![]() Or, for jpg files: "write image jpg 1xme5.jpg". At anytime type: "write image png "1xme5.png" ". Or "hide selected" or "hide not selected"Ģ5. A useful command "display selected" Done now it should hide the a,b and c chains, and show only the two hemes. (if you type "hem and has" you will get no atoms, since no atom can be in two different groups at once.) Now type "cpk color cpk"Ģ4. Now select the two hemes: Type "select hem or has"Ģ3. Type "cpk off" the cartoon should still be there.Ģ2. now select chain a by typing "select :a"Ģ1. To select residue 4 in chain c, type "select 4:c"Ģ0. Now color these residues a different color. Now select the leucine residues in chain c by typing "select leu:c" or "select leu and :c"ġ7. Try it out by typing "spacefilling 20% wireframe 40". If you use just 80, it is a different scale and gives you tiny spheres.īall-and-stick is a combination of cpk (or spacefilling) and wireframe. #COLOR TERMINUS JMOL TRIAL#Trial and error will quickly get you the thickness you want. You will see the backbone command re-appear. This backbone is very thin, so type "wireframe 80". One way to show the actual backbone is to type "wireframe only select backbone display selected"ġ5. "Trace" is similar to backbone but provides a smooth curve."Wireframe" traces the 3 backbone atoms, along with the sidechains. Now change chain c to backbone: Type "select :c cpk off cartoon off backbone"īackbone does not trace the backbone atoms, but provides one centered point for each amino acid at the alpha carbon (CA). See the link to Jmol colors: You can see that the blue used in "color by chain" is actually or ġ4. Jmol can use standard colors for each chemical element, or for chains. So, "color lime", "color ", or "color " all do the same thing. (where each digit can be A-F or 0-9, so-called hexadecimal). ![]() Any 3 numbers between 0 and 255, gives you over 16 million shades of color. Colors can also be written according to RGB: which is white. e.g, salmon, deeppink, darkblue, lightblue, etc. Many names of colors are recognized by Jmol. You can separate commands by a semi colon rather than hitting "return" each time.ġ3. One is pale blue, one is pale green, and one is pale pink.ġ2. Drag the molecule around so that you can see the three different chains. Now the N-terminus is blue and the C-terminus is red.ġ1. ![]() To color by rainbow colors, type "color group". To color each chain differently, type "color chain". To color the protein by "structure", means alpha helices are magenta, beta-strands are gold, etc. To change the appearance of the molecule, in general, you must first "select" something, and then "render" it, e.g by color.ġ0. Now you should see the protein appear in the window.ĩ. Or, type "load pdb_files/" into the Console.Ĩ. Look for the "pdb_files" folder and open it.ħ. At the upper left, under the Jmol "File" menu, click "Open"Ħ. Go to the "File" menu at the upper left of the Jmol window, and click on "Console". If necessary, make the window larger by dragging the lower right corner.ģ. Drag the window to the left side of the screen. Find the file "Jmol.jar" file in the jmol folder. ![]()
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |