Re: [Jmol-users] Rapamycin
Also, this is a good use of =RAP? at http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm [image: Inline image 1] On Fri, Jul 22, 2016 at 8:05 AM, Robert Hanson wrote: > Great idea, Angel. > > load ==RAP > > > -- Robert M. Hanson Larson-Anderson 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 -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports.http://sdm.link/zohodev2dev___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Rapamycin
Great idea, Angel. load ==RAP -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports.http://sdm.link/zohodev2dev___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Rapamycin
Sorry, something was preventing models from loading --only in some browsers. I have changed to a newer Jmol version (14.6). Please force reload of the page and it should work now > > a little fun: browse rapamycin structures at PDB: > > > > http://biomodel.uah.es/JSmol/rapamycin.htm > > -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports.http://sdm.link/zohodev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Rapamycin
D yes not load anything for me?? > On Jul 19, 2016, at 3:03 PM, Angel Herráez wrote: > > a little fun: browse rapamycin structures at PDB: > > http://biomodel.uah.es/JSmol/rapamycin.htm > > > > -- > What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic > patterns at an interface-level. Reveals which users, apps, and protocols are > consuming the most bandwidth. Provides multi-vendor support for NetFlow, > J-Flow, sFlow and other flows. Make informed decisions using capacity planning > reports.http://sdm.link/zohodev2dev > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports.http://sdm.link/zohodev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Rapamycin
a little fun: browse rapamycin structures at PDB: http://biomodel.uah.es/JSmol/rapamycin.htm -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports.http://sdm.link/zohodev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Rapamycin
Hello After a few weeks' online exam marking, I was beginning to feel like a zombie. So I was interested to read about rapamycin, and the flat files issues. I loaded a flat-looking mol file obtained from inchi data into the Jmol app (v12.2) and then entered model kit and minimised. The result looks quite good. I have put it onto a web page as an exercise: http://www.biotopics.co.uk/jsmol/rapamycin.html How does it look to you? Richard Steane -Original Message- From: Philip Bays Sent: Tuesday, July 19, 2016 5:56 PM To: Jmol Jmol Subject: Re: [Jmol-users] Rapamycin Yea. I had just found that. > On Jul 19, 2016, at 12:38 PM, Angel Herráez wrote: > > Hi Phil > > Going to PubChem, Compound Summary for CID 5284616 > has a "download" menu that offers no 3D structure but says "Protein-bound > 3D structures" -- their format are not helpful, but you can search in PDB > for > rapamycin and will find this ligand as RAP > > Hence, Jmol console > load ==RAP > and you have it! > > Of course, you can browse the different proteins to check the actual > "real" > 3D structure they bind > > · > Dr. Angel Herráez > Biochemistry and Molecular Biology, > Dept. of Systems Biology, University of Alcalá > E-28871 Alcalá de Henares (Madrid), Spain > > > -- > What NetFlow Analyzer can do for you? Monitors network bandwidth and > traffic > patterns at an interface-level. Reveals which users, apps, and protocols > are > consuming the most bandwidth. Provides multi-vendor support for NetFlow, > J-Flow, sFlow and other flows. Make informed decisions using capacity > planning > reports.http://sdm.link/zohodev2dev > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports.http://sdm.link/zohodev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports.http://sdm.link/zohodev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Rapamycin
Yea. I had just found that. > On Jul 19, 2016, at 12:38 PM, Angel Herráez wrote: > > Hi Phil > > Going to PubChem, Compound Summary for CID 5284616 > has a "download" menu that offers no 3D structure but says "Protein-bound > 3D structures" -- their format are not helpful, but you can search in PDB for > rapamycin and will find this ligand as RAP > > Hence, Jmol console > load ==RAP > and you have it! > > Of course, you can browse the different proteins to check the actual "real" > 3D structure they bind > > · > Dr. Angel Herráez > Biochemistry and Molecular Biology, > Dept. of Systems Biology, University of Alcalá > E-28871 Alcalá de Henares (Madrid), Spain > > > -- > What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic > patterns at an interface-level. Reveals which users, apps, and protocols are > consuming the most bandwidth. Provides multi-vendor support for NetFlow, > J-Flow, sFlow and other flows. Make informed decisions using capacity planning > reports.http://sdm.link/zohodev2dev > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports.http://sdm.link/zohodev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Rapamycin
Hi Phil Going to PubChem, Compound Summary for CID 5284616 has a "download" menu that offers no 3D structure but says "Protein-bound 3D structures" -- their format are not helpful, but you can search in PDB for rapamycin and will find this ligand as RAP Hence, Jmol console load ==RAP and you have it! Of course, you can browse the different proteins to check the actual "real" 3D structure they bind · Dr. Angel Herráez Biochemistry and Molecular Biology, Dept. of Systems Biology, University of Alcalá E-28871 Alcalá de Henares (Madrid), Spain -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports.http://sdm.link/zohodev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Rapamycin
I have looked at it a little more. Turns out that the exported structures do load into JSmol (…. 06.30) with the odd exception of the .spardir. It will load by dropping it one the JSmol window, but will not with the load local file. For that I get a “no atoms found” error. That is true of the structure I was working with and with n-hexane. A file reading glitch in the load sequence? > On Jul 19, 2016, at 12:19 PM, Otis Rothenberger wrote: > > Phil, > > Resolver is string entry “smart,” so you can use load $IDENTIFIER from the > console or a script. You might need the InChI= in the IDENTIFIER string. When > I tried this, it was flat! > > While CORINA docs state that there is no atom limit, you have to get through > CORINA’s ensemble creation front door. I suspect, that this step is failing > with the return of the 2D. Recall that CORINA needs to break molecules into > known ensembles which are then reassembled as 3D. FYI, CORINA DOCS. > > I have no clue what’s going on in SPARTAN. > > Otis > > -- > Otis Rothenberger > o...@chemagic.org > http://chemagic.org > >> On Jul 19, 2016, at 11:49 AM, Philip Bays wrote: >> >> I was intrigued by the structure of the macrolide rapamycin after reading >> the article in C&EN yesterday. So I went after the 3-D structure. >> >> I could not find it in any of the databases used by standard JSmol so I went >> off the Wikipedia and copied the smiles and inche strings. >> >> Using the console I was able to load from the smiles string, though the >> image was flat. Thinking Spartan would be faster at minimization, I >> exported from JSmol as a mol file which I loaded into Spartan and minimized. >> It was fast, but the result was ridiculous; a part of the molecule >> threaded through the macrocycle. >> >> I went back to JSmol and used the minimization function to begin a 3-D >> structure. I did not let it go to completion, but exported it as a mol file >> to load into Spartan. Spartan minimized it. I saved it as Spartan directory >> and as a mol file. For the mol file I was told that there were 8 >> unidentified atoms that were counted as dummy atoms. Neither would load >> into JSmol. It takes a while, but JSmol minimizes the structure to >> something reasonable. >> >> I then tried to load the inche string from the JSmol console using load >> inche “string”. Got a load error. What is the proper syntax for this and >> what is going on with Spartan?? >> >> >> Phil >> >> >> Philip Bays >> Emeritus Professor of Chemistry >> Saint Mary's College >> Notre Dame, IN 46556 >> pb...@saintmarys.edu >> >> >> >> -- >> What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic >> patterns at an interface-level. Reveals which users, apps, and protocols are >> consuming the most bandwidth. Provides multi-vendor support for NetFlow, >> J-Flow, sFlow and other flows. Make informed decisions using capacity >> planning >> reports.http://sdm.link/zohodev2dev >> ___ >> Jmol-users mailing list >> Jmol-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/jmol-users > > > -- > What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic > patterns at an interface-level. Reveals which users, apps, and protocols are > consuming the most bandwidth. Provides multi-vendor support for NetFlow, > J-Flow, sFlow and other flows. Make informed decisions using capacity planning > reports.http://sdm.link/zohodev2dev > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports.http://sdm.link/zohodev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Rapamycin
Phil, Resolver is string entry “smart,” so you can use load $IDENTIFIER from the console or a script. You might need the InChI= in the IDENTIFIER string. When I tried this, it was flat! While CORINA docs state that there is no atom limit, you have to get through CORINA’s ensemble creation front door. I suspect, that this step is failing with the return of the 2D. Recall that CORINA needs to break molecules into known ensembles which are then reassembled as 3D. FYI, CORINA DOCS. I have no clue what’s going on in SPARTAN. Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On Jul 19, 2016, at 11:49 AM, Philip Bays wrote: > > I was intrigued by the structure of the macrolide rapamycin after reading the > article in C&EN yesterday. So I went after the 3-D structure. > > I could not find it in any of the databases used by standard JSmol so I went > off the Wikipedia and copied the smiles and inche strings. > > Using the console I was able to load from the smiles string, though the image > was flat. Thinking Spartan would be faster at minimization, I exported from > JSmol as a mol file which I loaded into Spartan and minimized. It was fast, > but the result was ridiculous; a part of the molecule threaded through the > macrocycle. > > I went back to JSmol and used the minimization function to begin a 3-D > structure. I did not let it go to completion, but exported it as a mol file > to load into Spartan. Spartan minimized it. I saved it as Spartan directory > and as a mol file. For the mol file I was told that there were 8 > unidentified atoms that were counted as dummy atoms. Neither would load into > JSmol. It takes a while, but JSmol minimizes the structure to something > reasonable. > > I then tried to load the inche string from the JSmol console using load inche > “string”. Got a load error. What is the proper syntax for this and what is > going on with Spartan?? > > > Phil > > > Philip Bays > Emeritus Professor of Chemistry > Saint Mary's College > Notre Dame, IN 46556 > pb...@saintmarys.edu > > > > -- > What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic > patterns at an interface-level. Reveals which users, apps, and protocols are > consuming the most bandwidth. Provides multi-vendor support for NetFlow, > J-Flow, sFlow and other flows. Make informed decisions using capacity planning > reports.http://sdm.link/zohodev2dev > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports.http://sdm.link/zohodev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Rapamycin
I was intrigued by the structure of the macrolide rapamycin after reading the article in C&EN yesterday. So I went after the 3-D structure. I could not find it in any of the databases used by standard JSmol so I went off the Wikipedia and copied the smiles and inche strings. Using the console I was able to load from the smiles string, though the image was flat. Thinking Spartan would be faster at minimization, I exported from JSmol as a mol file which I loaded into Spartan and minimized. It was fast, but the result was ridiculous; a part of the molecule threaded through the macrocycle. I went back to JSmol and used the minimization function to begin a 3-D structure. I did not let it go to completion, but exported it as a mol file to load into Spartan. Spartan minimized it. I saved it as Spartan directory and as a mol file. For the mol file I was told that there were 8 unidentified atoms that were counted as dummy atoms. Neither would load into JSmol. It takes a while, but JSmol minimizes the structure to something reasonable. I then tried to load the inche string from the JSmol console using load inche “string”. Got a load error. What is the proper syntax for this and what is going on with Spartan?? Phil Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports.http://sdm.link/zohodev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
