How can I use the selection matrix in Pymol to select atoms by their number within a cofactor?

05 December 2020 2 5K Report

I work with photochemical reaction centers (like Photosystems I & II) and it can be helpful to use PyMol to create useful pictures of them. With these proteins, the chlorophylls do all the work, so it is often these cofactors that are the center of attention. However, chlorophylls have lengthy phytyl tails that can make these depictions crowded, so scientists will selectively remove these tails in PyMol and opt for a depiction that only shows the porphyrin ring/ central Mg atom.

I'm having trouble selecting the atoms I want to remove from these cofactors and hiding them. I recall a coworker selecting the atoms within a cofactor by number but I cannot remember how he did it. I need to be able to do this with all the chlorophylls in the protein (there are ~60) so I can't do them 1 at a time. I need to write script. Unfortunately, I am very new to using PyMol. Help!

Martin Klvana

cmd.select("idx. 1") # selects atom with index 1

cmd.hide("everything", "sele") # hides the selected atom with index 1

Annemarie Honegger

An example: I load the Structure of the green algal photosystem I supercomplex with light-harvesting complex I 6JO6, full of chlorophyll groups:

fetch 6JO6

color white, organic

by clicking on one of the many ligands in the complex, I learn which atom I hit:

/6JO6/JH/8/CLA`616/C2B, this is short for /object/segment/chain/resn`resi/name

by "select sele, resn CLA" I select all ligands of the type CLA (CHLOROPHYLL A)

by "select sele, resn CLA and resi 616 and chain '8'" I select only the one i initially clicked on.

by "hide everything, not sele", you hide everything except your selection

You might actually name that selection something different, zB "myCLA", so it will not get overwritten whsn you select something else:

select myCLA, resn CLA and resi 616 and chain '8'

In this particular Chlorophyll, the tail was not resolved. you might instead look at

/6JO6/PH/Z/CLA`602/C12

here, I copy the group into a separate object: chloroA

create chloroA, /6JO6/PH/Z/CLA`602/

you can now hide 6JO6 and remove or hide any atoms you do not want to see from object chloroA, without altering the original object

What is the best way to keep an anaerobic chamber anoxic in the absence of hydrogen?

How to analyze a particular region of my simulation box in GROMACS?

How do I increase the yield of my PCR product?

Is There Any Feasible Method To Test Fluorescent Compounds Other Than Fluorescence Spectrometers ??

How to repeat an operation on an atom selection for multiple times in PyMol?

Why almost every element would be metallized in sufficiently high pressure and low temperature?

PACYC PCR not working after several attempts. Would anyone have any suggestions?

How to address this issue in the analysis of Real-Time PCR results?

Runs of nucleotides in Sanger sequencing?

Can thermal cycler machines be problematic during PCR?

Calculating volume of DNA required from DNA concentration?