20. The RMSD value can be improved by either improving the
quality of the restraints (i.e., additional experimental information), or by fine tuning the sampling parameters. The number
of iterations can also be increased to maximize the search space
of the program.
4 Notes
1. A comprehensive PyMOL tutorial can be found at: https://
www.mrc-lmb.cam.ac.uk/rlw/text/MacPyMOL_tutorial.
html.
2. The sequence of the protein can be edited using PyMOL
through the command:
alter, resv += X
where should be modified to reflect the object
or chain to be altered, and the plus sign should be swapped to
minus if X is to be deducted from the sequence number. When
using this command, can refer to any selection,
e.g. the object name, segment ID, chain ID or the currently
highlighted selection. For more information, consult the
PyMOL documentation for the Alter command (https://
pymolwiki.org/index.php?title¼Alter&redirect¼no).
3. For cross-linking modeling, residues will need to have the atom
that will be involved in distance measurements. For example,
LYS-LYS cross-links can be measured from Cα, Cβ, or Nζ
atoms. If using the sidechain amide Nζ atom, you will need
to have this atom included in all sidechain models. The Mutagenesis tool of PyMOL can be used to quickly regenerate all
sidechain atoms, swap between common sidechain rotamers or
switch residue types (https://pymolwiki.org/index.php/
Mutagenesis).
4. FASTA is a text-based format for displaying sequence information of proteins or nucleotides (see also https://zhanglab.ccmb.
med.umich.edu/FASTA/). In PyMOL, you can save the
sequence information in FASTA format for any object or selection using the “save” command (https://pymolwiki.org/
index.php/Save).
5. T-Coffee is a quick and easy-to-use multiple sequence alignment tool [46]. A tutorial is available on the webserver website
at: http://tcoffee.crg.cat/apps/tcoffee/tutorial.html.
6. Homology modeling can be performed using the MODELLER software [47]. A detailed tutorial can be found at: https://
salilab.org/modeller/tutorial/.
Mass Spectrometry-Based Protein Modelling
237
quality of the restraints (i.e., additional experimental information), or by fine tuning the sampling parameters. The number
of iterations can also be increased to maximize the search space
of the program.
4 Notes
1. A comprehensive PyMOL tutorial can be found at: https://
www.mrc-lmb.cam.ac.uk/rlw/text/MacPyMOL_tutorial.
html.
2. The sequence of the protein can be edited using PyMOL
through the command:
alter
where
or chain to be altered, and the plus sign should be swapped to
minus if X is to be deducted from the sequence number. When
using this command,
e.g. the object name, segment ID, chain ID or the currently
highlighted selection. For more information, consult the
PyMOL documentation for the Alter command (https://
pymolwiki.org/index.php?title¼Alter&redirect¼no).
3. For cross-linking modeling, residues will need to have the atom
that will be involved in distance measurements. For example,
LYS-LYS cross-links can be measured from Cα, Cβ, or Nζ
atoms. If using the sidechain amide Nζ atom, you will need
to have this atom included in all sidechain models. The Mutagenesis tool of PyMOL can be used to quickly regenerate all
sidechain atoms, swap between common sidechain rotamers or
switch residue types (https://pymolwiki.org/index.php/
Mutagenesis).
4. FASTA is a text-based format for displaying sequence information of proteins or nucleotides (see also https://zhanglab.ccmb.
med.umich.edu/FASTA/). In PyMOL, you can save the
sequence information in FASTA format for any object or selection using the “save” command (https://pymolwiki.org/
index.php/Save).
5. T-Coffee is a quick and easy-to-use multiple sequence alignment tool [46]. A tutorial is available on the webserver website
at: http://tcoffee.crg.cat/apps/tcoffee/tutorial.html.
6. Homology modeling can be performed using the MODELLER software [47]. A detailed tutorial can be found at: https://
salilab.org/modeller/tutorial/.
Mass Spectrometry-Based Protein Modelling
237