Pymol Notes - from Carrie Go to directory where pdb files are located. Command: mkpy make pymol file File name? whatever.py Base name? What you called the pdb files, minus the number.include dashes etc. #of structures? how many pdb files you wrote Residues to superposition? 10-15,20-25 i.e. upper stems or lower or all Atoms? c*,n* Match at carbon and nitrogen Target? click on structure # 1 should say that whatever.py was created succesfully Back to terminal window, Command: pymol pymol windows (2) will open- move to right hand screen The following are all in black pymol window: @whatever.py this will source the file you just made. Use this to start over at any point quit End pymol reset centers structures, calculates center of mass, returns view to full picture hide hides all from view show stick shows structures in theses different ways dots surface dots spheres mesh lines cartoon show sticks,(name c*,n*) shows sticks on only carbons and nitrogen show mesh,(resi 30-31) show mesh only on two residues zoom (resi 25-29) zoom in on residues 25029 help show lists commands show displays all active models color blue,(name p*) colors all phospates blue color blue,(resi 25) color residue 25 blue color blue,(name p*,op*) will color backbone blue If you color backbone and then 'show cartoon' or the cartoon will be the color of the backbone show dots,(name p*,op*) show dots on backbone only. to have them different colors than the residues you must color the p*,op* set bg_rgb,(1,1,1) changes background from black to white. hide (resi 1-3) hides residues 1-3 hide (*///*/q*) hides pseudo atoms delete all removes all structure from memory. keeps previous commands in command history list The dots, lines, sticks, cartoons etc can be modified easily. under the 'settings' pull down menu click on 'Edit all...'. There you can change thickness of cartoons, ribbons, sticks, lines and density of dots. here are some short-cuts. set line_width,2 thickens line width for easier viewing set dot_density,3 increase the density of dots ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From Dr. Summers' Notes: File: chem/summers/pymol/example2 # Hierarchical: model/segment/chain/residue/atom # Example: # res/atom # chain/res/atom # chain/res/ # /seg/chain// # /model/seg/chain # /model/seg # /model//chain/res # model////atom fit (Two///25-125/c,ca,n), (One///25-125/c,ca,n) fit (Three///25-125/c,ca,n), (One///25-125/c,ca,n) fit (Four///25-125/c,ca,n), (One///25-125/c,ca,n) #reset origin and clipping planes for superposed structures: reset hide show lines,(name c,ca,n) # Two ways to do the same thing: show lines,(resn phe and name c*) color brown,(resn phe) show lines,(trp/c*,n*) color red,(trp/) # Hierarchical: model/segment/chain/residue/atom # Example: # res/atom # chain/res/atom # chain/res/ # /seg/chain// # /model/seg/chain # /model/seg # /model//chain/res # model////atom fit (Two///25-125/c,ca,n), (One///25-125/c,ca,n) fit (Three///25-125/c,ca,n), (One///25-125/c,ca,n) fit (Four///25-125/c,ca,n), (One///25-125/c,ca,n) #reset origin and clipping planes for superposed structures: reset hide show lines,(name c,ca,n) # Two ways to do the same thing: show lines,(resn phe and name c*) color brown,(resn phe) show lines,(trp/c*,n*) color red,(trp/) File: Example-High-Res.py # Example-High-Res.py:q! # MFS, HHMI-UMBC delete all load final001.pdb hide # Assign Secondary Structure (if not in the PDB file): util.ss # Set for high resolution (1x,0.75x): viewport 1000,750 set antialias = 1 # Draw the image: color red show cartoon show stick,(resn trp and name c*,n*) color green,(resn trp) show stick,(resn phe and name c*) color brown,(resn phe) # Ray trace the image for high quality: ray ############ IMPORTANT ########## # After the image appears, click on the titlebar (not the image itself), hit , then: # png bigfile.png