[Chimera-users] Preference/default for H-bond representation

Markus Heller mheller at cdrd.ca
Mon Jan 16 10:21:45 PST 2017


Fantastic, Eric!

Thanks

From: Eric Pettersen [mailto:pett at cgl.ucsf.edu]
Sent: Friday, January 13, 2017 5:39 PM
To: Markus Heller
Cc: chimera-users at cgl.ucsf.edu BB
Subject: Re: [Chimera-users] Preference/default for H-bond representation

Hi Markus,
          I’ll make sure to include it in the ChimeraX implementation when I get there.  To get ChimeraX where it needs to go I can’t put too much work into the current Chimera but nonetheless I added a “lineType” option to the hbonds/findhbonds command so that at least in the command version you can get dashed H-bonds without code modifications.  The valid options for the lineType are:  solid, dashed, dotted, dash-dot, and dash-dot-dot.  The option will be available in the next daily build.

—Eric

          Eric Pettersen
          UCSF Computer Graphics Lab


On Jan 12, 2017, at 1:55 PM, Markus Heller <mheller at cdrd.ca<mailto:mheller at cdrd.ca>> wrote:

Great Eric, thanks.  Works as advertised.

Any chance of making this more straightforward in ChimeraX or future Chimera releases?


From: Eric Pettersen [mailto:pett at cgl.ucsf.edu]
Sent: Thursday, January 12, 2017 12:47 PM
To: chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu> BB
Cc: Markus Heller
Subject: Re: [Chimera-users] Preference/default for H-bond representation

On Jan 12, 2017, at 12:28 PM, Elaine Meng <meng at cgl.ucsf.edu<mailto:meng at cgl.ucsf.edu>> wrote:

There must be some place in the code to change it to always dashed, but somebody else would have to advise on that…

To have all hydrogen bonds start out dashed, after line 991 of <your Chimera>/share/FindHBond/base.py (which should be “pbg.lineWidth = lineWidth”) add:

          pbg.lineType = chimera.Dash

with the same indentation as the preceding line.  On a Mac, “<your Chimera>” will be Chimera.app/Contents/Resources.

—Eric

          Eric Pettersen
          UCSF Computer Graphics Lab

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