[Chimera-users] usage of mcopy

[Eric Pettersen]

If there’s some reason that setting the angle back with “angle adjust” won’t work in your scheme, you can explicitly disable the caching by doing this after the “angle adjust”:

import BuildStructure
BuildStructure._bondAngleCache = {}

—Eric

> On Nov 23, 2016, at 10:08 AM, Jiying Jia <jiajiyingxibei at gmail.com> wrote:
> 
> By the way, I use the "if" after adjustment of angle because in my whole program there're another criterion <http://www.baidu.com/link?url=y10dPHkFYzBREucobuDAs73RgoMsopt2igSS2z1gFoRQdH8p_0rDvcC35wzy5wYkxaCY8B6_PKjkhyJalktpwbPcXofDXlxlm6QUKk36GtPrcGqeBqh7C0_f2gL5Gi6C>.
> 
> ------------------
> Best Wishes!
> Jiying Jia
> 
> On Wed, Nov 23, 2016 at 6:51 PM, Jiying Jia <jiajiyingxibei at gmail.com <mailto:jiajiyingxibei at 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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