Add protonation modification ASPprot, GLUprot, HISprot1 and HISprot2 … #59
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…in mon_lib_list.cif
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Did you do any test (hydrogen generation, refinement etc) using this? Please update links_and_mods.cif as well, by doing See #49 for details. |
…in links_and_mods.cif
keitaroyam
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keitaroyam
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I think modifications should be minimum. Please see specific comments.
(Changes should be made in list/mon_lib_list.cif and then copied to links_and_mods.cif)
links_and_mods.cif
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| ASPprot change CA CB CG OD1 chi2 180.000 20.0 6 | ||
| ASPprot change O C CA N sp2_sp3_1 0.000 20.0 6 |
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These changes are irrelevant and may be removed.
links_and_mods.cif
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| GLUprot change CB CG CD OE1 chi3 180.000 20.0 6 | ||
| GLUprot change O C CA N sp2_sp3_1 0.000 20.0 6 |
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These changes are unnecessary
links_and_mods.cif
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| loop_ | ||
| _chem_mod_tor.mod_id | ||
| _chem_mod_tor.function | ||
| _chem_mod_tor.atom_id_1 | ||
| _chem_mod_tor.atom_id_2 | ||
| _chem_mod_tor.atom_id_3 | ||
| _chem_mod_tor.atom_id_4 | ||
| _chem_mod_tor.id | ||
| _chem_mod_tor.new_value_angle | ||
| _chem_mod_tor.new_value_angle_esd | ||
| _chem_mod_tor.new_period | ||
| HISprot1 change CA CB CG CD2 chi2 90.000 20.0 6 | ||
| HISprot1 change O C CA N sp2_sp3_1 0.000 20.0 6 | ||
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links_and_mods.cif
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| loop_ | ||
| _chem_mod_tor.mod_id | ||
| _chem_mod_tor.function | ||
| _chem_mod_tor.atom_id_1 | ||
| _chem_mod_tor.atom_id_2 | ||
| _chem_mod_tor.atom_id_3 | ||
| _chem_mod_tor.atom_id_4 | ||
| _chem_mod_tor.id | ||
| _chem_mod_tor.new_value_angle | ||
| _chem_mod_tor.new_value_angle_esd | ||
| _chem_mod_tor.new_period | ||
| HISprot2 change CA CB CG CD2 chi2 90.000 20.0 6 | ||
| HISprot2 change O C CA N sp2_sp3_1 0.000 20.0 6 | ||
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Has anybody tested this? |
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I did for neutron.
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On 11 Feb 2025, at 15:04, GaribMurshudov ***@***.***> wrote:
Has anybody tested this?
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Have we addressed concerns raised by Keitaro? I guess @flong-mrc might need to look into this |
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OK, I manually removed the unnecessary torsion angle changes. We can merge this if you are happy with it. Acedrg may be updated later. |
GaribMurshudov
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GaribMurshudov
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I hope these were tested.
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mon_lib_list.cif