środa, 20 grudnia 2017

Thesis stuff - PyMOL - how to remove alternative conformation; renumbering, measuring distances with 2 decimals

I'm wondering if I should start a new blog, thesis related.. And written in English. Should I? Or can I still keep everything here? Will it be messy?

Sometimes I'm googling stuff. How to do something.. And I'm forgetting then. Or writing on paper. But better to keep it on-line, so other googlers can find it, too ;) Thanks for http://randomthesisstuff.blogspot.co.uk/ useful! Another great one - http://www.keepcalmandpublishpapers.com/

So PyMOL, alternative conformation. It makes messy some of my calculations to keep alternative conformations, so to remove it, simply type:

PyMOL>remove not (alt ''+A)
PyMOL>alter all, alt=''

But it's choosing conformation A, not that with higher occupancy!

See here - https://pymolwiki.org/index.php/Property_Selectors#Alternate_Locations

Alternatively in Phenix - Model tools - pdb tools - options - remove alternate conformers, but it gave me the same output as PyMOL, conformation A, not higher occupancy.

You can do it in Coot, but then (probably?) have to go from residue to residue (with double occupancy), I didn't find how to do it for whole structure.

Extensions - Modelling - Residues with Alt Confs... (will show you which residues have alternative conformations)

Then you can go:

Edit - Residue Info - in the first column after residue name it shows occupancy. I deleted one with lower occupancy (by delete residue/monomer).

Coming back to PyMOL.

Another thing - renumbering. When your pdb starts not from one. Example - when it starts at 51:

alter name_of_pdb, resi=str(int(resi)-50)

it will subtract 50 from all residues, so will starts at 1 instead of 51.

See here - https://pymolwiki.org/index.php?title=Alter&redirect=no#Renumber_the_amino_acids_in_a_protein.2C_so_that_it_starts_from_0_instead_of_its_offset_as_defined_in_the_structure_file

How to measure a distance?
Go to wizard->measuring

It's set to show just 1 decimal, if you want to see two, then:

set label_distance_digits, 2

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