Difference between revisions of "Useful chimera commands"

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(Created page with " ==Command line== You might like to make a small molecules (eg. HEM) part of the surface of the protein instead of separate: surfcat one #1:1-290 surf one probeRadius 1....")
 
 
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You might want to color by partial charge:
 
You might want to color by partial charge:
  
   rangecolor charge,a min blue 0 white max red sel
+
   rangecolor charge,a min red 0 white max blue sel
 +
  rangecolor charge,a -1.0 red 0.0 white 1.0 blue sel
  
 
This command will color the selected atoms by there charge.
 
This command will color the selected atoms by there charge.
 +
 +
 +
== Example Command-line script to save an image ==
 +
open ../poses_clust_int.mol2
 +
open ../rec.crg.pdb
 +
surface #1
 +
  color orange #1:.B
 +
  color byhet,a #1:.B
 +
  focus #0
 +
  transp 80,s #1
 +
  sop cap off
 +
  set bg_color white
 +
  unset depthCue
 +
  set silhouette
 +
set bg_color white
 +
unset depthCue
 +
set silhouette
 +
focus #0
 +
turn y 160
 +
  turn x 20
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~display
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display #0.1
 +
copy file ./C648_1.png png width 3840.0  height 1941.0 supersample 1
 +
# this copy command will save the image, give the full path where you want to save the image
 +
# you may want to ajust the width and height.
 +
copy file C:\Users\user\Desktop\name\system\public_structures\complex/image25.png png width 801.0  height 849.0 supersample 1
 +
 +
Here are some tutorials:
 +
*[[Chimera Tutorial (AMPC)]]
 +
*[[Chimera Tutorial (Delta opioid receptor)]]

Latest revision as of 03:10, 24 March 2020

Command line

You might like to make a small molecules (eg. HEM) part of the surface of the protein instead of separate:

 surfcat one #1:1-290
 surf one probeRadius 1.4

You might want to color by partial charge:

 rangecolor charge,a min red 0 white max blue sel
 rangecolor charge,a -1.0 red 0.0 white 1.0 blue sel

This command will color the selected atoms by there charge.


Example Command-line script to save an image

open ../poses_clust_int.mol2
open ../rec.crg.pdb
surface #1
 color orange #1:.B
 color byhet,a #1:.B
 focus #0
 transp 80,s #1
 sop cap off
 set bg_color white
 unset depthCue
 set silhouette
set bg_color white
unset depthCue
set silhouette
focus #0
turn y 160
 turn x 20
~display
display #0.1
copy file ./C648_1.png png width 3840.0  height 1941.0 supersample 1
# this copy command will save the image, give the full path where you want to save the image
# you may want to ajust the width and height. 
copy file C:\Users\user\Desktop\name\system\public_structures\complex/image25.png png width 801.0  height 849.0 supersample 1

Here are some tutorials: