RmsdByResidue - Revision history

Cchem: 1 revision

2018-12-10T03:24:51Z

1 revision

Zhentg: /* Introduction */

2018-11-12T06:32:22Z

Introduction

Cchem: 3 revisions

2016-12-12T03:26:18Z

3 revisions

Zhentg: /* Introduction */

2016-12-09T08:56:47Z

Introduction

Zhentg at 06:47, 8 December 2016

2016-12-08T06:47:11Z

Zhentg at 06:46, 8 December 2016

2016-12-08T06:46:20Z

Cchem: 2 revisions

2016-08-22T02:06:17Z

2 revisions

Zhentg at 08:08, 10 August 2016

2016-08-10T08:08:35Z

Zhentg: Created page with " #load library from pymol import cmd, stored import sys import os #function to judge if a file exists def is_non_zero_file(fpath): return os.path.is..."

2016-08-10T08:06:41Z

Created page with "<source lang="python"> #load library from pymol import cmd, stored import sys import os #function to judge if a file exists def is_non_zero_file(fpath): return os.path.is..."

New page

<source lang="python">
#load library
from pymol import cmd, stored
import sys
import os

#function to judge if a file exists
def is_non_zero_file(fpath):
return os.path.isfile(fpath) and os.path.getsize(fpath) > 0

#function to switch atom names within a residue
def switchName(residueSelection, atomName1, atomName2):
"""
switch the name of two atoms
"""
cmd.alter(residueSelection+" and name "+atomName1, 'name="gzt"')
cmd.alter(residueSelection+" and name "+atomName2, 'name="'+atomName1+'"')
cmd.alter(residueSelection+" and name gzt", 'name="'+atomName2+'"')

#function to change atom names of some residues with symetric sidechain
def flipAtomName(targetResidueSelection):
"""
switch the atom names of specific residues
"""
# Create flipped residue
cmd.create("flippedRes",targetResidueSelection+" and not alt B")
targetResidueCa=cmd.get_model("flippedRes and name CA")
for g in targetResidueCa.atom:
# print g.resn
if g.resn=='ARG':
switchName("flippedRes", "NH1", "NH2")
elif g.resn=='HIS':
switchName("flippedRes", "ND1", "CD2")
switchName("flippedRes", "CE1", "NE2")
elif g.resn=='ASP':
switchName("flippedRes", "OD1", "OD2")
elif g.resn=='PHE':
switchName("flippedRes", "CD1", "CD2")
switchName("flippedRes", "CE1", "CE2")
elif g.resn=='GLN':
switchName("flippedRes", "OE1", "NE2")
elif g.resn=='GLU':
switchName("flippedRes", "OE1", "OE2")
elif g.resn=='LEU':
switchName("flippedRes", "CD1", "CD2")
elif g.resn=='ASN':
switchName("flippedRes", "OD1", "ND2")
elif g.resn=='TYR':
switchName("flippedRes", "CD1", "CD2")
switchName("flippedRes", "CE1", "CE2")
elif g.resn=='VAL':
switchName("flippedRes", "CG1", "CG2")
cmd.sort()
# cmd.label("flippedRes","name")
return "flippedRes"

#main function
def rmsdByRes(referenceProteinChain,sel, targetProteinChain):
"""
Update
Zhenting Gao on 7/28/2016

USAGE

rmsf referenceProteinChain, targetProteinChain, selection [,byres=0], [reference_state=1]

Calculate the RMSD for each residue pairs from two chains of the same protein from two crystal structures.

Workflow
Read reference and target pdb files
Align two structures
sel target, proA and chain A
#define target protein chain
sel refrence, proB and chain A
#define reference protein chain
align target, reference
#automatical alignment
Clean attributes
otherwise rms_cur will fail

"""
# Create temporary objects, exclude alternative conformation B
cmd.create("ref_gzt", referenceProteinChain+" and polymer and not alt B")
cmd.alter("ref_gzt", "chain='A'")
cmd.alter("ref_gzt", "segi=''")
cmd.create("target_gzt", targetProteinChain+" and polymer and not alt B")
cmd.alter("target_gzt", "chain='A'")
cmd.alter("target_gzt", "segi=''")
# cmd.align("target_gzt","ref_gzt",object="align")
# parameters
outputText=""
res2Check=['HIS','ASP','ARG','PHE','GLN','GLU','LEU','ASN','TYR','VAL']

# select alpha carbon of selected residues in reference structure
calpha=cmd.get_model(sel+" and name CA and not alt B")

for g in calpha.atom:
# print g.resi+g.resn
if cmd.count_atoms("ref_gzt and polymer and resi "+g.resi)==cmd.count_atoms("target_gzt and polymer and resi "+g.resi):
rmsdRes=cmd.rms_cur("ref_gzt and polymer and resi "+g.resi,"target_gzt and polymer and resi "+g.resi)
rmsdResCa=cmd.rms_cur("ref_gzt and polymer and resi "+g.resi+" and name ca","target_gzt and polymer and resi "+g.resi+" and name ca")
rmsdResBackbone=cmd.rms_cur("ref_gzt and polymer and resi "+g.resi+" and name ca+n+c+o","target_gzt and polymer and resi "+g.resi+" and name ca+n+c+o")
# calculate minimum rmsd
rmsdResMin=rmsdRes
if g.resn in res2Check:
flippedRes=flipAtomName("target_gzt and polymer and resi "+g.resi)
rmsdFlippedRes=cmd.rms_cur("ref_gzt and polymer and resi "+g.resi,flippedRes)
if rmsdFlippedRes<rmsdRes:
rmsdResMin=rmsdFlippedRes

# print cmd.count_atoms("ref_gzt and polymer and resi "+g.resi),cmd.count_atoms("target_gzt and polymer and resi "+g.resi)
outputText+="%s,%s,%s,%.3f,%.3f,%.3f,%.3f\n" % (targetProteinChain,g.resn,g.resi,rmsdRes,rmsdResCa,rmsdResBackbone,rmsdResMin)

print outputText
# Destroy temporary objects
cmd.delete("ref_gzt target_gzt align res_gzt "+flippedRes)

# Save data into csv
outputFile='rmsdByRes_'+sel+'.csv'
f=open(outputFile,'a')
if not is_non_zero_file(outputFile):
f.write("targe,residueName,residueId,allAtomRMSD,rmsdResCa,rmsdResBackbone,allAtomRMSDMin\n")
f.write(outputText)
f.close()
print "Results saved in "+outputFile

cmd.extend("rmsdByRes",rmsdByRes)

</source>

[[Category:Script Library]]

@@ Line 5: / Line 5: @@
 == Introduction ==
-RMSD between two structures of the same protein
+RMSD between two structures of the same protein. The concept is similar as RMSF between two structures.
 *programming
 **Platform

@@ Line 8: / Line 8: @@
 *programming
 **Platform
-****PyMOL
+***PyMOL
-*****rms_cur
+****rms_cur
 **Feature
 ***Output
-					® RMSD of all atoms of each residues pairs
+****RMSD of all atoms of each residues pairs
-					® Least RMSD of all atoms of each residues pairs
+****Least RMSD of all atoms of each residues pairs
-						◊ symmetry of Phe, Tyr, His, Asp, Glu, Gln, Asn, Arg, Leu and Val needs to be considered
+*****symmetry of Phe, Tyr, His, Asp, Glu, Gln, Asn, Arg, Leu and Val needs to be considered
-							} switch the atom name and then calculate the RMSD again
+******switch the atom name and then calculate the RMSD again
-						◊ Selected least RMSD of a residue pair for report
+******Selected least RMSD of a residue pair for report
-					® RMSD of backbone atoms of each residues pairs
+*******RMSD of backbone atoms of each residues pairs
-					® RMSD of C alpha atoms of each residues pairs
+*******RMSD of C alpha atoms of each residues pairs
-				□ With defined residues pairs
+*****With defined residues pairs
-					® Residue pair can be limited to within binding site
+******Residue pair can be limited to within binding site
-			§ Workflow
+**Workflow
-				□ Read reference and target pdb files
+***Read reference and target pdb files
-					® #two structures should be superposed before using this function
+****two structures should be superposed before using this function
-			§ Note
+*Note
-				□ Python
+**Python
-				□ PyMOL
+**PyMOL
-					® Clean attributes
+***Clean attributes
-						◊ otherwise rms_cur will fail
+****otherwise rms_cur will fail
-					® How to get residue name?
+***How to get residue name?
-						◊ residue name, residue index and etc. can only be read from an atom
+****residue name, residue index and etc. can only be read from an atom
+*Reference
+**https://sourceforge.net/p/pymol/mailman/message/32710889/
 == Usage ==

@@ Line 42: / Line 42: @@
 == Required Arguments ==
-* '''sel1''' = first selection
+Text
 == Optional Arguments ==
-* '''output''' = accepts Screen/Print/None (default N)
+Text
 == Examples ==
-'''example #1'''
+Text
 == The Code ==
 <source lang="python">

← Older revision		Revision as of 06:46, 8 December 2016
Line 1:		Line 1:
		+	{{Infobox script-repo
		+	\|type = script
		+	\|author = [[User:zhentg\|Zhenting Gao]]
		+	}}
		+
		+	== Introduction ==
		+	RMSD between two structures of the same protein
		+	*programming
		+	**Platform
		+	****PyMOL
		+	*****rms_cur
		+	**Feature
		+	***Output
		+	® RMSD of all atoms of each residues pairs
		+	® Least RMSD of all atoms of each residues pairs
		+	◊ symmetry of Phe, Tyr, His, Asp, Glu, Gln, Asn, Arg, Leu and Val needs to be considered
		+	} switch the atom name and then calculate the RMSD again
		+	◊ Selected least RMSD of a residue pair for report
		+	® RMSD of backbone atoms of each residues pairs
		+	® RMSD of C alpha atoms of each residues pairs
		+	□ With defined residues pairs
		+	® Residue pair can be limited to within binding site
		+	§ Workflow
		+	□ Read reference and target pdb files
		+	® #two structures should be superposed before using this function
		+	§ Note
		+	□ Python
		+	□ PyMOL
		+	® Clean attributes
		+	◊ otherwise rms_cur will fail
		+	® How to get residue name?
		+	◊ residue name, residue index and etc. can only be read from an atom
		+
		+
		+
		+	== Usage ==
		+	*Open PyMOL
		+	*Load PDB files
		+	*run this Python script inside PyMOL
		+	*call the function
		+	**rmsdByRes pdb1, resSelection, pdb2
		+
		+	== Required Arguments ==
		+	* '''sel1''' = first selection
		+	* '''sel2''' = second selection
		+	* '''max_dist''' = max distance in Angstroms
		+
		+
		+	== Optional Arguments ==
		+	* '''output''' = accepts Screen/Print/None (default N)
		+	* '''sidechain''' = limits (Y) results to sidechain atoms (default N)
		+	* '''show''' = shows (Y) individual distances in pymol menu (default=N)
		+
		+
		+	== Examples ==
		+	'''example #1'''
		+	<source lang="python">
		+	PyMOL>pairwise_dist 1efa and chain D, 1efa and chain B, 3, output=S, show=Y
		+
		+	1efa/D/DC/13/OP1 to 1efa/B/TYR/47/OH: 2.765
		+	1efa/D/DC/13/OP2 to 1efa/B/LEU/6/N: 2.983
		+	1efa/D/DC/13/OP2 to 1efa/B/LEU/6/CB: 2.928
		+	1efa/D/DT/14/O4' to 1efa/B/ALA/57/CB: 2.827
		+	1efa/D/DT/14/OP1 to 1efa/B/ASN/25/OD1: 2.858
		+	1efa/D/DT/14/OP1 to 1efa/B/GLN/54/NE2: 2.996
		+	1efa/D/DT/14/OP2 to 1efa/B/SER/21/OG: 2.517
		+	1efa/D/DC/15/N4 to 1efa/B/GLN/18/NE2: 2.723
		+	1efa/D/DA/16/N6 to 1efa/B/GLN/18/NE2: 2.931
		+
		+	Number of distances calculated: 9
		+	</source>
		+	== The Code ==
	<source lang="python">		<source lang="python">
	#load library		#load library

← Older revision		Revision as of 08:08, 10 August 2016
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	[[Category:Script Library]]		[[Category:Script Library]]
		+	[[Category:Structural_Biology_Scripts]]
		+	[[Category:Pymol-script-repo]]

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