On Nov 23, 2016, at 10:08 AM, Jiying Jia <jiajiyingxibei@gmail.com> wrote:

By the way, I use the "if" after adjustment of angle because in my whole program there're another criterion.

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Best Wishes!

Jiying Jia

On Wed, Nov 23, 2016 at 6:51 PM, Jiying Jia <jiajiyingxibei@gmail.com> wrote:

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

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