many attached hydrogens are included in backbone. From the code....
Where should the nucleic acid backbone atoms stop?
Bob
// everything from here on is backbone
// protein backbone
//
"OXT", // 64 - second carbonyl oxygen, C-terminus only
// protein backbone hydrogens
//
"H", // 65 - amino hydrogen
// these appear on the N-terminus end of 1ALE & 1LCD
"1H", // 66 - N-terminus hydrogen
"2H", // 67 - second N-terminus Hydrogen
"3H", // 68 - third N-terminus Hydrogen
"HA", // 69 - H on alpha carbon
"1HA", // 70 - H on alpha carbon in Gly only
"2HA", // 71 - 1ALE calls the two GLY hdrogens 1HA & 2HA
// Terminal nuclic acid
"H5T", // 72 - 5' terminus hydrogen which replaces P + O1P + O2P
"O5T", // 73 - 5' terminus oxygen which replaces P + O1P + O2P
"O1P", // 74 - first equivalent oxygen on phosphorus of phosphate
"OP1", // 75 - first equivalent oxygen on phosphorus of phosphate --
new designation
"O2P", // 76 - second equivalent oxygen on phosphorus of phosphate
"OP2", // 77 - second equivalent oxygen on phosphorus of phosphate
-- new designation
"O4'", // 78 - sugar ring 4' oxygen ... not present in +T ... maybe
others
"O2'", // 79 - sugar 2' oxygen, unique to RNA
// nucleic acid backbone hydrogens
//
"1H5'", // 80 - first equivalent H on sugar 5' carbon
"2H5'", // 81 - second equivalent H on sugar 5' carbon
"H4'", // 82 - H on sugar ring 4' carbon
"H3'", // 83 - H on sugar ring 3' carbon
"1H2'", // 84 - first equivalent H on sugar ring 2' carbon
"2H2'", // 85 - second equivalent H on sugar ring 2' carbon
"2HO'", // 86 - H on sugar 2' oxygen, unique to RNA
"H1'", // 87 - H on sugar ring 1' carbon
"H3T", // 88 - 3' terminus hydrogen
// add as many as necessary
"HO3'", // 89 - 3' terminus hydrogen (new)
"HO5'", // 90 - 5' terminus hydrogen (new)
"HA2",
"HA3",
"HA2",
"H1",
"H2",
"H3",
"H5'",
"H5''",
"H2'",
"H2''",
"HO2'",
Frieda Reichsman wrote:
>On Jun 12, 2008, at 9:38 AM, Sérgio Ceroni da Silva wrote:
>
>
>
>>I think there is a bug in 11.5.38 and 11.5.39 (not sure when it
>>started,
>>but old versions didn't have it):
>>using "select dna and backbone" selects also some H from the DNA
>>bases.
>>Tested on 1CGP, 1JVE, 1Z04.
>>
>>
>>
>
>I have seen some similar, strange behavior with hydrogens and DNA
>bases vs. backbone, making it very difficult to work with the
>structure. I assumed that the PDB files I was using were not correctly
>naming the hydrogen atoms, but I'm not sure. Bob, I can send files if
>that would be helpful.
>
>Frieda
>
>
>//////////////////////////////////////
>
>Frieda Reichsman, PhD
>Molecules in Motion
>Interactive Molecular Structures
>http://www.moleculesinmotion.com
>413-253-2405
>
>//////////////////////////////////////
>
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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