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@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@gmail.com <mailto: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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