From: Timothy D. <mol...@ma...> - 2006-09-21 17:02:05
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On Sep 21, 2006, at 4:52 AM, Annemarie Honegger wrote: >> Date: Tue, 19 Sep 2006 20:43:58 -0400 >> From: Eric Martz <em...@mi...> >> Subject: [Jmol-users] Lots of bugs in Jmol: fix some before v11? >> >> Some standard amino acids are not included in protein. > > I agree with Eric that frequently found postranslational > modifications such as phosphorylations > and substitutions introduced to facilitate phasing such as > Selenomethioneine in place of > Methioneine should not prevent an amino acid from being treated as > part of a protein. > I do not have a comprehensive list, but the ones that come to my mind > are: > > MSE Selenomethionine > CSE Selenocysteine > PTR Phosphotyrosine > SEP Phosphoserine > TPO Phosphothreonine > HYP 4-hydroxyproline > 5HP Pyroglutamic acid; 5-hydroxyproline > PCA Pyroglutamic Acid > LYZ 5-hydroxylysine > GLX Glu or Gln > ASX Asp or Asn > GLA gamma-carboxy-glutamic acid > if I recall correctly, Jmol does not use the group name to determine membership in the pre-defined set 'protein.' it uses a minimum set of atoms (i.e., N, C, O, CA). so as long as modified residues still use the standard nomenclature for backbone atoms, they should be included in 'protein' already. is this not happening? or am I wrong about Jmol's behavior here? best, tim -- Timothy Driscoll em: mo...@vb... Virginia Bioinformatics Institute ph: 540-231-3007 Bioinformatics I: M-1 im: molvisions Washington St., Blacksburg, VA 24061 "Anyone who considers arithmetical methods of producing random digits is, of course, in a state of sin." - J von Neumann |