Rot

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rot is a top level plop command used to interact with rotamer libraries.

It contains a number of sub-commands:

Contents

[edit] rot dir

Set the local directory to look for rotamer libraries in. All libraries must be either in the datadir or here and this library cannot be changed multiple times in a run to load libraries from different locations.

rot dir <directory name> 

[edit] rot assign

This is the method for defining libraries for arbitrary residues. The libraries are combined combinatorically using the minimum ofac cutoff in the sidechain prediction. Those sections seperated by a "newgrp" command are not combined combinatorically and the multiple regions are treated as seperate sidechains. Must be run after loading the pdb. <Residue Name> : External residue name (all caps) <Library Name> : Sidechain library name without the .side ext. Can use included FREE10,FREE20 ... libraries for free rotation of a single bond. (do not include .side in name). <backbone libray name> : The backbone library for this residue (optional). Don't include the .back in the name. Zmat atoms in this libary must match the ones in the ligand. <bonds in residue> : Bonds can be specified in three ways "default" simply means to use the zmat atom specified in the library. Individual bonds can be identified using either the atoms name on either side of the bond (4chars ie "_C1_ _C2_") or the "zmat" followed by the zmat atom corresponding to the torsional rotation (ie "zmat _C3_"). For cases in wich free rotation is not used, the zmat method is prefered as it gives a defined 0 position for the rotation. newgrp : Command for seperating the residue into multiple regions with seperate sidechain libraries. The libraries in the above command not seperated by newgrp commands are combined combinatorically, while those seperated by this command are treated as seperate residues with independent sidechains.

rot assign res <Residue Name> &
backlib <backbone library name>
sidelib <Library Name1> <bonds in residue for lib 1> &
sidelib <Library Name2> <bonds in residue for lib 2> &
newgrp &
sidelib <Library Name4> <bonds in residue for lib 4> &
sidelib <Library Name5> <bonds in residue for lib 5> &

Example: This example creates a residue type SIA with two independent sidechains. The first has three freely rotatable bonds which will be combined combinatorically into a single library (SIA__1). Note that different resolutions can be combined, with lower resolution in this case for a polar hydrogen. The second region or independent sidechain combines a prebuilt library for a ring with a freely rotatable bond.

rot assign res SIA &
sidelib FREE10 _C6_ _C7_ &
sidelib FREE10 _C7_ _C8_ &
sidelib FREE30 _C7_ _O7_ &
newgrp &
sidelib SIA_R1 zmat _C2_ &
zmat _C4_ &
zmat _C1_ &
zmat _O4_ &
zmat 1H3_ &
sidelib FREE10 _C2_ _C1_ &

If the SIA_R1 library was build specifically for this ligand (such as with PlopRotTemp.py ) and the zmat atoms in it correspond to the ones you want to use you could use the following

newgrp &
sidelib SIA_R1 default &
sidelib FREE10 _C2_ _C1_ &

When the PDB is being loaded the program will search in the data directory and the local directory for files called <RESNAME>.rot.assign and use these to break complicated residues into smaller parts and assign rotmer libraries to them. As many of the non-bonded cutoffs are dependent on residue-residue distances this can effect the energies if cutoffs are enabled (you can disable them by setting them to 1000A).

rot assign all

The command "rot assign all," has been made obsolete. Now the program will always run as if this command was run


[edit] rot trrot

Gives the rotation and translation difference between these residues in the current and native structure:

rot trrot <atom type> <residue list (2words)> 
rot trrot heavy A:1 A:2

[edit] rot trrot

Gives all atoms within this % of combined vdw radii (steric clashes)

rot clash <ofac_min> 
rot clash 0.75 

[edit] rot sft

interface to the sidechain flexibility test

rot sft <ofac> <moveable residues (2 words)> <flexible sidechains (2 words)>
rot sft 0.65 _:1 _:1 within5.0 _:1 

[edit] rot restable

Add a line directly to the restable. Probably only for really power users.

rot restable <line>
rot restable GLY GLY G GLY trans 0 gly 0

[edit] Programmers notes

All ligands without an entry in the restable, and therefore without rotamer libraries have a rank of -100 for all of their atoms regardless of whether they have main chain and sidechain atoms defined in the template. All ligands with rotamer libraries are ranked like protein residues. This is essential for proper function with a variety of applications.

Rotamer libraries are combined in side_first to take advantage of the fact that they can pruned for backbone contacts at the same time as they are merged together combinatorically. If this is not the desired behavior (ie the backbone will change before you run side_first again) then use the prebuild_libraries function. The libraires are generally not written, although they are in memory. To actually write out the combined library use "write_libs yes" in your sidechain prediction. Also for this reason side_rot_standard (now in side_first_init) must be run every time side_first is run. Otherwise plop will use the already built library instead of building a new one for the new system configuration. Backbone libraries are not created in this fashion and are simply read in and used.

Splitting residues is dealt with by exanding residues in places and moving the other residues down. Any backbone library information is transfered to the first child.

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