[chimerax-users] [Chimera-users] [External] Re: Clip surface but not atoms

[Elaine Meng]

Sorry, one more tip:  just realized that the MLP map (volume model) is shown as isosurfaces, and if you make the cap transparent you can see the blobs from the map!  So you would need also to hide the map (hide #2) to make it look decent. 

At least for me, hiding the map has the annoying side effect of resetting the cap color, so best to "hide #2" before coloring the cap (#1.1.1).  E.g. something like

mlp map true; wait 1
hide #2
color sample #1.1.1 map #2 palette lipophilicity range -20,20; wait 1
transparency #1.1.1 50

The wait commands are useful if this is in a command file rather than entered one by one, to make sure the previous command is done before going to the next.

Elaine

> On Jul 27, 2020, at 1:18 PM, Pufall, Miles A <miles-pufall at uiowa.edu> wrote:
> 
> That is very nice - particularly is you can make the cap translucent (so you can see what the ligand might be interacting with.
> M
> 
>> On Jul 27, 2020, at 3:15 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> 
>> Another thing users might not know is that one can also color the planar surface cap by the MLP, e.g. by saving the lipophilicity map and then using a separate command to recolor the surface including the cap. E.g. adding the following commands to my previous example:
>> 
>> mlp map true
>> color sample #1.1 map #2 palette lipophilicity range -20,20
>> 
>> This is not to say it would make a better figure... just giving options.  :-)
>> 
> 
>> 
>>> On Jul 27, 2020, at 12:16 PM, Pufall, Miles A <miles-pufall at uiowa.edu> wrote:
>>> 
>>> Thanks Elaine!  I’ll save the full string of commands you sent.
>>> 
>>> Tom’s guidance helped a lot - the figure came out just how I wanted it.
>>> 
>>> <699C644F-6A5E-47A1-9559-30329A1B5105.png>
>>> 
>>> Thanks again - 
>>> 
>>> M
>>> 
>>> 
>>>> On Jul 27, 2020, at 2:14 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>>>> 
>>>> Hi Miles,
>>>> In case it's useful, here's a little example that works in the current daily build.  This protein has oleic acid (residue name OLA) in a buried pocket.  The example turns off clipping for the parent model #1 (the atomic model, which includes any ribbon and atom/bond displays) but leaves it on for the molecular surface model #1.1.
>>>> 
>>>> open 1g74
>>>> surface
>>>> clip front 0 position :ola
>>>> clip model #!1 false
>>>> hide ~:ola target ar
>>>> style :ola ball
>>>> 
>>>> Probably you'd want to use the Right Mouse modes to translate and rotate the clipping plane interactively since it's hard to get the position you want with commands only.
>>>> 
>>>> Elaine
>>>> 
>>>> 
>>>>> On Jul 25, 2020, at 7:12 AM, Pufall, Miles A <miles-pufall at uiowa.edu> wrote:
>>>>> 
>>>>> Cool - thanks!  Downloading now - will let you know if all is well.
>>>>> 
>>>>> Miles
>>>>> 
>>>>> 
>>>>>> On Jul 24, 2020, at 10:32 PM, Tom Goddard <goddard at sonic.net> wrote:
>>>>>> 
>>>>>> Hi Miles,
>>>>>> 
>>>>>> I added the ability to turn off clipping for specific models, in tonight's ChimeraX builds.  It only effects clip planes that rotate with the models, not the near / far camera clip planes:
>>>>>> 
>>>>>> clip model #!1 off
>>>>>> 
>>>>>> The molecular surface of atomic model #1 is a submodel #1.1.  So I use "#!1" in this command instead of #1 so the command acts on only model #1 and not its child models #1.1, 1.2,...  You also will want to turn of surface caps
>>>>>> 
>>>>>> surface cap false
>>>>>> 
>>>>>> so that the hole left in the clipped surface is not covered by a cap.
>>>>>> 
>>>>>> Tom
>>>>>> 
>>>>>> 
>>>>>>> On Jul 24, 2020, at 11:35 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>>>>>>> 
>>>>>>> Hi Miles!
>>>>>>> I remember meeting you at UCSF years ago.  I hope you are well.
>>>>>>> 
>>>>>>> This unfortunately is one of the features often needed for figures but that is not yet available in ChimeraX, the ability to clip one model (e.g. the surface) without clipping the other (e.g. the ligand atoms).
>>>>>>> 
>>>>>>> I've listed it in the Missing Features section of the ChimeraX download page as "per-model clipping." It is one of the things on the To-Do list and is a ticket in our database.  I will add your e-mail address to the notification list for that ticket.
>>>>>>> 
>>>>>>> For now, you would still need to use Chimera for per-model clipping.  Sorry about that,
>>>>>>> Elaine
>>>>>>> -----
>>>>>>> Elaine C. Meng, Ph.D.
>>>>>>> UCSF Chimera(X) team
>>>>>>> Department of Pharmaceutical Chemistry
>>>>>>> University of California, San Francisco
>>>>>>> 
>>>>>>>> On Jul 24, 2020, at 10:32 AM, Pufall, Miles A <miles-pufall at uiowa.edu> wrote:
>>>>>>>> 
>>>>>>>> Hi!
>>>>>>>> I’ve used Chimera for years (though not recently) and am switching to ChimeraX.  I’m looking to display the ligand binding pocket with the ligand, and the tutorial you have is great.  I generated this picture, which is really close to what I want.  It shows the ligand, and the pocket, and I’m able to slice it with the interactive side view tool to get to this point.  However, the left side of the ligand is slightly clipped. I’ve played with rotation and with moving the slice plane, but can’t find an orientation that shows the pocket so nicely (without any surface in the foreground) and not ligand clipping.  My question is: is there a way to tell ChimeraX to clip the surface but not the ligand?
>>>>>>>> Thanks!
>>>>>>>> Miles
>>>>>>>> 
>>>>>>>> <DAC_binding_pocket.png>
>>>>>>>> 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimerax-users/attachments/20200727/69e429d9/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: mlpclip.png
Type: image/png
Size: 262365 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimerax-users/attachments/20200727/69e429d9/attachment-0001.png>