Preference/default for H-bond representation - Chimera-users - RBVI Mailing Lists

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Preference/default for H-bond representation

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Markus Heller

10 Jan 2017 10 Jan '17

2:08 p.m.

Hello, Is there a way to set the preference for H-bonds to be represented as dashed lines, not as solid lines? I don't seem to be able to find anything in the Preferences or the documentation. Thanks and Cheers Markus

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Elaine Meng

12 Jan 12 Jan

12:28 p.m.

Hi Markus, Although there is something like that for distance monitors (Save button in the Distances tool), unfortunately there isn’t for H-bond pseudobonds, nor is there an option in the findhbond command or dialog to make them dashed in the first place. That leaves changing them after the fact, e.g. the following command would make all pseudobonds dashed: setattr g lineType 2 You can also specify subsets but only by endpoint atoms, not by the pseudobond group name. GUI ways to make them dashed: (A) Pseudobond Panel (under Tools… General Controls), choose “hydrogen bonds” and click “attributes…” on the right, and in the attributes dialog change “line style” - OR - (B) select any H-bond pseudobond, click green magnifying glass icon to open Selection Inspector, Inspect: pseudobond group, change “line style” How I know to use”setattr” command “g” (pseudobond group” and the attribute name “lineType” and its possible values are by seeing in either of the above dialogs that it is a pseudobond group attribute, and then mousing over “line type” in the dialog to show balloon help with the attribute name and possible values. There must be some place in the code to change it to always dashed, but somebody else would have to advise on that... Sorry for the inconvenience, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

On Jan 10, 2017, at 2:08 PM, Markus Heller wrote:

Hello, Is there a way to set the preference for H-bonds to be represented as dashed lines, not as solid lines? I don't seem to be able to find anything in the Preferences or the documentation. Thanks and Cheers Markus

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Eric Pettersen

12:46 p.m.

On Jan 12, 2017, at 12:28 PM, Elaine Meng 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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Markus Heller

1:55 p.m.

Great Eric, thanks. Works as advertised. Any chance of making this more straightforward in ChimeraX or future Chimera releases? From: Eric Pettersen [mailto:pett@cgl.ucsf.edu] Sent: Thursday, January 12, 2017 12:47 PM To: chimera-users@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 mailto:meng@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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Eric Pettersen

13 Jan 13 Jan

5:38 p.m.

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 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@cgl.ucsf.edu] Sent: Thursday, January 12, 2017 12:47 PM To: chimera-users@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 mailto:meng@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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Markus Heller

16 Jan 16 Jan

10:21 a.m.

Fantastic, Eric! Thanks From: Eric Pettersen [mailto:pett@cgl.ucsf.edu] Sent: Friday, January 13, 2017 5:39 PM To: Markus Heller Cc: chimera-users@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 mailto:mheller@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@cgl.ucsf.edu] Sent: Thursday, January 12, 2017 12:47 PM To: chimera-users@cgl.ucsf.edumailto:chimera-users@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 mailto:meng@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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Elaine Meng
Eric Pettersen
Markus Heller