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August 17, 2019

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tim hockswender
Unregistered guest
Posted on Wednesday, January 18, 2017 - 3:43 pm:   

How can I best utilize the NMR view capability of WebMO? I load my GAMESS log file but don't see the correct NMR spectrum.
Any advice appreciated, even id WebMO is not appropriate.
JR Schmidt
Moderator
Username: Schmidt

Post Number: 546
Registered: 11-2006
Posted on Wednesday, January 18, 2017 - 3:45 pm:   

If you send me your output file via email or post it, I will take a look. It is possible that GAMESS has made a few tweaks to the output format.
timhockswender
Unregistered guest
Posted on Friday, January 20, 2017 - 9:14 am:   

Great- I will attach results.
application/octet-streamNMR Run Output
3-bromo-1-propene.log (62.2 k)


I can see a 13C spectrum but not H.
JR Schmidt
Moderator
Username: Schmidt

Post Number: 547
Registered: 11-2006
Posted on Friday, January 20, 2017 - 10:04 am:   

Tim,

The spectrum is parsed and displayed correctly -- with a caveat. NMR calculations calculate the ABSOLUTE NMR chemical shift, NOT the shift relative to TMS. In some cases (combinations of method/basis set), WebMO knows the TMS shift and can display the shift relative to TMS.

In general, though, you need to calculate the TMS H shift yourself and enter that to get the "normal" shift relative to TMS.

The reason you are not seeing anything is that the absolute chemical shifts for H are off the default scale. If you expand the range, you will see the peaks.

The solution is to do a NMR calculation for TMS!
timhockswender
Unregistered guest
Posted on Saturday, January 21, 2017 - 11:12 am:   

Thanks, If I enter the TMS shift (32.596) and click on 'shift spectrum' the display no longer shows any NMR info nor the 'data box' where I entered the shift factor. Also, the top View when I click on Data Viewer is empty/blank with the top right showing not a number for the title/ledgend:-(NaN Nan). ?
JR Schmidt
Moderator
Username: Schmidt

Post Number: 548
Registered: 11-2006
Posted on Monday, January 23, 2017 - 12:25 pm:   

Odd. I cannot reproduce this. I enter a shift and the NMR data in the table updates appropriately. The resulting NMR spectrum appears fine. What version of WebMO are you using?
timhockswender
Unregistered guest
Posted on Monday, January 23, 2017 - 2:24 pm:   

I'm using 17.0. On Win10. Puzzling. What should be in the Data Viewer top plot?
I can send a screenshot of how the Absolute NMR Shifts item will not expand but don't see how this might help.
My thought is to re-install. Agree?
Timhockswender
Unregistered guest
Posted on Monday, January 23, 2017 - 7:33 pm:   

To check, I wanted to run upgrade.py but the script seems to insist that I need to backup first but I don't see the specifics as to how. I have nothing worth backing up so should I just delete the WebMO directory?
JR Schmidt
Moderator
Username: Schmidt

Post Number: 549
Registered: 11-2006
Posted on Tuesday, January 24, 2017 - 11:00 am:   

If you are not concerned with backups (see the FAQ for details), just say 'yes' to proceed.
timhockswender
Unregistered guest
Posted on Tuesday, January 24, 2017 - 2:21 pm:   

I reinstalled v17 and the errors persist.
After attempting to re-scale after entering the shift factor leads to no spectrum and no box to change anything.
JR Schmidt
Moderator
Username: Schmidt

Post Number: 550
Registered: 11-2006
Posted on Tuesday, January 24, 2017 - 2:22 pm:   

Entering the shift CHANGES the values displayed in the Table. You still need to click the "View" to see the spectrum.
timhockswender
Unregistered guest
Posted on Sunday, February 05, 2017 - 6:02 pm:   

I can enter the values but once I doo so, the box and all options go away so that the View icon and all else, are gone. The little triangle is there but clicking it does not cause the box to come up.
JR Schmidt
Moderator
Username: Schmidt

Post Number: 552
Registered: 11-2006
Posted on Sunday, February 05, 2017 - 9:20 pm:   

What browser / OS are you using?
Tim
Unregistered guest
Posted on Monday, February 06, 2017 - 1:44 pm:   

I am using Win10 and Edge.
Will Polik
Moderator
Username: Polik

Post Number: 33
Registered: 7-2000
Posted on Thursday, February 16, 2017 - 3:32 pm:   

Win 10 and Edge seem to work fine for us for displaying NMR spectra, or at least the same as all other OS/browser combinations.

Please do the following:
1) Enter a shift and click the "Shift NMR Spectrum" icon (writing).
2) Click the "View" icon (magnifying glass) to display the updated values.
3) On the dataviewer tab, click the "Reset Zoom" icon (magnifying glass in upper-left), which will expand the spectrum to display it in its entirety.

Make sure you do these three steps in the prescribed order!

Note, however, that WebMO 17.0.010 has a bug in the calculation of offset values. After applying the offset, the peak positions are negated. For example, if a peak is located at 27 and an offset of 20 is applied, then the peak is calculated (and displayed) to be at -7, instead of at 7.

We will fix the calculated value in the next update.

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