 most interaction with PyMOL is via a scripting language, not all functions are available from menus  keyword followed optionally by one or more comma-separated arguments, e.g. color red, hetatm – colors all non- protein atoms red, color red – all atoms are red  in most cases 1 st argument is specific to command used, while the 2 nd argument is the name of the object/selection, e.g. show spheres, resi 1

commonly used commands more in PyMol

 download 1PD8, 1PD9 and 1PDB in PDB format  load them into Pymol as objects log_open log.pml load 1PD8.pdb, ter load 1PD9.pdb, bi load 1PDB.pdb, apo  Alignment align ter, apo align bi, apo Pymol

 PDB files having ss from programs like DSSP  PyMOL has reasonably fast ss assignment using dss selection - To change assignments manually, the best way is to use the alter command as follows: show cartoon alter 40-52/, ss='L' # assign residues as loop alter 52-65/, ss='S' # assign residues as sheet alter 65-72/, ss='H' # assign residues as helix rebuild # regenerate the cartoon

 download 1PD8, 1PD9 and 1PDB in PDB format  load them into Pymol as objects log_open log.pml load 1PD8.pdb, ter load 1PD9.pdb, bi load 1PDB.pdb, apo  Alignment align ter, apo align bi, apo  Alter Secondary structure alter (ter and (resi 59-60), ss='L' rebuild Pymol

 Object (ter, bi and apo)  Show car, ter  Select 1, resn ALA and name N  # Select backbone nitrogens from alanine residues  Show spheres, 1  Select 2, resi 1:20  #select residues 1-20  Show sticks, 2  select 3, elem O and not name OH  # Select all oxygen atoms except hydroxyls

propertyshortexample symbole. chemical symbol,select polar, symbol o+n namen. atom names, select carbons, n. ca+cb+cg+cd resnr. residue names, select aas, resn asp+glu+asn+gln resii. residue numbers, select mults10, resi chainc.chain ID ss- secondary structure type, select allstrs, ss h+s+l+""

 and, or, not etc.  how would you select resid 27 and resid 28? propertyshortexample not s1! s1atoms that are not included in s1 and&atoms included in both s1 and s2 or|atoms included in either s1 or s2 in-s1 atoms whose name, resi, resn, chain match s2 atoms likel.s1 atoms whose name, resi match s2 atoms

propertyshortexample s1 around Xs1 a. Xatoms with centers within X Angstroms of the center of any atom in s1 select near10, resi 10 around 5 s1 expand Xs1 e. XExpands s1 by all atoms within X Angstroms of the center of any atom in s1 select near10x, near10 expand 3 s1 within X of s2s1 w. X of s2 Selects atoms in s1 that are within X Angstroms of the s2 byres s1br. s1 Expands selection to complete residues select cmplt, byres near10 neighbor s1nbr. s1atoms directly bonded to s1 select vic, nbr. resi 10 s1 extend Xs1 ? XExtends s1 by X bonds connected to atom in s1 select connect_x, near10 extend 3

# selects atoms that are part of chain a, but not # residue number 125. select chain a and (not resi 125) # The following two selections are equivalent select (name cb or name cg1 or name cg2) and chain A select name cb+cg1+cg2 and chain A # PyMOL will expand its logical selection out # from the innermost parentheses byres ((chain a or (chain b and (not resi 125))) around 5)

 select residue 301 in ter (name it CO4)  show it as stick, zoom at it  Save this selection as molecule in file co4-1.pdb 1. select CO4, (ter and resn CO4) 2. show stick, CO4 3. Save co4-1.pdb, co4 4. load co4-1.pdb, co4 #create new co4 object 5. Show surface, co4 6. show sticks, byres ((ter and ((resn CO4) x; 3.5))) Pymol

 PyMOL creates an object-name to locate data when you load a data file.  Making selections is a way of pointing to a subset of that data.  Selections are in parentheses in control panel.  When you delete a selection-name, the data are still found under the object-name, but the data are no longer organized as the selection. In contrast, after you delete an object, you must reload the data to have access to it again. delete  PyMOL can hold several objects at the same time disable, enable 1

 Named selections are static. Only atoms that exist at the time the selection is defined are included in the selection, even if atoms which are loaded subsequently fall within the selection criterion 2

# EXAMPLE 1: Show hydrogen bonds between protein # and ligands (which must have hydrogens) load 1PD8.pdb,ter CO4 as a ligand h_add ter select don, (elem n,o and (neighbor hydro)) select acc, (elem o or (elem n and not (neighbor hydro))) dist HBA, (co4 and acc),(ter and don), 3.2 dist HBD, (co4 and don),(ter and acc), 3.2 delete don delete acc hide (hydro) hide labels,HBA hide labels,HBD

1. h_add ter 2. select HD, (elem n,o and (neighbor hydro)) 3. select HA, (elem o or (elem n and not (neighbor hydro))) 4. dist HBD, (co4 and HD), (ter and HA), 3.5 #distant name = (selection1), (selection2), cutoff distant (selections are in the same obj) 5. dist HBA, (co4 and HA), (ter and HB), dist X, (ter and (resi 301 and name; C5')), (ter and (resi 31 and name; CE2)), 4.5

 bg white  set bg_rgb, [120, 12, 30]  set dash_width, 5  set dash_radius, 10  label (resi 301 and name; o3'), "CO4"  label (resi 31 and name; CA), “Phe31”  set label_font_id, 10  set label_color, red

 PyMOL script – text file with commands, each at one line  *.pml  useful feature: get_view command  run script from  or from command line as pymol aaa.pml  save the image ray png