Talk:Ramachandran plot

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Molecular Biology: MCB

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OMEGA misdefined[edit]

In the first figure, Omega is shown for residue i-1. It should be shown above phi, on the next C-N bond, not where it is now. I cite Ramachandran, 1968 -- [[1]] Hansonrstolaf (talk) 17:43, 17 June 2012 (UTC)[reply]

free software[edit]

Someone please add a list of (free) software that can calculate the Ramachandran plot for a given PDB (or whatever) file. Smoe

I added a link to this page: http://www.fos.su.se/~pdbdna/input_Raman.html --Sven.hovmoeller (talk) 18:29, 4 March 2009 (UTC)[reply]

I note that Jmol does this. Hansonrstolaf (talk) 17:43, 17 June 2012 (UTC)[reply]

plot[edit]

Please, someone do the plot again, axis title and values are missing !! Currently the plot does not help for much

introductory info[edit]

Please someone define psi.

This article doesn't really address anything useful... I still have no idea how a Ramachandran plot is obtained or why. Please add some introductory information, or link to articles with appropriate background. 128.148.31.211 (talk) 17:36, 2 December 2008 (UTC)jbk[reply]

Can someone kwnoledgable indicates what are Phi and Psy angle are. Preferably with a drawing. AlainD (talk) 15:08, 20 August 200

I agree, this article is deeply flawed because the introduction immeditely starts out in technical jargon whose terms are not defined. It needs a plain english language introduction before jumping into greek (literally and figuratively). See comments below (Initial Rework of Page). Lapabc (talk) 13:56, 9 August 2011 (UTC)[reply]

Brackets[edit]

Opera does not render the equation. This article needs to be rewritten it is unstructured... —Preceding unsigned comment added by 76.28.6.229 (talk) 23:14, 30 July 2008 (UTC)[reply]

My browser (Firefox) shows all the brackets in the math formula facing right (as opening, or left, square brackets), though the source seems to indicate that they should be paired. D021317c 04:18, 1 October 2007 (UTC)[reply]

It's supposed to be like that: pi is excluded because it is identified with -pi. Remember these are angles! Tomixdf 06:06, 1 October 2007 (UTC)[reply]

I've switched that notation to the standard ) notation as this is clearer. http://en.wikipedia.org/wiki/Interval_%28mathematics%29 —Preceding unsigned comment added by Indiedan (talk • contribs) 14:18, 19 October 2007 (UTC)[reply]

This article needs more background and explanation. —Preceding unsigned comment added by 76.28.6.229 (talk) 17:18, 5 April 2008 (UTC)[reply]

How can i calculate the amino acids present seperately in all 4 areas of ramachandran plot?[edit]

Please some one add the procedure to calculate the amino acids present in different areas of ramachandran plot and also tell the criteria of amino acids to be in defferent areas of plot. thanks —Preceding unsigned comment added by 111.68.111.82 (talk) 10:31, 14 March 2011 (UTC)[reply]

Initial Rework of this page[edit]

I've started on a rework that tries to address the many very good points about what was incomplete or misleading in the earlier version.Dcrjsr (talk) 20:14, 15 May 2011 (UTC)[reply]

Improved inline citations and added generic reference. Also reorganized to add subheadings. Dcrjsr (talk) 18:37, 20 May 2011 (UTC)[reply]

As stated previously, this article needs a non-technical, jargon-free introductory paragraph. Then let the technical discussion flow. Further, there should NEVER be a refernce embedded in the text. This article contained references embedded in each of the first four sentences, making it even harder for people to cut through the jargon. (I corrected this problem and changed them to citations with the references showing up in... the Reference Section) Lapabc (talk) 14:09, 9 August 2011 (UTC)[reply]

I do not know where to add this, but the picture of the definitions Psi and Phi (and Omega) consists of one too many C(+1) atoms. One should be replaced be the correct C(-1) atom.

How is the values of Phy and Psy dihedral angle being counted?[edit]

Please clarify how the zero value, positive and negative values of phy and psy are being calculated? Where is the frame of reference? Which way I have to look at the atoms to count the dihedral angles? We need at least four atoms to define a dihedral angle. Which four atoms we are using for phy? and which four atoms for psy? and from which orientation we have to look at the structure to count the positive or negative sense of phy and psy? can anybody please clear these things up? 2409:4060:11E:BADD:0:0:1430:F0AC (talk) 14:59, 26 April 2021 (UTC)[reply]