Question: How to calculate the center of mass
0
gravatar for M.O.L.S
4 days ago by
M.O.L.S10
M.O.L.S10 wrote:

Please can I have some ideas as I just don't get it. We usually come here, after countless Google searches, not as a first resort =)

What is the center of mass of an atomic coordinate of protein? I'd like to program it using biopython

Is there a formula for it? Why is this important? How is it related to the mean?

ADD COMMENTlink modified 4 days ago • written 4 days ago by M.O.L.S10

How is this related to bioinformatics?

ADD REPLYlink written 4 days ago by Kevin Blighe53k

As posed, the question is not related to bioinformatics.

A simple Google search returns plenty of info, especially when the interest appears to be general.

ADD REPLYlink written 4 days ago by Mensur Dlakic2.9k

Yes, the interest is general, but I don't think the knowledge is. I could be wrong.

ADD REPLYlink written 4 days ago by M.O.L.S10

Just out of interest: how is something involving "atomic coordinate of protein" not related to bioinformatics? This is only the case if you ignore the whole field of structural bioinformatics. Even if its golden era is over [or maybe it isn't, I have not worked in it for a while], it is still a valid and somewhat active field. Not everything is genomics/transcriptomics.

Had OP written "center of mass of atomic coordinate", i.e. without explicitly mentioning protein, it could be a cheminformatics question, but I'd still have given that the benefit of the doubt...

ADD REPLYlink written 4 days ago by cschu1811.9k

The original question has been edited.

ADD REPLYlink modified 3 days ago • written 4 days ago by Kevin Blighe53k

Hm, ok. What I don't like, though, is it just says modified, which might be anything really. Maybe there should be a way to see the original pre-modified version or editing should not be possible or ... I mean, right now it looks as if someone posed a perfectly legit question only to be jumped on by a power user/mod. [It looks like this, not saying this is how it is.]

Edit: added missing "if" to "as if"

ADD REPLYlink modified 3 days ago • written 3 days ago by cschu1811.9k

Oh yeh I know - the forum system is not the greatest.

ADD REPLYlink written 3 days ago by Kevin Blighe53k

I think it is the set up for the Kabsch Algorithm or the orthogonal Procrustes problem. Is the centroid and the center of mass the same thing?

ADD REPLYlink modified 4 days ago • written 4 days ago by M.O.L.S10

With all due respect, I am not convinced that you have done countless Google searches. A single Google search with "center of mass protein biopython" returned this as a first hit. There is a section "Coarse Grain Structure" towards the end that shows a simple Biopython solution:

from Bio.Struct.Geometry import center_of_mass
ADD REPLYlink written 4 days ago by Mensur Dlakic2.9k
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