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PyMOL Visualization¶

PyMOL作为最流行的分子结构可视化的工具之一，在PyRosetta中内置了相关的服务可以直接和PyMOL进行工作联动。这使得我们可以实时观察结构和打分的变化。这大大有助于理解采样和计算过程中发了什么。

一、PyMOLRosettaServer的配置¶

PyRosetta的一大特点在于可以使用PyMOL作为可视化的窗口，实时观测采样的过程。首先安装PYMOL, 通过conda可以轻松获取。

运行命令:

conda install -c schrodinger pymol

启动PyMOl命令:

pymol

图形界面菜单栏-点击-File>Edit pymolrc. 在其中添加:（路径根据自己PyRosetta安装的地址进行填写。）

run /opt/miniconda3/envs/pyrosetta/lib/python3.6/site-packages/pyrosetta/PyMOLRosettaServer.py

重启PyMOL后如有以下字样说明配置成功:

PyMOL>run /opt/miniconda3/envs/pyrosetta/lib/python3.7/site-packages/pyrosetta/PyMOLRosettaServer.py

PyMOL <---> PyRosetta link started!

at 127.0.0.1 port 65000

(图片来源: 知乎Rosetta研习社)

二、使用PyMOL观察建模结果¶

2.1 发送Pose至PyMOL¶

在前面章节中，我们已经学会如何得到Pose的4种方法，那就先来生成Pose，并发送到PyMOL中进行观察。

In [1]:

# 读入Pose;
from pyrosetta import pose_from_pdb,init,create_score_function
init()
pdb_pose = pose_from_pdb('./data/pose_demo.pdb')

PyRosetta-4 2021 [Rosetta PyRosetta4.conda.mac.cxx11thread.serialization.python37.Release 2021.26+release.b308454c455dd04f6824cc8b23e54bbb9be2cdd7 2021-07-02T13:01:54] retrieved from: http://www.pyrosetta.org
(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.
core.init: {0} Checking for fconfig files in pwd and ./rosetta/flags
core.init: {0} Rosetta version: PyRosetta4.conda.mac.cxx11thread.serialization.python37.Release r288 2021.26+release.b308454c455 b308454c455dd04f6824cc8b23e54bbb9be2cdd7 http://www.pyrosetta.org 2021-07-02T13:01:54
core.init: {0} command: PyRosetta -ex1 -ex2aro -database /opt/miniconda3/lib/python3.7/site-packages/pyrosetta/database
basic.random.init_random_generator: {0} 'RNG device' seed mode, using '/dev/urandom', seed=1700255855 seed_offset=0 real_seed=1700255855 thread_index=0
basic.random.init_random_generator: {0} RandomGenerator:init: Normal mode, seed=1700255855 RG_type=mt19937
core.chemical.GlobalResidueTypeSet: {0} Finished initializing fa_standard residue type set.  Created 984 residue types
core.chemical.GlobalResidueTypeSet: {0} Total time to initialize 0.690504 seconds.
core.import_pose.import_pose: {0} File './data/pose_demo.pdb' automatically determined to be of type PDB
core.conformation.Conformation: {0} Found disulfide between residues 2 11
core.conformation.Conformation: {0} current variant for 2 CYS
core.conformation.Conformation: {0} current variant for 11 CYS
core.conformation.Conformation: {0} current variant for 2 CYD
core.conformation.Conformation: {0} current variant for 11 CYD
core.conformation.Conformation: {0} Found disulfide between residues 5 25
core.conformation.Conformation: {0} current variant for 5 CYS
core.conformation.Conformation: {0} current variant for 25 CYS
core.conformation.Conformation: {0} current variant for 5 CYD
core.conformation.Conformation: {0} current variant for 25 CYD

PyRosetta和PyMOL的交互主要通过PyMOLMover这个模块进行实现。

In [2]:

# 展示如何发送pose到pymol中
from pyrosetta.rosetta.protocols.moves import PyMOLMover
pymover = PyMOLMover()
pymover.update_energy(True)
pymover.apply(pdb_pose)

此处截图可见，Pose已经发送至PyMOL窗口。

(图片来源: 知乎Rosetta研习社)

2.2 调用PyMOLMover进行能量分析¶

PyMOLMover还有一些跟能量或性质进行着色管理，PyMOLMover能量展示相关的api函数:

send_hbonds
send_energy/send_RAW_Energies
send_polars(注意:不兼容新版本的pymol)

In [3]:

# 对pose先进行能量计算（必须执行）
scoring = create_score_function('ref2015')
scoring(pdb_pose)

core.scoring.etable: {0} Starting energy table calculation
core.scoring.etable: {0} smooth_etable: changing atr/rep split to bottom of energy well
core.scoring.etable: {0} smooth_etable: spline smoothing lj etables (maxdis = 6)
core.scoring.etable: {0} smooth_etable: spline smoothing solvation etables (max_dis = 6)
core.scoring.etable: {0} Finished calculating energy tables.
basic.io.database: {0} Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv
basic.io.database: {0} Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv
basic.io.database: {0} Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv
basic.io.database: {0} Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv
basic.io.database: {0} Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv
basic.io.database: {0} Database file opened: scoring/score_functions/rama/fd/all.ramaProb
basic.io.database: {0} Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb
basic.io.database: {0} Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt
basic.io.database: {0} Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt
basic.io.database: {0} Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt
basic.io.database: {0} Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt
basic.io.database: {0} Database file opened: scoring/score_functions/P_AA_pp/P_AA
basic.io.database: {0} Database file opened: scoring/score_functions/P_AA_pp/P_AA_n
core.scoring.P_AA: {0} shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.
basic.io.database: {0} Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop
basic.io.database: {0} Database file opened: scoring/score_functions/elec_cp_reps.dat
core.scoring.elec.util: {0} Read 40 countpair representative atoms
core.pack.dunbrack.RotamerLibrary: {0} shapovalov_lib_fixes_enable option is true.
core.pack.dunbrack.RotamerLibrary: {0} shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.
core.pack.dunbrack.RotamerLibrary: {0} Binary rotamer library selected: /opt/miniconda3/lib/python3.7/site-packages/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin
core.pack.dunbrack.RotamerLibrary: {0} Using Dunbrack library binary file '/opt/miniconda3/lib/python3.7/site-packages/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.
core.pack.dunbrack.RotamerLibrary: {0} Dunbrack 2010 library took 0.208031 seconds to load from binary

Out[3]:

-43.150585937778

In [4]:

# 显示所有氢键的情况:
pymover.send_hbonds(pdb_pose)

(图片来源: 知乎Rosetta研习社)

In [5]:

# 发送pose的能量着色到pymol中
pymover.send_energy(pdb_pose)

蓝色代表这个残基的能量越低(favorable energy)，残基着色越红代表能量越高(unfavorable energy)

(图片来源: 知乎Rosetta研习社)

除了整体着色以外，也可以支持仅对某个能量项进行着色，比如，我目前最关心分子内部的溶剂化能（看看哪些区域有很大暴露的疏水氨基酸，这会导致蛋白质折叠不稳定）。运行结果表示，β折叠片上的氨基酸侧链上的疏水原子有比较好的packing，暴露的疏水面积较α-螺旋上的少。

In [6]:

# 发送某个能量打分项到pymol中
pymover.send_energy(pdb_pose,'fa_sol')

2.3 调用PyMOLObserver进行实时轨迹观察¶

除了静态的分析能量，在PyMOLMover中可以调用PyMOL Observer实时观察并记录构象变化的过程。

其中两个关键的模块:

AddPyMOLObserver_to_conformation，每当Pose发生构象变化时，用观察器记录构象并输出到PyMOL窗口。
AddPyMOLObserver_to_energies，仅当能量发生变化时，用观察器记录构象并输出到PyMOL窗口。

In [7]:

# loading a pose;
from pyrosetta import pose_from_pdb,init,create_score_function
init()
peptide_pose = pose_from_pdb('./data/4jfx_peptide.pdb')

# 对pose先进行能量计算（必须执行）
scoring = create_score_function('ref2015')
scoring(peptide_pose)

PyRosetta-4 2021 [Rosetta PyRosetta4.conda.mac.cxx11thread.serialization.python37.Release 2021.26+release.b308454c455dd04f6824cc8b23e54bbb9be2cdd7 2021-07-02T13:01:54] retrieved from: http://www.pyrosetta.org
(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.
core.init: {0} Checking for fconfig files in pwd and ./rosetta/flags
core.init: {0} Rosetta version: PyRosetta4.conda.mac.cxx11thread.serialization.python37.Release r288 2021.26+release.b308454c455 b308454c455dd04f6824cc8b23e54bbb9be2cdd7 http://www.pyrosetta.org 2021-07-02T13:01:54
core.init: {0} command: PyRosetta -ex1 -ex2aro -database /opt/miniconda3/lib/python3.7/site-packages/pyrosetta/database
basic.random.init_random_generator: {0} 'RNG device' seed mode, using '/dev/urandom', seed=1831499113 seed_offset=0 real_seed=1831499113 thread_index=0
basic.random.init_random_generator: {0} RandomGenerator:init: Normal mode, seed=1831499113 RG_type=mt19937
core.import_pose.import_pose: {0} File './data/4jfx_peptide.pdb' automatically determined to be of type PDB

Out[7]:

12.957104631992078

In [8]:

#AddPyMOLObserver(pose, True)
from pyrosetta.rosetta.protocols.moves import AddPyMOLObserver_to_conformation, AddPyMOLObserver_to_energies
from pyrosetta.rosetta.protocols.minimization_packing import MinMover
from pyrosetta.rosetta.core.kinematics import MoveMap

In [9]:

# 创建pymol构象变化观察器;
AddPyMOLObserver_to_conformation(peptide_pose, True)

# 创建pymol能量变化观察器;（只能选其一）
# AddPyMOLObserver_to_energies(peptide_pose, True)

# 对多肽进行能量最小化;
mp = MoveMap()
mp.set_bb(True)
mp.set_chi(True)
min_mover = MinMover()
min_mover.movemap(mp)
min_mover.apply(peptide_pose)

core.scoring.ScoreFunctionFactory: {0} SCOREFUNCTION: ref2015

(图片来源: 知乎Rosetta研习社)

在后面的一些章节中，还可以是用一些特殊的残基选择器得到可以再PyMOL中进行选择的命令语句，配合使用也可以进行相应的可视化功能。

In [ ]: