[Chimera-users] usage of mcopy

Jiying Jia jiajiyingxibei at gmail.com
Wed Nov 23 09:51:59 PST 2016

```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
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]
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
%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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```