[Chimera-users] usage of mcopy

[Eric Pettersen]

Hi Jiying,
	This is kind of a bug and kind of a feature.  Chimera remembers the adjustments made with the “adjust angle” command so that if you adjust the same angle several times, they are consistent in direction/magnitude.  However if you adjust the angle without using the “adjust angle” command (e.g. via mcopy), then the remembered adjustments are no longer in sync and you get the weird results you’re seeing.
	So, the easiest way for you to get the outcome you want is to instead of using mcopy, revert to the old angle simply by using “adjust angle” with the old value.

—Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Nov 23, 2016, at 9:51 AM, Jiying Jia <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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