Few bugs on Mac OS X - El Capitan

[zuccomac]

Please describe the problem or enhancement:

Reading an GAMESS v 2013 and 2014 optimization/frequency output the bonds are generally invisible. Only few are drawn and it appears sometimes the window with warning below. I think because rungms wrote a long line with all the nodes of our cluster. But it is new.

### If this is a bug report please list the steps required to reproduce the problem:

Opening a file.

What version are you running?

Version 7.7

What OS are you using? (please include 32/64 bit and if Linux the specific distribution)

Mac OS X El Capitan

[brettbode]

Hmm... There is something unusual about the file you are reading in. Can you attach it here or send it to me via email ([email protected])?

[brettbode]

Ok I do see the warning. You are correct it is from the kickoff line. I will try to work around that so warnings aren't produced by output outside of the main program.

I think the issue with bond display has to do with the preferences for the bond tolerance. MacMolPlt is simply using the interatomic distance to "guess" at bonds. I would suggest going to the "Global Preferences" and the "File" pane. Hit the "Factory Defaults" button and then "Ok" and try to open the file again. That seems to work ok for me. You can also reapply the auto-bonding for an open window using the "Set Bonds..." item under the "Molecule" menu. In that dialog you can among other choices adjust the tolerance (left for tighter tolerance, fewer bonds, right for longer distances to be considered a bond).

[zuccomac]

Brett,

On 27 Oct 2016, at 16:47, Brett Bode [email protected] wrote:

Ok I do see the warning. You are correct it is from the kickoff line. I will try to work around that so warnings aren't produced by output outside of the main program.

Ok
I think the issue with bond display has to do with the preferences for the bond tolerance. MacMolPlt is simply using the interatomic distance to "guess" at bonds. I would suggest going to the "Global Preferences" and the "File" pane. Hit the "Factory Defaults" button and then "Ok" and try to open the file again. That seems to work ok for me. You can also reapply the auto-bonding for an open window using the "Set Bonds..." item under the "Molecule" menu. In that dialog you can among other choices adjust the tolerance (left for tighter tolerance, fewer bonds, right for longer distances to be considered a bond).

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Well, just before my email, I tried to enlarge the bond tolerances but it hasn’t had any result. In your opinion could be related to new El Capitan OS? Before upgrading your package was a pack-horse of my visualisations…
Anyway I try again.
m.

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Marino Vetuschi Zuccolini
[email protected]
[email protected]
Professor / Geochemist
Laboratory of Geochemistry [LGCH]

DISTAV - Università di Genova
Tel. ++39 010 3538308 Fax. ++39 010 352169
Corso Europa 26, 16132 - Genova - Italy

[brettbode]

I would not expect it to have anything to do with the OS upgrade. The only thing that might possibly impact it is if the user preferences file was somehow corrupted. You could try trashing or just moving the prefs file (~/Library/Preferences/MacMolPlt.Prefs.xml) out of the way and see if that helps.

I would try adjusting that slider to the right more. It is somewhat sensitive to get it just right.

[zuccomac]

Brett,

On 27 Oct 2016, at 23:02, Brett Bode [email protected] wrote:

I would not expect it to have anything to do with the OS upgrade. The only thing that might possibly impact it is if the user preferences file was somehow corrupted. You could try trashing or just moving the prefs file (~/Library/Preferences/MacMolPlt.Prefs.xml) out of the way and see if that helps.

You are absolutely right!! Doing so all is up and running.
I would try adjusting that slider to the right more. It is somewhat sensitive to get it just right.

Thank you

m.

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Marino Vetuschi Zuccolini
[email protected]
[email protected]
Professor / Geochemist
Laboratory of Geochemistry [LGCH]

DISTAV - Università di Genova
Tel. ++39 010 3538308 Fax. ++39 010 352169
Corso Europa 26, 16132 - Genova - Italy

[brettbode]

Great! I will leave this open until I fix the unnecessary warning message.

[brettbode]

I have checked in code that disables the warning during the initial parsing phase to avoid the kickoff line triggering the message. This will be included in the next release.