In PyMol how can I determine:
1) the diameter of a membrane protein at the height of the membrane and/or the area in that plane (so that I can estimate how much space the protein takes in the membrane and how many lipids it displays)
and
2) the distance of a residue (or protein bound metal) to the membrane surface?
Hi Josy,
In PyMol you can go to (in the very top control panel with File, Edit, etc) Wizard -> Measurement. Then a menu will appear below the object window (bottom right ish). You can then click on the button that defaults to "Distances" to change between distances, angles, dihedrals, and more.
1) If you don't need average diameter, just a simple measurement, just take a few distance measurements across the width of the protein. Sometimes it's easiest to use a surface representation to see the most extended regions. If you're looking for more accurate measurements I would use a program that calculates volume/diameter/etc.
2) Simply use Wizard -> Measurement -> Distances. Click on the residue (or metal) and then on an atom in the membrane surface.
Good luck!
Hi Kyle, Thank you for your fast answer! The options you gave I am aware of (and I have done that), but I was looking for a way to do it more precisely. Can you give me some names of programs that could do that? Thanks again!
Hi Josy,
Apologies, I should've just included some programs in the initial answer. One of the better programs (and has a web interface, but requires you register with them) is Crysol.
- Crysol will give you the estimated Radius of Gyration (Rg) of a PDB file. An Rg is a good measure of the compactness of a macromolecule because it is the root mean square distance from each atom of the protein to its centroid. This doesn't require SAXS data, just leave that field blank. (https://www.embl-hamburg.de/biosaxs/crysol.html)
- FOXS - https://modbase.compbio.ucsf.edu/foxs/ (Does almost exactly the same thing as Crysol). This doesn't require SAXS data, so just leave that blank.
- MOLEMAN2 from USF Uppsala Software Factory has a bunch of utilities for investigating properties of PDB files. specifically check out how they calculate Rg's and the other dimensions of a PDB: http://xray.bmc.uu.se/usf/dim_vol_tut.html
- Mol_Volume will calculate the volume of the macromolecule, http://www.ks.uiuc.edu/Development/MDTools/molvolume/
- HydroPro (for hydrodynamic radius) - http://leonardo.inf.um.es/macromol/programs/hydropro/hydropro.htm
- Pymol itself has some utilities for finding surface area I believe.
Hopefully those help!
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