > # bug fix: multiple isosurface cavities incorrect in a multimodel > environment > # bug fix: isosurface cavity not filled completely > > > Christian Baerlocher wrote: > >> Thanks Bob, >> >> I have just downloaded version 11.2.5 and tested it: Unfortunately, >> I still have the same problem.... >> It works fine the first time, but when load the second model, it >> draws the wrong range. When I go back to the first model: wrong >> again. >> >> (I hope I am not doing something silly!) >> >> Christian >> >> P.S. Should I send you a test file? >> >> >> On Jul 23, 2007, at 2:04 PM, Bob Hanson wrote: >> >> >> >>> It was a bug in the isosurface POCKET and CAVITY subcommands. Fixed >>> for >>> 11.2.5 and 11.3.5 >>> >>> >>> Christian Baerlocher wrote: >>> >>> >>> >>>> Hi, >>>> >>>> I have upgraded to Jmol 11.2.4 and now my script for the cavity >>>> drawings in zeolites does not work properly anymore. >>>> >>>> I load two models from an xyz file and select the models using >>>> something like this >>>> >>>> >>>> >>>> I works fine if you draw the channels for model one, but for >>>> model 2 >>>> it seems to mix model 1 into it as well. >>>> >>>> It works also fine for both models for the "normal" isosurfaces. >>>> >>>> Has anything changed with select/ignore in the new version? I have >>>> tried several options but none seems to work >>>> >>>> I use Jmol.js >>>> >>>> Thanks for your help >>>> >>>> Christian >>>> >>>> >>>> >>>> ------------------------------------------------------------------- >>>> -- >>>> ---- >>>> This SF.net email is sponsored by DB2 Express >>>> Download DB2 Express C - the FREE version of DB2 express and take >>>> control of your XML. No limits. Just data. Click to get it now. >>>> http://sourceforge.net/powerbar/db2/ >>>> _______________________________________________ >>>> Jmol-users mailing list >>>> Jmo...@li... >>>> https://lists.sourceforge.net/lists/listinfo/jmol-users >>>> >>>> >>>> >>>> >>> -- >>> Robert M. Hanson >>> Professor of Chemistry >>> St. Olaf College >>> Northfield, MN >>> http://www.stolaf.edu/people/hansonr >>> >>> >>> If nature does not answer first what we want, >>> it is better to take what answer we get. >>> >>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 >>> >>> >>> >>> -------------------------------------------------------------------- >>> -- >>> --- >>> This SF.net email is sponsored by: Splunk Inc. >>> Still grepping through log files to find problems? Stop. >>> Now Search log events and configuration files using AJAX and a >>> browser. >>> Download your FREE copy of Splunk now >> http://get.splunk.com/ >>> _______________________________________________ >>> Jmol-users mailing list >>> Jmo...@li... >>> https://lists.sourceforge.net/lists/listinfo/jmol-users >>> >>> >> >> >> --------------------------------------------------------------------- >> ---- >> This SF.net email is sponsored by: Splunk Inc. >> Still grepping through log files to find problems? Stop. >> Now Search log events and configuration files using AJAX and a >> browser. >> Download your FREE copy of Splunk now >> http://get.splunk.com/ >> _______________________________________________ >> Jmol-users mailing list >> Jmo...@li... >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> > > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > > > > ---------------------------------------------------------------------- > --- > This SF.net email is sponsored by: Splunk Inc. > Still grepping through log files to find problems? Stop. > Now Search log events and configuration files using AJAX and a > browser. > Download your FREE copy of Splunk now >> http://get.splunk.com/ > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users |