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@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@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