[Chimera-users] Showing/Hiding/Fading

[Gustaf Olsson]

Hi Elaine

I was trying to avoid splitting the model into several models though after trying a range of different combinations of commands, using the “split” command or the “surfcat” command does not allow me to easily “hide” and “re-display” the coulomb surface. I am assuming that either I manage to mangle the atom_selection or it gets mangled when I mock about with the split/join stuff however I am unable to perform the task I was aiming for. So, rather then spending several hours solving this, I just created two different models and loading them. I am trying to accomplish the desired effect right now.

I do want to have the surface transparent and not hidden at some point because I want to fade the created surface into frame while spinning the model. With one issue solved I will now see if I can get through the initial recordings without issues.

A big thank you for you answers and patience, feels like a personal support contact at this point!

Best regards
// Gustaf


> On 12 Jun 2018, at 19:31, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi Gustaf,
> Chimera uses some default rules as to what set of atoms is enclosed in the same surface, but you can specify different sets to enclose without using “split”.  E.g.
> 
> surfcat blob #0:17.het
> surface blob
> 
> … where “blob” is just the name you gave it. Surface categories and “surfcat” command explained here:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/surface.html#surfcats>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/msms.html>
> 
> Splitting and combining creates and removes models, which may result in atoms no longer “knowing” which surface they go with, which may be the problem. I wouldn’t use that approach simply to control the display.  I’d try using “surfcat” as mentioned above, or you could simply open your structure twice and delete everything except :17.het from one copy.  Then hide and show parts or all of model #0 or model #1 as needed.
> 
> I don’t really understand your script.  Seems like if you combine #0.1 and #0.2 and then close them, you would no longer have a model #0.1.  You can see what models you have by looking in the Model Panel (open from Favorites menu).  Also you can just hide/show the surface with
> 
> ~surface
> surface blob
> ~surface
> surface #0:17.het
> 
> … rather than trying to make it 100% transparent.  “~surface” does not delete the model, it just hides the surface of the specified set of atoms.
> 
> You can also hide/show the model as a whole, same as using the “S”hown checkbox in the Model Panel.  It is a little trickier to hide a molecular surface but not the atomic model since they have the same model number, but the fancy command to do it is something like:
> 
> ~modeldisp #0 & ~ @*
> 
> (undisplay model #0 that doesn’t have any atoms)
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
>> On Jun 12, 2018, at 1:07 AM, Gustaf Olsson <gustaf.olsson at lnu.se> wrote:
>> 
>> 
>> Hello Chimera users and developers, I’m back again.
>> 
>> So my movie rendering is progressing though I have of course run into more problems. I have one PDB file open, I need to create a surface around one molecule that is close to other molecules so running the surface command directly does not work as intended. I therefore have to split the PDB file and calculate a surface around a single molecule. All is well, however after this I run into some problems trying to clean up the script. I assume that I am defining the modelID incorrectly though I cannot figure out how.
>> 
>> The following works:
>> 
>>   split #0 atoms :17.het
>>   surface probeRadius 0.5 vertexDensity 20.0 :17.het
>>   coulombic -5 red 0 white 5 blue :17.het
>>   wait
>>   combine #0.1-2 modelId 0 close true
>>   surftransparency 100 #0.1
>> 
>> This splits the model putting one residue (17) in a separate model, I calculate the surface without issue, color it by coulombic charges. I then have to combine the models (the single residue (17) and the rest of the residues) and close the old “residue 17” model. I then need to hide the newly created surface to display it at a later point in the movie. The script above works, however this does not seem very neat.
>> 
>> I have experimented with different other commands, including transparency
>> 
>>   transp 100,s #0.1
>> 
>> Which also works well, as long as I split and combined the models. However, I have to combine the model for this to work!
>> 
>>   split #0 atoms :17.het
>>   surface probeRadius 0.5 vertexDensity 20.0 :17.het
>>   coulombic -5 red 0 white 5 blue :17.het
>>   wait
>>   combine #0.1-2 modelId 0 close true
>>   surftransparency 100 #0.1
>> 
>> Everything but hiding the surface works.
>> 
>>   transp 100,s #0.1
>> 
>> This does not work either in this case. I am assuming that I am not defining the model ID correctly for the surface and this is why I cannot hide it? I also tried using surfcat:
>> 
>>   surfcat templ :17.het
>>   surf probeRadius 0.5 vertexDensity 20.0 templ
>>   coulombic -5 red 0 white 5 blue templ
>>   wait
>>   surftransparency 100 templ 
>> 
>> or any of the following:
>> 
>>   surftransparency 100 #0
>>   surftransparency 100 :17.het
>>   surftransparency 100 #0:17.het
>>   transp 100,s #0
>> 
>> Hides the created surface, what am I doing wrong in defining the surface to hide it and show it again?
>> 
>> Thank you for any input and best regards
>> // Gustaf
>