## RE: [Jmol-users] Add NMR parameters to "measurements"

 RE: [Jmol-users] Add NMR parameters to "measurements" From: Miguel - 2004-03-31 10:05:18 ```Too many words ... I don't understand :-) Are these properties specifically per atom? Or general to the entire model? Miguel > Hi Miguel, > > =09OK, so the output file has some lines that look a bit like this - > one for each atom: > ... > Calculating GIAO nuclear magnetic shielding tensors. > SCF GIAO Magnetic shielding tensor (ppm): > 1 C Isotropic =3D 126.6540 Anisotropy =3D 21.4588 > XX=3D 119.2320 YX=3D 2.2126 ZX=3D -0.5824 > XY=3D 1.7272 YY=3D 138.4056 ZY=3D 6.3864 > XZ=3D -1.5981 YZ=3D 7.0991 ZZ=3D 122.3243 > Eigenvalues: 117.7671 121.2349 140.9598 > 2 C Isotropic =3D 25.5825 Anisotropy =3D 100.8347 > XX=3D 3.0461 YX=3D 33.1351 ZX=3D -63.5814 > XY=3D 39.6564 YY=3D 27.3781 ZY=3D 16.4905 > XZ=3D -61.6212 YZ=3D 10.3607 ZZ=3D 46.3234 > Eigenvalues: -58.0816 42.0235 92.8057 > ... > 17 H Isotropic =3D 26.2132 Anisotropy =3D 13.5495 > XX=3D 33.4604 YX=3D 2.6961 ZX=3D 4.6178 > XY=3D -0.6098 YY=3D 26.5118 ZY=3D 2.2945 > XZ=3D 4.8633 YZ=3D 3.5607 ZZ=3D 18.6673 > Eigenvalues: 16.6260 26.7674 35.2462 > ... > > I'm looking to > - extract the value for =22Isotropic=22 (probably just for C and H) > - scale by a number depending on the atom type > - produce these numbers in a list, or show on the structure next to the= > relevant atom > > > Thanks, > =09Mike >> -----Original Message----- >> From: Miguel =5Bmailto:miguel=40jmol.org=5D >> Sent: 31 March 2004 10:33 >> To: jmol-users=40lists.sourceforge.net >> Subject: Re: =5BJmol-users=5D Add NMR parameters to =22measurements=22= >> >> >> > =09I'm running NMR chemical shift calculations in >> gaussian98. I can >> > fish the isotropic chemical shifts from the output file and do the >> > necessary >> > scaling. >> > >> > =09Can you say whether it'd be a big effort to get these >> numbers read >> > from within Jmol, and shown on the structure as >> measurements next to the >> > appropriate atom, or possibly in a list (including atom numbers)? >> >> Mike, >> >> I *suspect* that added them will be easy. >> >> I am not a chemist and am not familiar with these parameters. >> >> You need to give me a little more background information ... >> 50 words or >> less. >> >> Are they general parameters that describe the entire model? >> >> Or are they specific to a single atom? >> >> Or are they specific to a single bond? >> >> Or something else? >> >> >> Miguel >> >> >> >> ------------------------------------------------------- >> This SF.Net email is sponsored by: IBM Linux Tutorials >> Free Linux tutorial presented by Daniel Robbins, President and CEO of >> GenToo technologies. Learn everything from fundamentals to system >> administration.http://ads.osdn.com/?ad_id=3D1470&alloc_id=3D3638&op=3D= click >> _______________________________________________ >> Jmol-users mailing list >> Jmol-users=40lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> > -------------------------------------------------- Miguel Howard miguel=40howards.org c/Pe=F1a Primera 11-13 esc dcha 6B 37002 Salamanca Espa=F1a Spain -------------------------------------------------- telefono casa 923 27 10 82 movil 650 52 54 58 -------------------------------------------------- To call from the US dial 9:00 am Pacific US =3D home 011 34 923 27 10 82 12:00 noon Eastern US =3D cell 011 34 650 52 54 58 6:00 pm Spain -------------------------------------------------- ```

 RE: [Jmol-users] Add NMR parameters to "measurements" From: - 2004-03-31 09:48:26 Attachments: application/ms-tnef ```Hi Miguel, OK, so the output file has some lines that look a bit like this - one for each atom: ... Calculating GIAO nuclear magnetic shielding tensors. SCF GIAO Magnetic shielding tensor (ppm): 1 C Isotropic = 126.6540 Anisotropy = 21.4588 XX= 119.2320 YX= 2.2126 ZX= -0.5824 XY= 1.7272 YY= 138.4056 ZY= 6.3864 XZ= -1.5981 YZ= 7.0991 ZZ= 122.3243 Eigenvalues: 117.7671 121.2349 140.9598 2 C Isotropic = 25.5825 Anisotropy = 100.8347 XX= 3.0461 YX= 33.1351 ZX= -63.5814 XY= 39.6564 YY= 27.3781 ZY= 16.4905 XZ= -61.6212 YZ= 10.3607 ZZ= 46.3234 Eigenvalues: -58.0816 42.0235 92.8057 ... 17 H Isotropic = 26.2132 Anisotropy = 13.5495 XX= 33.4604 YX= 2.6961 ZX= 4.6178 XY= -0.6098 YY= 26.5118 ZY= 2.2945 XZ= 4.8633 YZ= 3.5607 ZZ= 18.6673 Eigenvalues: 16.6260 26.7674 35.2462 ... I'm looking to - extract the value for "Isotropic" (probably just for C and H) - scale by a number depending on the atom type - produce these numbers in a list, or show on the structure next to the relevant atom Thanks, Mike > -----Original Message----- > From: Miguel [mailto:miguel@...] > Sent: 31 March 2004 10:33 > To: jmol-users@... > Subject: Re: [Jmol-users] Add NMR parameters to "measurements" > > > > I'm running NMR chemical shift calculations in > gaussian98. I can > > fish the isotropic chemical shifts from the output file and do the > > necessary > > scaling. > > > > Can you say whether it'd be a big effort to get these > numbers read > > from within Jmol, and shown on the structure as > measurements next to the > > appropriate atom, or possibly in a list (including atom numbers)? > > Mike, > > I *suspect* that added them will be easy. > > I am not a chemist and am not familiar with these parameters. > > You need to give me a little more background information ... > 50 words or > less. > > Are they general parameters that describe the entire model? > > Or are they specific to a single atom? > > Or are they specific to a single bond? > > Or something else? > > > Miguel > > > > ------------------------------------------------------- > This SF.Net email is sponsored by: IBM Linux Tutorials > Free Linux tutorial presented by Daniel Robbins, President and CEO of > GenToo technologies. Learn everything from fundamentals to system > administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > https://lists.sourceforge.net/lists/listinfo/jmol-users > ```
 RE: [Jmol-users] Add NMR parameters to "measurements" From: - 2004-03-31 11:37:39 Attachments: application/ms-tnef ```Sorry, Miguel. Considering Christoph's response, should we end this discussion? It seems he's identified the issue and gone a long way to solving it... Many thanks,=09 Mike > -----Original Message----- > From: Miguel [mailto:miguel@...] > Sent: 31 March 2004 11:12 > To: jmol-users@... > Subject: RE: [Jmol-users] Add NMR parameters to "measurements" >=20 >=20 > Too many words ... I don't understand :-) >=20 > Are these properties specifically per atom? > Or general to the entire model? >=20 >=20 > Miguel >=20 > > Hi Miguel, > > > > OK, so the output file has some lines that look a bit=20 > like this - > > one for each atom: > > ... > > Calculating GIAO nuclear magnetic shielding tensors. > > SCF GIAO Magnetic shielding tensor (ppm): > > 1 C Isotropic =3D 126.6540 Anisotropy =3D 21.4588 > > XX=3D 119.2320 YX=3D 2.2126 ZX=3D -0.5824 > > XY=3D 1.7272 YY=3D 138.4056 ZY=3D 6.3864 > > XZ=3D -1.5981 YZ=3D 7.0991 ZZ=3D 122.3243 > > Eigenvalues: 117.7671 121.2349 140.9598 > > 2 C Isotropic =3D 25.5825 Anisotropy =3D 100.8347 > > XX=3D 3.0461 YX=3D 33.1351 ZX=3D -63.5814 > > XY=3D 39.6564 YY=3D 27.3781 ZY=3D 16.4905 > > XZ=3D -61.6212 YZ=3D 10.3607 ZZ=3D 46.3234 > > Eigenvalues: -58.0816 42.0235 92.8057 > > ... > > 17 H Isotropic =3D 26.2132 Anisotropy =3D 13.5495 > > XX=3D 33.4604 YX=3D 2.6961 ZX=3D 4.6178 > > XY=3D -0.6098 YY=3D 26.5118 ZY=3D 2.2945 > > XZ=3D 4.8633 YZ=3D 3.5607 ZZ=3D 18.6673 > > Eigenvalues: 16.6260 26.7674 35.2462 > > ... > > > > I'm looking to > > - extract the value for "Isotropic" (probably just for C and H) > > - scale by a number depending on the atom type > > - produce these numbers in a list, or show on the structure=20 > next to the > > relevant atom > > > > > > Thanks, > > Mike > >> -----Original Message----- > >> From: Miguel [mailto:miguel@...] > >> Sent: 31 March 2004 10:33 > >> To: jmol-users@... > >> Subject: Re: [Jmol-users] Add NMR parameters to "measurements" > >> > >> > >> > I'm running NMR chemical shift calculations in > >> gaussian98. I can > >> > fish the isotropic chemical shifts from the output file=20 > and do the > >> > necessary > >> > scaling. > >> > > >> > Can you say whether it'd be a big effort to get these > >> numbers read > >> > from within Jmol, and shown on the structure as > >> measurements next to the > >> > appropriate atom, or possibly in a list (including atom = numbers)? > >> > >> Mike, > >> > >> I *suspect* that added them will be easy. > >> > >> I am not a chemist and am not familiar with these parameters. > >> > >> You need to give me a little more background information ... > >> 50 words or > >> less. > >> > >> Are they general parameters that describe the entire model? > >> > >> Or are they specific to a single atom? > >> > >> Or are they specific to a single bond? > >> > >> Or something else? > >> > >> > >> Miguel > >> > >> > >> > >> ------------------------------------------------------- > >> This SF.Net email is sponsored by: IBM Linux Tutorials > >> Free Linux tutorial presented by Daniel Robbins, President=20 > and CEO of > >> GenToo technologies. Learn everything from fundamentals to system > >>=20 > = administration.http://ads.osdn.com/?ad_id=3D1470&alloc_id=3D3638&op=3Dcl= ick > >> _______________________________________________ > >> Jmol-users mailing list > >> Jmol-users@... > >> https://lists.sourceforge.net/lists/listinfo/jmol-users > >> > > >=20 >=20 > -------------------------------------------------- > Miguel Howard miguel@... > c/Pe=F1a Primera 11-13 esc dcha 6B > 37002 Salamanca > Espa=F1a Spain > -------------------------------------------------- > telefono casa 923 27 10 82 movil 650 52 54 58 > -------------------------------------------------- > To call from the US dial 9:00 am Pacific US =3D > home 011 34 923 27 10 82 12:00 noon Eastern US =3D > cell 011 34 650 52 54 58 6:00 pm Spain > -------------------------------------------------- >=20 >=20 > ------------------------------------------------------- > This SF.Net email is sponsored by: IBM Linux Tutorials > Free Linux tutorial presented by Daniel Robbins, President and CEO of > GenToo technologies. Learn everything from fundamentals to system > administration.http://ads.osdn.com/?ad_id=1470&alloc_id638&op=3Dclick > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > https://lists.sourceforge.net/lists/listinfo/jmol-users >=20 ```
 RE: [Jmol-users] Add NMR parameters to "measurements" From: Miguel - 2004-03-31 14:07:30 ```Mike wrote: > Sorry, Miguel. Considering Christoph's response, should we end this > discussion? It seems he's identified the issue and gone a long way to > solving it... Fine. I'll coordinate with Christoph. Miguel ```
 Re: [Jmol-users] Add NMR parameters to "measurements" From: Christoph Steinbeck - 2004-03-31 14:46:56 ```> BTW, the web site advertises users of Jmol. You may know that > Bruker bundles this in their new NMR software, TopSpin > (http://www.bruker-biospin.de/NMR/nmrsoftw/prodinfo/topspin/index.html). No, I did not know this. This is quite interesting since I had quite=20 some contacts with the Bruker NMR people in the last 10 years. They=20 never mentioned anything. Anyway, in this context I would like to remark that I had problems=20 finding any mentioning of the Jmol copyright license on the Jmol website. After 10 clicks or so I gave up. I then started up Jmol and went to the Help menu. Again nothing. Maybe this should be placed more prominently. Now, is it GPL or LGPL? Cheers, Chris --=20 Dr. rer. nat. habil. Christoph Steinbeck (c.steinbeck@...) Groupleader Junior Research Group for Applied Bioinformatics Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de) Z=FClpicher Str. 47, 50674 Cologne Tel: +49(0)221-470-7426 Fax: +49 (0) 221-470-7786 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. ```
 Re: [Jmol-users] Add NMR parameters to "measurements" From: E.L. Willighagen - 2004-03-31 15:05:58 ```=2D----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On Wednesday 31 March 2004 16:46, Christoph Steinbeck wrote: > > BTW, the web site advertises users of Jmol. You may know that > > Bruker bundles this in their new NMR software, TopSpin > > (http://www.bruker-biospin.de/NMR/nmrsoftw/prodinfo/topspin/index.html). > > No, I did not know this. This is quite interesting since I had quite > some contacts with the Bruker NMR people in the last 10 years. They > never mentioned anything. > > Anyway, in this context I would like to remark that I had problems > finding any mentioning of the Jmol copyright license on the Jmol > website. After 10 clicks or so I gave up. > I then started up Jmol and went to the Help menu. Again nothing. > Maybe this should be placed more prominently. > > Now, is it GPL or LGPL? LGPL. If only it was GPL :))) Cool nevertheless. Egon =2D --=20 egonw@... PhD on Molecular Representation in Chemometrics Nijmegen University http://www.cac.sci.kun.nl/people/egonw/ GPG: 1024D/D6336BA6 =2D----BEGIN PGP SIGNATURE----- Version: GnuPG v1.0.7 (SunOS) iD8DBQFAat43d9R8I9Yza6YRAu67AJ9vg37X+zNXBri5tsXm2Y7U2+3I6ACgyvzm w7uMeqcMy6WJtVaf34famWA=3D =3DXOjW =2D----END PGP SIGNATURE----- ```
 RE: [Jmol-users] Add NMR parameters to "measurements" From: Miguel - 2004-03-31 10:05:18 ```Too many words ... I don't understand :-) Are these properties specifically per atom? Or general to the entire model? Miguel > Hi Miguel, > > =09OK, so the output file has some lines that look a bit like this - > one for each atom: > ... > Calculating GIAO nuclear magnetic shielding tensors. > SCF GIAO Magnetic shielding tensor (ppm): > 1 C Isotropic =3D 126.6540 Anisotropy =3D 21.4588 > XX=3D 119.2320 YX=3D 2.2126 ZX=3D -0.5824 > XY=3D 1.7272 YY=3D 138.4056 ZY=3D 6.3864 > XZ=3D -1.5981 YZ=3D 7.0991 ZZ=3D 122.3243 > Eigenvalues: 117.7671 121.2349 140.9598 > 2 C Isotropic =3D 25.5825 Anisotropy =3D 100.8347 > XX=3D 3.0461 YX=3D 33.1351 ZX=3D -63.5814 > XY=3D 39.6564 YY=3D 27.3781 ZY=3D 16.4905 > XZ=3D -61.6212 YZ=3D 10.3607 ZZ=3D 46.3234 > Eigenvalues: -58.0816 42.0235 92.8057 > ... > 17 H Isotropic =3D 26.2132 Anisotropy =3D 13.5495 > XX=3D 33.4604 YX=3D 2.6961 ZX=3D 4.6178 > XY=3D -0.6098 YY=3D 26.5118 ZY=3D 2.2945 > XZ=3D 4.8633 YZ=3D 3.5607 ZZ=3D 18.6673 > Eigenvalues: 16.6260 26.7674 35.2462 > ... > > I'm looking to > - extract the value for =22Isotropic=22 (probably just for C and H) > - scale by a number depending on the atom type > - produce these numbers in a list, or show on the structure next to the= > relevant atom > > > Thanks, > =09Mike >> -----Original Message----- >> From: Miguel =5Bmailto:miguel=40jmol.org=5D >> Sent: 31 March 2004 10:33 >> To: jmol-users=40lists.sourceforge.net >> Subject: Re: =5BJmol-users=5D Add NMR parameters to =22measurements=22= >> >> >> > =09I'm running NMR chemical shift calculations in >> gaussian98. I can >> > fish the isotropic chemical shifts from the output file and do the >> > necessary >> > scaling. >> > >> > =09Can you say whether it'd be a big effort to get these >> numbers read >> > from within Jmol, and shown on the structure as >> measurements next to the >> > appropriate atom, or possibly in a list (including atom numbers)? >> >> Mike, >> >> I *suspect* that added them will be easy. >> >> I am not a chemist and am not familiar with these parameters. >> >> You need to give me a little more background information ... >> 50 words or >> less. >> >> Are they general parameters that describe the entire model? >> >> Or are they specific to a single atom? >> >> Or are they specific to a single bond? >> >> Or something else? >> >> >> Miguel >> >> >> >> ------------------------------------------------------- >> This SF.Net email is sponsored by: IBM Linux Tutorials >> Free Linux tutorial presented by Daniel Robbins, President and CEO of >> GenToo technologies. Learn everything from fundamentals to system >> administration.http://ads.osdn.com/?ad_id=3D1470&alloc_id=3D3638&op=3D= click >> _______________________________________________ >> Jmol-users mailing list >> Jmol-users=40lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> > -------------------------------------------------- Miguel Howard miguel=40howards.org c/Pe=F1a Primera 11-13 esc dcha 6B 37002 Salamanca Espa=F1a Spain -------------------------------------------------- telefono casa 923 27 10 82 movil 650 52 54 58 -------------------------------------------------- To call from the US dial 9:00 am Pacific US =3D home 011 34 923 27 10 82 12:00 noon Eastern US =3D cell 011 34 650 52 54 58 6:00 pm Spain -------------------------------------------------- ```