Talk:Root mean square deviation of atomic positions

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I think this topic is misnamed as a use of RMSD, when actually it covers the specific topic of Macromolecular structure alignment. RMSD is and can be used for several other applications in bioinformatics, such as X-ray diffraction data, CryoEM image comparison, seqeunce alignments, and proteomics, because it is such a general tool. The current title implies it is some ultra-important use of the RMSD, when it really is not. --vossman 20:57, 20 May 2007 (UTC)

• Do you have any specific suggestions on how to improve this article? I am in favour of moving most of the material to the new article, "Macromolecular structure alignment", but I wish to make sure the information currently in this article is not lost along the way. RMSD for structure alignment is an "ultra-important" use in the field. I know, I use it everyday. --Thorwald 23:19, 7 June 2007 (UTC)

Looking for tools?

Where are they? --141.14.26.125 16:42, 31 October 2007 (UTC)

Move it or merge it?

The 2007 discussion above on this fizzled. The topic seems important, but there's already an article on root-mean-square deviation, and this application in bioinformatics should be named for the application, not for the generic technique used. Move it? Merge it some place? Any bioinformatics people listening? Dicklyon (talk) 03:33, 5 November 2011 (UTC)

RMSD described in this article is different than the generic root-mean-square deviation in that optimal translation and rotation, and permutation of identical particles, if any, is assumed and must be found by the algorithm that calculates the RMSD. The application is rigid body structural alignment (superposition, actually). A merge into that article may be in order. Olli Niemitalo (talk) 21:26, 28 August 2013 (UTC)

Also molecular dynamics simulations can be analyzed/visualized based on an RMSD matrix that compares the atomic coordinates between simulation frames. That counts as structural superposition but not really as structural alignment, because a perfect alignment is known because it's the same molecule. But I guess it would be OK to wikilink from Molecular dynamics to a subsection on RMSD in Structural alignment. Olli Niemitalo (talk) 07:28, 30 August 2013 (UTC)

Another option is to move to "Root-mean-square deviation of atomic positions" for now, no extra effort required. Will do that. Olli Niemitalo (talk) 06:58, 1 September 2013 (UTC)

Requested move 26 April 2024

The following is a closed discussion of a requested move. Please do not modify it. Subsequent comments should be made in a new section on the talk page. Editors desiring to contest the closing decision should consider a move review after discussing it on the closer's talk page. No further edits should be made to this discussion.

The result of the move request was: moved. (non-admin closure) Safari Scribe^{Edits! Talk!} 15:52, 3 May 2024 (UTC)

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Root-mean-square deviation of atomic positions → Root mean square deviation of atomic positions – The hyphenation in the title appears non-standard for RMSD. A couple of the cites use partial hyphenation, but the consistency doesn't appear there. Engineerchange (talk) 17:04, 26 April 2024 (UTC)

See similar proposed move at Talk:Root-mean-square deviation. Note that root mean square also doesn't have hyphens. --Engineerchange (talk) 17:08, 26 April 2024 (UTC)

Why is it relevant that root mean square doesn't have hyphens? It's not being used as a prepositive modifier (see MOS:HYPHEN #3) in that title. Graham (talk) 01:14, 30 April 2024 (UTC)

• Support. Technically the hyphenated version is more correct in terms of punctuation, but it seems pretty clear by Google ngrams that that spelling is falling out of favour (see here). Though, I do note that even a cursory Google search and search via Google Scholar shows the hyphenated spelling is still used often enough. I don't think describing one as being a 'standard' spelling quite hits the mark. Probably more of a trend away from using hyphens to join descriptive nouns together overall (or whatever this type of hyphenation is called). I'll copy a shorter version of this comment to the other discussion as well. ― Synpath 18:00, 27 April 2024 (UTC)
• Whatever is decided at Talk:Root-mean-square deviation. Graham (talk) 02:52, 28 April 2024 (UTC)

The discussion above is closed. Please do not modify it. Subsequent comments should be made on the appropriate discussion page. No further edits should be made to this discussion.