Hi,

I want to use python script to adjust the bond angle randomly and only accept the case if the random new angle is larger than old one.

I use "mcopy" to recover the old angle if the new is smaller. But I encounter a problem: if I use "mcopy #old #new setting a" or "x" or "y", the after "adjust angle anglenew" command, the angle adjusted is not the anglenew, but a different one. I don't know why.

I hope anyone can solve my problem..

Below is the python script and init.mol2.

PYTHON SCRIPT:

import os

import time

import chimera

import random

from chimera import runCommand as rc

from chimera.tkgui import saveReplyLog

import MoleculeTransform

from MoleculeTransform import transform_atom_coordinates

import numpy as np

import sys

import re

#open initial conformation init.mol2

opened = chimera.openModels.open("init.mol2")# opened as model 0 in chimera

chimera.openModels.open("init.mol2") # opened as model 1 in chimera, used to store old conformation in monte carlo simulation

rho = opened[0]

print "angleold anglenew angle_after_adjust"

for pdbi in range(0,20):

random_atom = 1

an0 = rho.atoms[random_atom-1]

an1 = rho.atoms[random_atom]

an2 = rho.atoms[random_atom+1]

angleold = chimera.angle(an0.xformCoord(),an1.xformCoord(),an2.xformCoord())

anglenew = random.random()*180

rc("adjust angle %f %s %s %s"%(anglenew,an0.oslIdent(),an1.oslIdent(),an2.oslIdent()))

angleafter = chimera.angle(an0.xformCoord(),an1.xformCoord(),an2.xformCoord())

print str(angleold)+" "+str(anglenew)+" "+str(angleafter)

if anglenew>angleold:

rc("mcopy #0 #1 settings x")

else:

rc("mcopy #1 #0 settings x")

rc("close all")

rc("stop now")

INIT.MOL2:

@<TRIPOS>MOLECULE

init.mol2

3 2 3 0 0

NUCLEIC_ACID

NO_CHARGES

@<TRIPOS>ATOM

1 C 1.7324 -0.5083 0.8663 C.3 1 DA 0.0000

2 C -0.6180 0.4940 -0.0060 C.3 2 DA 0.0000

3 C 1.2450 0.9460 1.8950 C.3 3 DA 0.0000

@<TRIPOS>BOND

1 1 2 1

2 2 3 1

@<TRIPOS>SUBSTRUCTURE

1 DA 1 RESIDUE 4 A DA 1 ROOT

2 DA 2 RESIDUE 4 A DA 2

3 DA 3 RESIDUE 4 A DA 1