ProDy¶

10/03/2023¶

Original slides courtesy Ahmet Bakan

print view

In [1]:
%%html
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In [2]:
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ProDy stands for Protein Dynamics,

  • an API that is very suitable for interactive usage
  • comes with several command line applications

ProDy is designed for normal mode analysis, but also is

  • a powerful tool for handling macromolecular structures
  • useful for analysis of molecular dynamics trajectories
  • useful for sequence conservation and coevolution analysis (Evol)

This lecture contains:

  • an into to some ProDy conventions
  • handling protein structure files
  • an intro to some dynamics calculations
  • some ProDy design principles

Import from ProDy¶

In interactive sessions, the following is safe (no name conflicts)

In [3]:
from prody import *
checkUpdates()

C:\Users\mertg\anaconda3\lib\site-packages\Bio\pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module.
  warnings.warn(
@> ProDy v2.4.1 is available, you are using 2.3.1.

When developing software, prefer importing specific functions/classes or prefixing

In [4]:
import prody as pd
from prody import parsePDB

ProDy API naming conventions¶

Function names¶

ProDy functions start with an action verb followed by one or more names or an abbreviation/extension, i.e. doSomething:

  • parseEXT(): parse a file in EXT format, e.g. parsePDB, parseDCD
  • writeEXT(): write a file in EXT format, e.g. writePDB, writeDCD
  • fetchSTH(): download a file, e.g. fetchPDB, fetchMSA
  • calcSTH(): calculate something, e.g. calcRMSD, calcGyradius, calcANM
  • showSTH(): show a plotting of something, e.g. showCrossCorrelations, showProtein
  • saveSTH(): save a ProDy object instance to disk, e.g. saveAtoms
  • loadSTH(): save a ProDy object instance to disk, e.g. loadAtoms

Class names¶

Class names start with upper case letters and are abbreviations or words in camel case style, e.g. AtomGroup, Selection, ANM, etc.

Class method names¶

Class method naming is similar to function naming:

  • Class.numSomething: return number of the thing, e.g. AtomGroup.numAtoms returns number of atoms
  • Class.getSomething: return an attribute, e.g. AtomGroup.getNames returns atom names
  • Class.setSomething: set/update an attribute, e.g. AtomGroup.setNames sets atom names
  • Class.buildMatrix: builds a matrix, e.g. PCA.buildCovariance calculates covariance matrix

Usage example¶

In [5]:
ubi = parsePDB('1ubi')

@> PDB file is found in working directory (1ubi.pdb.gz).
@> 683 atoms and 1 coordinate set(s) were parsed in 0.01s.
In [6]:
ubi
Out[6]:
<AtomGroup: 1ubi (683 atoms)>

TIP: to see a list of available functions, just type the action word (calc, show, get, etc.), and use TAB completion.

In [7]:
ubi.numAtoms()
Out[7]:
683
In [8]:
calcGyradius(ubi)
Out[8]:
12.085104173005442

Visualization¶

In [9]:
%matplotlib inline
showProtein(ubi)
Out[9]:
<Axes3D:xlabel='x', ylabel='y'>
No description has been provided for this image

Better Visualization¶

In [10]:
import py3Dmol
showProtein(ubi)

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
jupyter labextension install jupyterlab_3dmol

Out[10]:
<py3Dmol.view at 0x16c7d6f6040>
In [ ]:
In [11]:
%%html
<div id="newatomcnt" style="width: 500px"></div>
<script>
$('head').append('<link rel="stylesheet" href="https://bits.csb.pitt.edu/asker.js/themes/asker.default.css" />');

    var divid = '#newatomcnt';
	jQuery(divid).asker({
	    id: divid,
	    question: "How many atoms does PDB 3ERK have?",
		answers: ["1023","2849","3016","4872"],
        server: "https://bits.csb.pitt.edu/asker.js/example/asker.cgi",
		charter: chartmaker})
    
$(".jp-InputArea .o:contains(html)").closest('.jp-InputArea').hide();


</script>

File handling¶

ProDy has a custom format for directly saving atom groups.

In [12]:
saveAtoms(ubi)
Out[12]:
'1ubi.ag.npz'

Can also read/write standard protein formats (PDB,PQR)

In [13]:
writePDB('ubi.pdb', ubi)
Out[13]:
'ubi.pdb'
In [14]:
parsePDB(writePDB('ubi.pdb', ubi))

@> 683 atoms and 1 coordinate set(s) were parsed in 0.01s.
Out[14]:
<AtomGroup: ubi (683 atoms)>

Structures and AtomGroups¶

Protein Data Bank (PDB) Structure files can be parsed using parsePDB. For a given PDB identifier, this function will download the file if needed.

In [15]:
ag = parsePDB('1vrt')

@> PDB file is found in working directory (1vrt.pdb.gz).
@> 7953 atoms and 1 coordinate set(s) were parsed in 0.07s.

Structure data parsed from the file is stored in an AtomGroup instance:

In [16]:
type(ag)
Out[16]:
prody.atomic.atomgroup.AtomGroup

Why AtomGroup?

  • not Molecule, because structures are usually made up from multiple molecules
  • not Structure, because PDB format is sometimes used for storing small-molecules

AtomGroup made sense for handling bunch of atoms, and is used by some other packages too.

Some AtomGroup methods¶

Check number of atoms and models (coordinate sets)

In [17]:
ag.numAtoms()
Out[17]:
7953
In [18]:
ag.numCoordsets()
Out[18]:
1

Getters¶

Use getSomething methods to access data parsed from the file

In [19]:
names = ag.getNames()
In [20]:
names
Out[20]:
array(['N', 'CA', 'C', ..., 'O', 'O', 'O'], dtype='<U6')
In [21]:
len(names)
Out[21]:
7953
In [22]:
print(names[0])

N
In [23]:
ag.getBetas()
Out[23]:
array([86.04, 85.23, 84.2 , ..., 64.55, 58.23, 46.98])

Note that get is followed by a plural name, and method returns a numpy array

Setters¶

Use setSomething methods to set attributes, but don't forget to pass an array or list with length equal to number of atoms

In [24]:
zeros = [0] * len(ag) # same as ag.numAtoms()
ag.setBetas(zeros)
In [25]:
ag.getBetas()
Out[25]:
array([0., 0., 0., ..., 0., 0., 0.])

Atom instances¶

You can get a handle for specific atoms by indexing

In [26]:
a0 = ag[0]
print(a0)

Atom N (index 0)

Note that getSomething and setSomething methods are available, but that thing is in singular form:

In [27]:
a0.getName()
Out[27]:
'N'
In [28]:
a0.getBeta() # we had just set it to zero
Out[28]:
0.0

Subset of atoms¶

Slicing an AtomGroup will return a handler called Selection for specified subset of atoms. Let's get every other atom:

In [29]:
eoa = ag[::2] # eoa: every other atom
print(eoa)

Selection 'index 0:7953:2'
In [30]:
print(len(eoa))
print(len(ag))

3977
7953

get and set methods in plural form are also available for Selection instances

In [31]:
eoa.getNames()
Out[31]:
array(['N', 'C', 'CB', ..., 'O', 'O', 'O'], dtype='<U6')

Hierarchical Views¶

Macromolecules have a hierarchical structure:

  • chain - a polypeptide or a nucleic acid chain
  • residue - an amino acid, nucleotide, small molecule, or an ion
  • atom - lowest level of hierarchy
  • segment - used by simulation programs and may be composed of multiple chains
In [32]:
ag.numChains()
Out[32]:
2
In [33]:
ag.numResidues()
Out[33]:
1233
In [34]:
showProtein(ag)

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
jupyter labextension install jupyterlab_3dmol

Out[34]:
<py3Dmol.view at 0x16c7d32b8e0>

Iterations¶

In [35]:
for ch in ag.iterChains():
    print('%s - %d residues' % (str(ch), ch.numResidues()))

Chain A - 688 residues
Chain B - 545 residues
In [36]:
for ch in ag.iterChains():
    print(ch)
    for res in ch:
        print(' |-%s' % res)
        break
    print('...')

Chain A
 |-PRO 4
...
Chain B
 |-ILE 5
...

Also iterAtoms (default), iterBonds, iterCoordsets, iterFragments, iterResidues, iterSegments

Indexing¶

Index with chain identifier to get a chain instance:

In [37]:
chA = ag['A']
print(chA)
type(chA)

Chain A
Out[37]:
prody.atomic.chain.Chain

Index with a pair of chain identifier and residue number to get a handle for a residue:

In [38]:
chA_res10 = ag['A', 10]
print(chA_res10)
type(chA_res10)

VAL 10
Out[38]:
prody.atomic.residue.Residue

Of course, plural forms of get and set methods and other methods are available:

In [39]:
chA_res10.getNames()
Out[39]:
array(['N', 'CA', 'C', 'O', 'CB', 'CG1', 'CG2'], dtype='<U6')
In [40]:
chA_res10.numAtoms()
Out[40]:
7
In [41]:
%%html
<div id="resname" style="width: 500px"></div>
<script>
$('head').append('<link rel="stylesheet" href="https://bits.csb.pitt.edu/asker.js/themes/asker.default.css" />');

    var divid = '#resname';
	jQuery(divid).asker({
	    id: divid,
	    question: "What is residue 12 of 3ERK?",
		answers: ["VAL","ALA","PHE","ARG"],
        server: "https://bits.csb.pitt.edu/asker.js/example/asker.cgi",
		charter: chartmaker})
    
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</script>

Atom Selections¶

The atom selection engine is what makes ProDy a powerful tool. Selection grammar is similar to that of VMD but with added flexibility of Python. AtomGroup.select method accepts selection arguments and returns a Selection instance:

In [42]:
sel = ag.select('protein and name CA')
print(sel)
print('# of atoms: %d' % sel.numAtoms())
set(sel.getNames())

Selection 'protein and name CA'
# of atoms: 925
Out[42]:
{'CA'}

Same as using the keyword 'ca' or 'calpha'

In [43]:
ag.select('ca') == ag.select('calpha') == ag.select('protein and name CA')
Out[43]:
True

Selecting by distance¶

You can make proximity based selections:

In [44]:
kinase = parsePDB('3erk')
bindingsite = kinase.select('within 5 of (hetero and not water)')
print('# of atoms: %d' % bindingsite.numAtoms())
print(set(bindingsite.getResnames()))

@> PDB file is found in working directory (3erk.pdb.gz).
@> 3016 atoms and 1 coordinate set(s) were parsed in 0.04s.

# of atoms: 98
{'LYS', 'CYS', 'ALA', 'SER', 'ILE', 'GLN', 'MET', 'HOH', 'SB4', 'ASP', 'LEU', 'VAL'}

exwithin excludes the initial selection

In [45]:
noligand = kinase.select('exwithin 5 of (hetero and not water)')
print('# of atoms: %d' % noligand.numAtoms())
print(set(noligand.getResnames()))

# of atoms: 73
{'LYS', 'CYS', 'ALA', 'SER', 'ILE', 'GLN', 'MET', 'HOH', 'ASP', 'LEU', 'VAL'}
In [46]:
%%html
<div id="withincnt" style="width: 500px"></div>
<script>
$('head').append('<link rel="stylesheet" href="https://bits.csb.pitt.edu/asker.js/themes/asker.default.css" />');

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Keyword arguments¶

Words used within the selection string that are not reserved keywords can be substituted with keyword arguments.

Select atoms that are close to a point in space:

In [47]:
import numpy as np
origin = np.zeros(3)
print(origin)
sel = ag.select('within 10 of origin', origin=origin)
sel

[0. 0. 0.]
Out[47]:
<Selection: 'index 3426 to 3437 3439 to 3461' from 1vrt (35 atoms)>
In [48]:
calcDistance(sel, origin)[:5]
Out[48]:
array([9.93856378, 9.16952812, 9.08634382, 9.79169985, 8.45576029])
In [49]:
ag.select('within 5 of center',center = calcCenter(ag))
Out[49]:
<Selection: 'index 4457 to 4...49 to 7353 7941' from 1vrt (19 atoms)>

Dot selection shorthand¶

Dot operator can also be used to make selections:

In [50]:
ag.calpha
Out[50]:
<Selection: 'calpha' from 1vrt (925 atoms)>
In [51]:
ag.name_CA_and_resname_ALA
Out[51]:
<Selection: 'name CA and resname ALA' from 1vrt (37 atoms)>

See full documentation of selection grammar at: https://prody.csb.pitt.edu/manual/reference/atomic/select.html

Coordinate Sets¶

AtomGroup can handle multiple models in a PDB file. Models are called coordinate sets.

In [52]:
ubi = parsePDB('2k39')

@> PDB file is found in working directory (2k39.pdb.gz).
@> 1231 atoms and 116 coordinate set(s) were parsed in 0.28s.
In [53]:
ubi.numCoordsets()
Out[53]:
116

Active coordinate set (ACS) can be queried or changed using getACSIndex and setACSIndex methods:

In [54]:
ubi.getACSIndex()
Out[54]:
0

Coordinates¶

Coordinates are numpy arrays

In [55]:
coords = ubi.getCoords()
coords.mean(axis=0)
Out[55]:
array([26.02865475, 25.60081316, 20.56833875])
In [56]:
ubi.setACSIndex(115)
ubi.getCoords().mean(axis=0)
Out[56]:
array([26.49875061, 26.09516897, 20.5057498 ])

Selections have their own active coordinate set indices:

In [57]:
ubi_ca = ubi.calpha
ubi_ca.getACSIndex()
Out[57]:
115
In [58]:
ubi_ca.setACSIndex(0)
print(ubi_ca.getACSIndex())
print(ubi.getACSIndex())

0
115

Operations with Atoms¶

Copying atoms¶

Call copy method to make a copy of AtomGroup or Selection instance

In [59]:
ag.copy()
Out[59]:
<AtomGroup: 1vrt (7953 atoms)>
In [60]:
ca = ag.select('ca')
ca.copy()
Out[60]:
<AtomGroup: 1vrt Selection 'ca' (925 atoms)>

AtomGroup addition¶

Lot's of customization has gone into ProDy classess handling atoms. Addition of AtomGoups (__add__) results in a new AtomGroup:

In [61]:
ag_copy = ag.copy()
moveAtoms(ag_copy, by=np.array([50, 50, 50]))
ag_copy['A'].setChid('C')
ag_copy['B'].setChid('D')
ag_new = ag + ag_copy
showProtein(ag_new)

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
jupyter labextension install jupyterlab_3dmol

Out[61]:
<py3Dmol.view at 0x16c7d391370>

AtomGroup membership¶

You can use in to see whether a Selection is in another one (enabled by implementing Selection.__contains__() method):

In [62]:
ag.calpha in ag.backbone
Out[62]:
True
In [63]:
ag.backbone in ag.protein
Out[63]:
True
In [64]:
ag.water in ag.protein
Out[64]:
False
In [65]:
ag.water in ag
Out[65]:
True

Selection operations¶

You can use bitwise operations on selections as follows:

In [66]:
chA = ag.chain_A
chB = ag.chain_B
In [67]:
print(chA & chB) # intersection

None
In [68]:
sel = chA | chB # union
In [69]:
sel.getSelstr()
Out[69]:
'(chain A) or (chain B)'
In [70]:
~chA #not
Out[70]:
<Selection: 'not (chain A)' from 1vrt (3461 atoms)>

Store Data in AtomGroup¶

You can store arbitrary atomic data in AtomGroup class and make it persistent on disk:

In [71]:
atoms = parsePDB('1p38')
atoms.getResnums()

@> PDB file is found in working directory (1p38.pdb.gz).
@> 2962 atoms and 1 coordinate set(s) were parsed in 0.03s.
Out[71]:
array([  4,   4,   4, ..., 771, 773, 776])
In [72]:
resnum_fract = atoms.getResnums() / 10.
resnum_fract
Out[72]:
array([ 0.4,  0.4,  0.4, ..., 77.1, 77.3, 77.6])
In [73]:
atoms.setData('resnumfract', resnum_fract)
atoms.getData('resnumfract')
Out[73]:
array([ 0.4,  0.4,  0.4, ..., 77.1, 77.3, 77.6])

Saving to Files¶

In [74]:
saveAtoms(atoms)
Out[74]:
'1p38.ag.npz'
In [75]:
atoms = loadAtoms('1p38.ag.npz')
atoms.getData('resnumfract')

@> Atom group was loaded in 0.03s.
Out[75]:
array([ 0.4,  0.4,  0.4, ..., 77.1, 77.3, 77.6])

PDB Access¶

Fetch PDB files¶

Can request multiple files at once. Will download to local directory.

In [76]:
fetchPDB('1p38', '1r39', '@!~#') # searches working directory, local resources, then downloads

@> WARNING '@!~#' is not a valid identifier.
Out[76]:
['1p38.pdb.gz', '1r39.pdb.gz', None]
In [77]:
fetchPDBviaHTTP('1p38')
fetchPDBviaFTP('1p38')

@> 1p38 downloaded (C:\Users\mertg\...\1p38.pdb.gz)
@> PDB download via HTTP completed (1 downloaded, 0 failed).
@> Connecting wwPDB FTP server RCSB PDB (USA).
@> pdb1p38.ent.gz download failed. 1p38 does not exist on ftp.wwpdb.org.
@> PDB download via FTP completed (0 downloaded, 1 failed).

Comparing and Aligning Structures¶

In [78]:
p38 = parsePDB('1p38')
bound = parsePDB('1zz2')

@> PDB file is found in working directory (1p38.pdb.gz).
@> 2962 atoms and 1 coordinate set(s) were parsed in 0.03s.
@> PDB file is found in working directory (1zz2.pdb.gz).
@> 2872 atoms and 1 coordinate set(s) were parsed in 0.02s.
In [79]:
showProtein(p38, bound)

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
jupyter labextension install jupyterlab_3dmol

Out[79]:
<py3Dmol.view at 0x16c0003f0a0>

Chain matching and RMSD¶

matchChains tries to match chains by sequence. Returns a list of all pairwise matches

In [80]:
apo_chA, bnd_chA, seqid, overlap = matchChains(p38, bound)[0]
print(bnd_chA)
print(seqid)
print(overlap)

@> WARNING no one-letter mapping found for <Residue: HOH 500 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 501 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 502 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 503 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 504 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 505 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 506 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 507 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 508 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 509 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 510 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 511 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 512 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 513 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 514 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 515 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 516 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 517 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 518 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 519 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 520 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 521 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 522 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 523 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 524 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 525 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 526 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 527 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 528 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 529 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 530 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 531 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 532 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 533 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 534 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 535 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 536 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 537 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 538 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 539 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 540 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 541 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 542 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 543 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 544 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 545 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 546 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 547 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 548 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 549 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 550 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 551 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 552 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 553 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 554 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 555 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 556 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 557 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 558 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 559 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 560 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 561 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 562 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 563 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 564 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 565 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 566 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 567 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 568 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 569 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 570 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 571 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 572 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 573 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 574 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 575 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 576 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 577 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 578 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 579 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 580 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 581 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 582 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 583 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 584 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 585 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 700 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 701 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 705 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 708 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 710 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 711 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 713 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 716 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 717 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 718 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 719 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 720 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 724 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 728 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 729 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 731 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 732 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 733 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 739 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 741 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 742 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 743 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 745 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 746 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 747 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 748 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 751 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 752 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 756 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 757 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 758 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 759 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 761 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 762 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 763 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 764 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 765 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 766 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 767 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 769 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 771 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 773 from Chain A from 1p38 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 776 from Chain A from 1p38 (1 atoms)> 
@> Checking AtomGroup 1p38: 1 chains are identified
@> WARNING no one-letter mapping found for <Residue: BOG 361 from Chain A from 1zz2 (20 atoms)> 
@> WARNING no one-letter mapping found for <Residue: B11 362 from Chain A from 1zz2 (33 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 363 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 364 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 365 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 366 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 367 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 368 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 369 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 370 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 371 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 372 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 373 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 374 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 375 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 376 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 377 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 378 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 379 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 380 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 381 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 382 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 383 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 384 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 385 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 386 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 387 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 388 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 389 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 390 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 391 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 392 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 393 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 394 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 395 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 396 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 397 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 398 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 399 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 400 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 401 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 402 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 403 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 404 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 405 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 406 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 407 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 408 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 409 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 410 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 411 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 412 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 413 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 414 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 415 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 416 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 417 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 418 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 419 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 420 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 421 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 422 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 423 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 424 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 425 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 426 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 427 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 428 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 429 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 430 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 431 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 432 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 433 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 434 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 435 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 436 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 437 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 438 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 439 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 440 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 441 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 442 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 443 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 444 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 445 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 446 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 447 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 448 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 449 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 450 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 451 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 452 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 453 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 454 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 455 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 456 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 457 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 458 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 459 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 460 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 461 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 462 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 463 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 464 from Chain A from 1zz2 (1 atoms)> 
@> WARNING no one-letter mapping found for <Residue: HOH 465 from Chain A from 1zz2 (1 atoms)> 
@> Checking AtomGroup 1zz2: 1 chains are identified
@> Trying to match chains based on residue numbers and names:
@>   Comparing Chain A from 1p38 (len=480) and Chain A from 1zz2 (len=442):
@> 	Failed to match chains (seqid=76%, overlap=70%).
@> Trying to match chains based on local sequence alignment:
@>  Comparing Chain A from 1p38 (len=480) and Chain A from 1zz2 (len=442):
@> 	Match: 442 residues match with 100% sequence identity and 92% overlap.

AtomMap Chain A from 1zz2 -> Chain A from 1p38
99.5475113122172
92.08333333333333

Match is alpha carbon only

In [81]:
print(len(apo_chA),len(bnd_chA),len(p38),len(bound))

337 337 2962 2872
In [82]:
set(apo_chA.getNames())
Out[82]:
{'CA'}
In [83]:
calcRMSD(apo_chA, bnd_chA)
Out[83]:
72.93023086946586

Align chains¶

superpose(mobile, target)

  • Finds minimal RMSD pose of mobile with respect to target
In [84]:
bnd_chA, transformation = superpose(bnd_chA, apo_chA)
calcRMSD(bnd_chA, apo_chA)

@> WARNING mobile is an AtomMap instance, consider assign weights=mobile.getFlags("mapped") if there are dummy atoms in mobile
@> WARNING target is an AtomMap instance, consider assign weights=target.getFlags("mapped") if there are dummy atoms in target
Out[84]:
1.862801490869549
In [85]:
showProtein(p38, bound)

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
jupyter labextension install jupyterlab_3dmol

Out[85]:
<py3Dmol.view at 0x16c7d3e1f10>

Building Biomolecules¶

PDB files often contain monomer coordinates, when the structure of the multimer can be obtained using symmetry operations. Let’s use some ProDy function to build tetrameric form of KcsA potassium channel:

In [86]:
# parse the monomer structure and PDB file header information
# the header includes transformations for forming tetramer
monomer, header = parsePDB('1k4c', header=True)
monomer

@> PDB file is found in working directory (1k4c.pdb.gz).
@> 4534 atoms and 1 coordinate set(s) were parsed in 0.04s.
Out[86]:
<AtomGroup: 1k4c (4534 atoms)>
In [87]:
showProtein(monomer, legend=True)

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
jupyter labextension install jupyterlab_3dmol

Out[87]:
<py3Dmol.view at 0x16c7d3fd9d0>

Building Biomolecules¶

In [88]:
without_K = monomer.not_name_K
without_K
Out[88]:
<Selection: 'not name K' from 1k4c (4527 atoms)>
In [89]:
tetramer = buildBiomolecules(header, without_K)
tetramer
Out[89]:
<AtomGroup: 1k4c Selection 'not name K' biomolecule 1 (18108 atoms)>
In [90]:
showProtein(tetramer)

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
jupyter labextension install jupyterlab_3dmol

Out[90]:
<py3Dmol.view at 0x16c7d344fa0>
In [ ]: