From: Otis R. <osr...@ch...> - 2011-03-01 00:53:19
|
Bob, I can get the translated coordinates and frame adjustments from the state script of your page, so I have no problem loading your adjusted data for Hen's file. But I have looked at that file for years and said, "Boy I'd like to translate the those coordinates." So, just as a Jmol learning exercise, how'd ya do it? I don't mean the details - just some gentle pointers. Otis -- Otis Rothenberger Department of Chemistry Illinois State University Normal, IL 61790-4160 http://chemagic.org |
From: Otis R. <osr...@ch...> - 2011-03-01 02:58:49
|
Incredible! Load, frame all, and the following is instructive and fun to watch: for (var i = 1; i < 35; i++) { var j = i+1;compare {model=j} {model=i} ROTATE TRANSLATE 0.0;delay .5 } Like I said. That file has been around for years, with lots of people asking about changing the C1 C2 fixed position. It's also nice to know the file's origin. Otis -- Otis Rothenberger Department of Chemistry Illinois State University Normal, IL 61790-4160 http://chemagic.org ---------------------------------------- From: "Robert Hanson" <ha...@st...> Sent: Monday, February 28, 2011 9:13 PM To: osr...@ch..., jmo...@li... Subject: Re: [Jmol-users] Finally! A nice cyclohexane chair/chair flip demo load http://wetche.cmbi.ru.nl/organic/cyclohexane/jm/chxinv.xyz for (var i = 1; i < 35; i++) { var j = i+1;compare {model=j} {model=i} ROTATE TRANSLATE 0.0 } There are 35 models. This runs through the models, rotating and translating each model to be the best match to the previous model in the set. Originally written for aligning proteins, it turns out the COMPARE command does a pretty fair job with simple reactions as well. Bob On Mon, Feb 28, 2011 at 6:52 PM, Otis Rothenberger <osr...@ch...> wrote: Bob, I can get the translated coordinates and frame adjustments from the state script of your page, so I have no problem loading your adjusted data for Hen's file. But I have looked at that file for years and said, "Boy I'd like to translate the those coordinates." So, just as a Jmol learning exercise, how'd ya do it? I don't mean the details - just some gentle pointers. Otis -- Otis Rothenberger Department of Chemistry Illinois State University Normal, IL 61790-4160 http://chemagic.org ---------------------------------------------------------------------------- -- Free Software Download: Index, Search & Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev _______________________________________________ Jmol-users mailing list Jmo...@li... https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 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: Robert H. <ha...@st...> - 2011-03-01 03:32:38
|
Well, if you like that.... load http://wetche.cmbi.ru.nl/organic/cyclohexane/jm/chxinv.xyz rotate x 90 frame all for (var i = 1; i < 35; i++) { var j = i+1;select {model=i}; color @{point(i*5 + 80, i*4 + 115, i*3 + 140)}; compare {model=j} {model=i} ROTATE TRANSLATE 0.5 } Nicely shows the C2 symmetry of the process. Bob On Mon, Feb 28, 2011 at 8:58 PM, Otis Rothenberger <osr...@ch...>wrote: > Incredible! > > Load, frame all, and the following is instructive and fun to watch: > > for (var i = 1; i < 35; i++) { var j = i+1;compare {model=j} {model=i} > ROTATE TRANSLATE 0.0;delay .5 } > > Like I said. That file has been around for years, with lots of people > asking about changing the C1 C2 fixed position. It's also nice to know the > file's origin. > > > Otis > > -- > Otis Rothenberger > Department of Chemistry > Illinois State University Normal, IL 61790-4160 > http://chemagic.org > > ------------------------------ > *From*: "Robert Hanson" <ha...@st...> > *Sent*: Monday, February 28, 2011 9:13 PM > *To*: osr...@ch..., jmo...@li... > *Subject*: Re: [Jmol-users] Finally! A nice cyclohexane chair/chair flip > demo > > > load http://wetche.cmbi.ru.nl/organic/cyclohexane/jm/chxinv.xyz > for (var i = 1; i < 35; i++) { var j = i+1;compare {model=j} {model=i} > ROTATE TRANSLATE 0.0 } > > There are 35 models. This runs through the models, rotating and translating > each model to be the best match to the previous model in the set. Originally > written for aligning proteins, it turns out the COMPARE command does a > pretty fair job with simple reactions as well. > > Bob > > > On Mon, Feb 28, 2011 at 6:52 PM, Otis Rothenberger <osr...@ch...>wrote: > >> Bob, >> >> I can get the translated coordinates and frame adjustments from the state >> script of your page, so I have no problem loading your adjusted data for >> Hen's file. But I have looked at that file for years and said, "Boy I'd like >> to translate the those coordinates." >> >> So, just as a Jmol learning exercise, how'd ya do it? I don't mean the >> details - just some gentle pointers. >> >> Otis >> >> -- >> Otis Rothenberger >> Department of Chemistry >> Illinois State University Normal, IL 61790-4160 >> http://chemagic.org >> >> >> >> >> >> >> >> ------------------------------------------------------------------------------ >> Free Software Download: Index, Search & Analyze Logs and other IT data in >> Real-Time with Splunk. Collect, index and harness all the fast moving IT >> data >> generated by your applications, servers and devices whether physical, >> virtual >> or in the cloud. Deliver compliance at lower cost and gain new business >> insights. http://p.sf.net/sfu/splunk-dev2dev >> _______________________________________________ >> Jmol-users mailing list >> Jmo...@li... >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> > > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > 1520 St. Olaf Ave. > Northfield, MN 55057 > http://www.stolaf.edu/people/hansonr > phone: 507-786-3107 > > > 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 > > > > ------------------------------------------------------------------------------ > Free Software Download: Index, Search & Analyze Logs and other IT data in > Real-Time with Splunk. Collect, index and harness all the fast moving IT > data > generated by your applications, servers and devices whether physical, > virtual > or in the cloud. Deliver compliance at lower cost and gain new business > insights. http://p.sf.net/sfu/splunk-dev2dev > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 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: Robert H. <ha...@st...> - 2011-03-01 02:13:18
|
load http://wetche.cmbi.ru.nl/organic/cyclohexane/jm/chxinv.xyz for (var i = 1; i < 35; i++) { var j = i+1;compare {model=j} {model=i} ROTATE TRANSLATE 0.0 } There are 35 models. This runs through the models, rotating and translating each model to be the best match to the previous model in the set. Originally written for aligning proteins, it turns out the COMPARE command does a pretty fair job with simple reactions as well. Bob On Mon, Feb 28, 2011 at 6:52 PM, Otis Rothenberger <osr...@ch...>wrote: > Bob, > > I can get the translated coordinates and frame adjustments from the state > script of your page, so I have no problem loading your adjusted data for > Hen's file. But I have looked at that file for years and said, "Boy I'd like > to translate the those coordinates." > > So, just as a Jmol learning exercise, how'd ya do it? I don't mean the > details - just some gentle pointers. > > Otis > > -- > Otis Rothenberger > Department of Chemistry > Illinois State University Normal, IL 61790-4160 > http://chemagic.org > > > > > > > > ------------------------------------------------------------------------------ > Free Software Download: Index, Search & Analyze Logs and other IT data in > Real-Time with Splunk. Collect, index and harness all the fast moving IT > data > generated by your applications, servers and devices whether physical, > virtual > or in the cloud. Deliver compliance at lower cost and gain new business > insights. http://p.sf.net/sfu/splunk-dev2dev > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 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 |