Jump to content
Main menu
Main menu
move to sidebar
hide
Navigation
Main page
Recent changes
Random page
Help
Special pages
SBGrid Resources
SBGrid Consortium
SBGrid Data Bank
Software Webinars
PyMOL Webinar
PyMOL Wiki
Search
Search
Appearance
Create account
Log in
Personal tools
Create account
Log in
Pages for logged out editors
learn more
Contributions
Talk
Editing
RmsdByResidue
(section)
Page
Discussion
English
Read
Edit
View history
Tools
Tools
move to sidebar
hide
Actions
Read
Edit
View history
General
What links here
Related changes
Page information
Appearance
move to sidebar
hide
Warning:
You are not logged in. Your IP address will be publicly visible if you make any edits. If you
log in
or
create an account
, your edits will be attributed to your username, along with other benefits.
Anti-spam check. Do
not
fill this in!
== Introduction == RMSD between two structures of the same protein. The concept is similar as RMSF between two structures. *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 *Reference **https://sourceforge.net/p/pymol/mailman/message/32710889/
Summary:
Please note that all contributions to PyMOL Wiki are considered to be released under the GNU Free Documentation License 1.2 (see
PyMOL Wiki:Copyrights
for details). If you do not want your writing to be edited mercilessly and redistributed at will, then do not submit it here.
You are also promising us that you wrote this yourself, or copied it from a public domain or similar free resource.
Do not submit copyrighted work without permission!
Cancel
Editing help
(opens in new window)
Search
Search
Editing
RmsdByResidue
(section)
Add topic