Dihedral/Dihedral angles in proteins
From Proteopedia
(Difference between revisions)
(trying the script in a Jmol Extension tag) |
(trying the script in a Jmol Extension tag) |
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<uploadedFileContents>1iy4_34-36.pdb</uploadedFileContents> | <uploadedFileContents>1iy4_34-36.pdb</uploadedFileContents> | ||
<pspeed>2</pspeed> | <pspeed>2</pspeed> | ||
| - | <script> | ||
| - | for (i=0;i<23;i++) { | ||
| - | if (i==0) { | ||
| - | load ""; | ||
| - | select visible and (34, 35.N, 35.H); | ||
| - | hide all; | ||
| - | rotateSelected {35.CA} {35.N} -12.7428; | ||
| - | calculate structure; // phi=-90 | ||
| - | } else { | ||
| - | load append ""; | ||
| - | select visible and (34, 35.N, 35.H); | ||
| - | hide all; | ||
| - | rotateSelected {35.CA} {35.N} @{-12.7428 + 15*i}; //phi rotation | ||
| - | calculate structure; | ||
| - | } | ||
| - | draw id @{"phi1_" + i} plane {35.N} {35.CA} {34.C}; | ||
| - | draw id @{"phi2_" + i} plane {35.N} {35.CA} {35.C}; | ||
| - | color $phi1* thistle; | ||
| - | color $phi2* plum; | ||
| - | } | ||
| - | draw psi2 plane fixed {35.CA} {35.C} {36.N}; | ||
| - | color $psi2 sandybrown; | ||
| - | background white; | ||
| - | color _H [xEEFFFF]; | ||
| - | wireframe 0.12; | ||
| - | font label 14 Sans bold; | ||
| - | |||
| - | select *.CA; color [x70AB70]; label "C\u03B1"; color label green; | ||
| - | select *.C; color [xBF9090]; label "C=O"; color label indianred; | ||
| - | select *.N; label N; | ||
| - | |||
| - | select all; | ||
| - | color bonds [x999999]; | ||
| - | select *.C,*.N; | ||
| - | define pepBonds selected; | ||
| - | color bonds [x404040]; | ||
| - | |||
| - | select (34,36) and sidechain; | ||
| - | color translucent 0.3; | ||
| - | color bonds translucent 0.3; | ||
| - | |||
| - | set echo vPhi 0% 100%; | ||
| - | set echo vPhi left; | ||
| - | font echo 22 serif italic; | ||
| - | set echo vPsi 0% 100%; | ||
| - | set echo vPsi left; | ||
| - | color $vP* black; | ||
| - | |||
| - | select all; | ||
| - | |||
| - | set AnimFrameCallback "jmolscript:showPhi()" | ||
| - | function showPhi() { | ||
| - | var k = '\u03D5 = ' + {35 and visible}.phi % 0 + '\u00B0'; // phi, degree | ||
| - | set echo vPhi; | ||
| - | echo @k; | ||
| - | } | ||
| - | set echo vPsi; | ||
| - | echo @{'|\u03C8 = ' + {35/1.1}.psi % 0 + '\u00B0'}; //constant | ||
| - | |||
| - | frame rewind; | ||
| - | moveto 0 {426 -575 698 151.19} 85 0 0 {109.5 -2.1 -4.584} 7.74 {0 0 0} 0 0 0 3 0 0; | ||
| - | anim mode loop 0 0; | ||
| - | anim fps 2; | ||
| - | |||
| - | set measurementLabels off; | ||
| - | set measurements 0.25; | ||
| - | color measurements magenta; | ||
| - | measure delete; | ||
| - | measure range 0 1.6 all (34, 35.N, 35.H) ((35,36) and not (35.N, 35.H, 35.CA)); | ||
| - | |||
| - | display all; | ||
| - | </script> | ||
</jmolApplet> | </jmolApplet> | ||
</jmol> | </jmol> | ||
Revision as of 19:35, 3 December 2014
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Dihedral angles in proteins: Phi and Psi
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