User talk:Bensaccount

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[edit] gpcr figure

Hi - I liked your GPCR figures, especially the mechanism one. Could you provide a little detail on how you constructed these? Thanks --smd 23:52, 21 February 2007 (UTC)

Thanks, I used DeepView and POV-Ray. Do you want an in depth tutorial? Bensaccount 02:29, 22 February 2007 (UTC)

If you have time, I would really appreciate it. I'm sure others would appreciate it as well. --smd 03:19, 23 February 2007 (UTC)

[edit] Molecular model tutorial

Heres a tutorial on how I make molecular models. If you copy it please give me some credit; it took some work to get it to look right, and I don't get any money for it. Enjoy:

1. Open the PDBs in DeepView and arrange.
2. Export as POV scene.
3. Copy and paste the following code:

//This code sets the camera:

camera { 
location < 0, 0, 20 >
look_at < 0, 0, 0 >
}

#declare cam_pos = <0, 0, 20>;


//This codes for the outline:
#declare dist = 1.03; 
#declare thick1 = 0.05; 
#declare linetex  = texture {pigment {rgb 0} finish {ambient 1}}

#declare trans = transform {rotate 90*clock*y}


#macro scalepoint(center,amt) 
        transform {trans}
        translate -center scale amt translate center
#end


#macro atom(center,rad,thick)
        union {
                sphere {center,rad transform {trans}}
                sphere {center,(rad+thick1) texture {linetex} scalepoint(cam_pos,dist)}  
                }
#end 


//The following does the color and shading:
#declare ATM_FINISH = finish {ambient rgb <1,1,1> }


#declare textgrey = texture {pigment {slope {vnormalize(<1000,1000,1000>)}
   color_map{[0.625 color rgb <.45,.45,.45>][0.626 color rgb <.5,.5,.5>]}}
   finish {ATM_FINISH}
   }

background { color rgb < 10,10,10 > }



//The fog gives the sense of distance that is lacking from most other molecular models:
fog {
  fog_type   2
  distance   4
  color      rgbt <0,0,0,.1>
  fog_offset 1
  fog_alt    .0001
  up <0,0,1>
}


//Here is where you put the objects:
object {atom(<0,0,0> .4, thick1)
texture {textgrey}
}

4. Search and replace

sphere {

with

object{atom(

5. Search and replace

_ }

with

_ , thick1)}

6. Search and replace

pigment{ colour red 0.75 green 0.75 blue 0.75} finish{ ATM_FINISH }

with

textgrey

Awesome, thanks again. I'd pretty much worked out a similar strategy, but yours is a little more succinct. --smd 05:33, 10 March 2007 (UTC)

BTW, Jmol can be modified to export pre-coded POV-Ray files like this. Bensaccount 20:27, 31 March 2007 (UTC)