[Chimera-users] Adding color key to hydrophobicity surface (preset 3)

[Boaz Shaanan]

Yes Elaine, but I usually explain these things in the figure legend. It worked for me so far. I may well use your suggestion though in the future.
Thanks again,
Boaz



Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel

E-mail: bshaanan at bgu.ac.il
Phone: 972-8-647-2220
Fax:   972-8-647-2992 or 972-8-646-1710





________________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Wednesday, April 3, 2019 8:14 PM
To: בעז שאנן
Cc: UCSF Chimera Mailing List
Subject: Re: [Chimera-users] Adding color key to hydrophobicity surface (preset 3)

Another problem is that the color key does not say what attribute is being shown!  That would require adding a 2D Label next to it saying “residue hydrophobicity” or something like that.  Further, it might be better to have “min” and “max” as the key labels instead of the numerical values, and for the border to switch between white or black as appropriate for the current background color…  so we’d punted all these judgment calls to the user.

Elaine

> On Apr 3, 2019, at 9:42 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>
> Hi Boaz,
> The problem is that there is no option to automatically place the color key.  The user has to interactively click and drag to create/size it, and then
> click and drag to move it around, and then deactivate the color key mouse mode so that using the mouse does the normal stuff (rotation, translation, zooming).  E.g. try command:
>
> surface; rangecolor kdHydrophobicity,s key min dodger blue 0 white max orange red
>
> … then place the color key as described above. You could make that an alias and use it instead of preset 3.
>
> Most users would not appreciate (or even understand what was happening or know to turn it off) if all they could do with the mouse was continually draw and redraw the color key instead of rotating the molecule.  Unfortunately we’ve seen based on publication figures that lots of people use this preset simply to show the molecular surface (instead of Actions… Surface… show, or the “surface” command) and have no idea where the coloring comes from.
>
> Perhaps if this preset brought up the Color Key tool with the corresponding settings filled in, but without the mouse mode turned on, that would help. Then, you could turn on the mouse mode, do the interactive stuff, and then turn the mouse mode off.  Still, it might be annoying to lots of people if this dialog appeared every time preset 3 was used.
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>> On Apr 3, 2019, at 6:21 AM, Boaz Shaanan <bshaanan at bgu.ac.il> wrote:
>>
>> Hi,
>> I find preset 3  as a very convenient tool but is it possible to add a color key to the hydrophobicity surface produced in this preset (as in the options for coloring electrostatic surface) ?
>> Thanks,
>>       Boaz
>>