1. Selections, Scripting and Command Language

2. ICM – The Basics # ICM The Basics aa=2.4 #You have just created a new ICM-shell variable aa and assigned a value of 2.4 to it. You can create a variable with a name which is not already in use in the ICM-shell, does not contain space or delimiters like ".","," and starts from a letter (e.g. 1aag is an illegal name, except for sequences). Let us go on: bb=2.*aa #Now you have created another ICM-shell variable bb and its value is probably 4.8. Find it out by typing: print " bb=", bb #or any of these commands: list "b*" list integers show bb

3. Basics (Contd) #The next step would be to type a conditional expression like: if (bb != 4.8) print "something went wrong" #or something even more elaborate: if (bb != 4.8) then print "something went wrong" else print "It really works" endif #You can always start a for-loop such as: cc={"sushi","sashimi","negi maki","toro","period."} for i=1,Nof(cc) # Nof returns the number of elements. # Index i runs from 1 to 5 print "*** I just like to eat ",cc[i] endfor

5. ICM Molecule Introduction display a_2. cpk # object selection (the second object) display a_1.1 ribbon green # molecule 1 from object 1 display a_1.2/his xstick # residue his12 shown as balls and sticks color a_/1.2/12/n* xstick blue # atoms: color nitrogens in blue prefix _ [ object(s) . ] molecule(s) / residue(s) / atom(s) or variable(s)

6. Making Selections The Prefix defines one of the three selection types: atoms, residues, molecules and objects ( a_.. ) free variables ( v_.. ) all variables ( V_.. )

19. Free and all variables Example: aa = v_//phi,psi # the backbone torsions unfix only aa unfix only v_/10:15/phi,psi

21. ICM Command Language Verbs: read, write delete rename show display undisplay color make set Nouns: object, sequence, alignment, map e.g. read object “…..ob” make sequence “ALKLPLKD” show sequence display ribbon

22. Scripting - An ICM script means a collection of ICM commands stored in a file which can be called from ICM-shell. call s_ScriptFileName [ only ] • invokes and executes an ICM-script file. End the script with the quit command, unless you want to continue to work interactively, or use it in other script. • option “only” allows you to suppress opening the script file if the call command is inside a block which is not executed. By default the script file is opened and loaded into the ICM history stack anyway, but the commands from the file are not executed. • Example: call _startup # execute commands from _startup file

31. Constants

32. Regular Expressions

38. Jump Controls • break <for-loop> or <while-loop> ... if ( <logical expression> ) break ... <end of loop>

39. Jump Controls • continue <for-loop> or <while-loop> ... if ( <logical expression> ) continue ... <end of loop>

40. Jump Controls • goto ... if ( <logical expression> ) goto <label> ... ... <label>: ...

41. Jump Examples

42. Logical Operations

43. Logical Operations (contd)

44. Comparison Operators