[ atomLabelStyle | alignMethod | atomSingleStyle | dcMethod | electroMethod | errorAction | ffMethod | gcMethod | highEnergyAction | interruptAction | mfMethod | minimizeMethod | pdbDirStyle | rejectAction | resLabelStyle | ribbonColorStyle | ribbonStyle | sequenceColorScheme | shineStyle | surfaceMethod | tzMethod | varLabelStyle | visitsAction | vwMethod | webEntrezOption | wireStyle | xrMethod ]

• the item number
• the item name
• "nextItem" string
• 0 (the same as "nextItem")

 
 resLabelStyle = 3              # 3-rd choice 
 resLabelStyle = "Ala 5"        # assign by string  
 resLabelStyle = "nextItem"     # go to the next item in the list  

1. "cb1" <== default
2. "cb1 q" (atomic charge)
3. "cb1:FC" (formal charge and chirality)
4. "cb1 all" (different atomic properties)
5. "cb1 mmff q"
6. "C" (chemical atom name for non-H and non-C atoms, formal charge and chirality)
7. "[C]" (chem. name, formal charge and chirality on a rectangle )

 
 build string "se his" 
 atomLabelStyle = "[C]" 
 wireStyle = "chemistry" 
 lineWidth = 3. 
 display atom label wire black # press Ctrl-A 
 color background white 
 write postscript "tm"         # save the results 
# 
 atomLabelStyle = "C" 
 display xstick  
 set type mmff                 # press Ctrl-A again 

1. "ZEGA"
2. "H-align" <- the best choice
3. "frame-H-align" # allows to align DNA sequence against protein sequence or protein sequence database

• gapFunction,
• accFunction,
• alignMinCoverage (0.5) - minimal ratio of the aligned residues with respect to the shorter sequence length.

1. "tetrahedron"
2. "cross"
3. "dot"

1. "exact" <- default
2. "unnormalized"

1. The "exact" density correlation penalty function uses the Pearson's correlation coefficient. The correlation coefficient is then shifted by +1 so that the function ranges from 0. to 2. rather than from 1. to -1. DC = 1 - Sum( D_i - < D > )( A_i - < A > )/( N * Rmsd( D )*Rmsd( A )) The term has analytical derivatives with respect to the internal coordinates and can be efficiently locally minimized. This term requires additional memory allocation equal to the current map size and is two times slower than the unnormalized term.
2. The "unnormalized" density correlation. Formula: DC = 1 - Sum( D_i - < D > )( A_i - < A > )/ N where D_i is a map value in point i , and A_i represents the density generated dynamically from atomic positions. The differences from the "exact" term are the following:
   • scaling is arbitrary in contrast to "exact" term. Therefore you have to estimate a reasonable dcWeight value if "dc" is optimized along with the other energy or penalty terms.
   • The "unnormalized" term does not require additional memory and is two times faster than the "exact" term. The term has analytical derivatives with respect to the internal coordinates and can be efficiently locally minimized.

1. "Coulomb"
2. "distance dependent" <- default
3. "MIMEL"
4. "boundary element"

1. The Coulomb electrostatics is defined as U = q₁ *q₂ /D*r₁₂ with D = dielConst .
2. In the distance-dependent dielectric model D in the above formula is set to dielConst*r, where r is an interatomic distance.
3. The "MIMEL" electrostatics allows to evaluate the free energy of a molecule in water environment by the Modified IMage ELectrostatics approximation at every iteration of the Monte Carlo, or search procedure. This energy will only be calculated for a static structure or at the end of local minimization ( so called "double energy scheme", see Abagyan and Totrov, 1994 section (e) on p.992, or Abagyan, Totrov and Kuznetsov, 1994 p. 10, for reference). ). The MIMEL energy consists of the Coulomb energy, which is calculated for all the atom pairs at the current dielConst value, and the electrostatic solvation energy which is a sum of "selfEnergy" and "crossEnergy" and is returned in the r_out real variable upon completion of the calculation in the show energy command. A more accurate evaluation of the electrostatic solvation energy can be obtained with the boundary element method.
4. The boundary element method provides an accurate solution of the Poisson equation. The dielectric boundary is defined by the accurate analytical molecular surface (skin) and all the local charges stay exactly where they are. The boundary element method does not rely on any 3D grid and is free from dependence on the grid size. The ICM implementation of the boundary element method is fast and accurate. During the local minimization the derivatives with respect to the internal coordinates are not calculated (similar to the MIMEL method). The distance dependent dielectric model is used during minimization instead. At the end of the local minimization the electrostatic energy is replaced by the more rigorous boundary element energy.

1. = "none" # error flag is set (see the Error() function)
2. = "break" <- default # exit from loops and macros
3. = "exit" # exit from a script into shell
4. = "quit" # quit ICM: useful for CGIs

1. = "ecepp" <- default
2. = "mmff"
3. = "icmff" a new experimental force field obtained by reparametrization of the mmff force field into the internal coordinate space and derivation of the parameters specific for a particular covalent geometry.

• "ecepp"
  • read library (if it is not included in your _startup.icm file)
  • modify terms with the set terms command.
  • use show energy , minimize, or montecarlo.
• "mmff" in cartesian space (free covalent geometry). The command requires at least the "vw,af,bb,bs" terms and needs correct atom types and charges.
  • read library mmff
  • assign atom types: set type mmff a_ . This operation requires correct
• chemical structure (when you build the molecule, make sure it is complete),
• bond types (check graphically with wireMethod=2, and change with the set bond type command), and
• formal charges (check graphically with the atomLabelStyle=3, and assign with the set charge formal .. command).
  • assign charges: set charge mmff a_
  • modify terms with the set terms command. The full set is: set terms "vw,el,to,af,bb,bs"
  • use show energy , minimize, or montecarlo.
• "mmff" in the internal coordinate space according to the current fixation. The use of the mmff force field is not recommended.
• "icmff". This new force field is designed to be used with the fixed covalent geometry and is faster than both mmff-cartesian and "ecepp". The icmff force field is still experimental and should be used with caution. The vacuum part of icmff requires only three terms: "vw,to,el". The solvation terms "sf,en" can be added. Icmff calculates parameters on the fly for a particular geometry. To use this force field use the following procedures:
• assign mmff types and charges, and load the mmff libraries (see above)
• to generate the starting conformation, minimize your molecule with ffMethod = 2 and minimize cartesian "14,to,bb,bs,af" .
• set ffMethod to 3 and set terms ""vw,to,el,sf,en" only .
• use show energy or montecarlo

1. "vw" <- default choice: current object interacts with the van der Waals field. Positive values repel, negative attract; Contribution from one non-hydrogen atom is Eatom = 1.*Egc
2. "density" : treats the m_gc map as positive electron density and pulls the object into it. The contributions of atoms are proportional to atomic number (the number of electrons), hydrogens are ignored: Eatom = -AtomicNumber*Egc
3. "field" : uses user-defined atomic field value, which can be set by the set field command and extracted with the Field (as_ ) command, as the relative weight of each atom. Anticipates that van der Waals type of the map (attractive negative values, repulsive positive) as in the first method. Eatom = Field(atom)*Egc

1. " heat"
2. " stackjump" <- default
3. " random"
4. " exit"

1. = "break loop"
2. = "break all loops" <- default
3. = "exit macro"
4. = "exit to the main macro"
5. = "exit all macros"

• "intermolecular" (or 1 ) <- default
• "all" (or 2)

1. "conjugate"
2. "newton"
3. "auto" <- default

1. "1abc.pdb"
2. "pdb1abc.ent" <-- current choice
3. "ab/pdb1abc.ent"
4. "ab/pdb1abc.ent.Z"
5. "ab/pdb1abc.ent.gz"
6. "PDB website"

1. " heat" <- default choice
2. " stackjump"
3. " random"
4. " exit"

1. "A5" <- default choice
2. "Ala 5"
3. "ALA 5"
4. "Ala"
5. "ALA"
6. "Alanine 5"
7. "5"
8. "A"
9. " A"
10. "Mol" - displays MOLECULAR name.

 
 nice "1eoc.a/" 
 make sequence a_1.1 
 read pdb sequence "3pcc.a/" 
 aa = Align(3pcc_a 1eoc_a) 
 ribbonColorStyle=3   # color gaps gray 
 color ribbon 
 ribbonColorStyle=4   # see alignment strength 
 color ribbon 

specifies type of representation when display ribbon command is used. Options are the following: "ribbon" <- default choice "cylinders" "pencils" "numbers"

1. "no color"
2. "residue type"
3. "icm-combo" <-- current choice
4. "consensus strength"
5. "greyscale"

1. "white" <- default
2. "color"

1. "constant tension"
2. "atomic solvation" <- default choice
3. "apolar"

1. "constant tension" means that the energy terms are just the product of the total solvent-accessible surface by the surfaceTension parameter. This term is intended to represent the surface energy if electrostatics takes the solvent polarization energy into account (see electroMethod )
2. "atomic solvation" option is designed to evaluate the solvation energy purely on the basis of the atomic accessible surfaces instead of using the proper electrostatic evaluation of the polarization free energy. This fast but approximate scheme was proposed by Wesson and Eisenberg, (1992) . Atomic surface parameters derived from the experimental vacuum-water transfer energies are given in the icm.hdt file.
3. "apolar" option is designed to evaluate the stabilization energy, which is the difference between denatured and folded states. The "atomic solvation" energy should be used with the van der Waals term while the "apolar" energy takes it into account and should be used without any other energy terms. The "apolar" atomic surface parameters were derived from the experimental octanol-water transfer energies and are given in the icm.hdt file.

1. "simple" : equal weight tethers to 3D points
2. "weighted" : individual weights are calculated from atomic B-factors by dividing 8*PI² by the B-factor value. All the weights additionally are multiplied by the tzWeight shell variable.
3. "z_only" : tethers are imposed only in the Z-direction towards the target Z-coordinate. These type of tethers pulls a molecule into a z-plane. This may be useful if you are trying to generate a flat projection of a three-dimensional molecule.
4. "function" : tethers can take a form of distance restraints with individual weights, upper and lower bounds. The three parameters are controlled by the following properties of the target atoms (not the source atoms as in the "weighted" case): individual weights are directly taked from bfactor values, the upper bounds from the area fields, and the lower bounds from the charge field. To set those values, use the set bfactor, set area and set charge commands respectively. applying linear force to atoms: to exert a constant force to an atom, set the formal charge of the target atom to a special value of 5. The b-factors will continue to serve as individual force constants and the direction of force will correspond to the vector from the origin to the target pdb-atom with this special value of formal charge.

 
build smiles "c1c(ccc(c1)N(=O)=O)N2CCC(CC2)=CC(=O)NNC(=O)Nc3cc(ccc3)C(F)(F)F" 
tzMethod = "z_only" 
set tether a_   # sets tethers to x,y,z=0. coordinates for each atom 
minimize "vw,tz" 200 
dsChem a_//!h* 
 
#linear force. Use interface to set the linear force flag (formal charge) and bfactors 
copy a_ "tzcopy" 
tzMethod = "function" # will use bfactor and formal charge features of a_tzcopy. atoms 
set tether a_/1/ca a_tzcopy./1/ca  # drag the target atom where you want 
set charge formal a_tzcopy./1/ca 5. # number 5. signals ICM to interpret it as linear force 
set bfactor a_tzcopy./1/ca 5000.    # the force constant 
set tether a_/1/cb a_tzcopy./1/cb   # combine with normal tethers. 
display tether a_ 
minimize v_//?vt* "tz"   

1. "greek" <- default choice
2. "name"
3. "value"

[ heat | stackjump | random | mcexit ]

1. "random"
2. "heat" <- default choice
3. "stackjump"
4. "exit"

• "heat" - double the simulation temperature
• "stackjump" - jump to the conformation of the least visited slot in the stack.
• "random" - randomize all free variables according to the mcJump parameter
• "exit" - exit the MC procedure

1. "exact" <- default choice: F_vw = A/r¹² - B/r⁶ . This is the usual van der Waals formula tending to infinity at r close to 0.
2. "soft": F_soft = F_vw , for F_vw <= 0. and F_soft = F_vw *(t/(t+F_vw )) for F_vw > 0. (repulsion). This form preserves the function for the most populated part of the curve but smoothly reaches the limit t (defined by the vwSoftMaxEnergy real system variable)
3. "old soft": another smooth approximation with the finite value at r=0, depending on the well depth.

1. "none"
2. "g:GenPept" <- default
3. "r:Report"
4. "f:FASTA"
5. "a:ASN.1"
6. "d:Entrez document summary"
7. "m:MEDLINE links"
8. "p:protein neighbors"
9. "n:nucleotide links"
10. "t:structure links"
11. "c:genome links"

1. "wire" <- default choice
2. "chemistry"
3. "tree"

1. "corr Fc:Fo" <- default
2. "corr Fc2:Fo2"