Missing hydrogens on C5' C in 4fen?

[russell-taylor]

Reduce places a pair of hydrogens on the C atom in C5', but Hydrogenate does not.

[russell-taylor]

Per Jane, the hydrogens should always be placed.

[dcliebschner]

Oddly, I cannot reproduce this. I tried it on residue C of chain B. Can you let me know which residue is missing the pair of hydrogens?

[russell-taylor]

Sorry about that. When I run original and new reduce on 4fen.pdb, reduce places two hydrogens on C5' U B 77 but reduce2 does not. Also C5' G B 78. Also C5' C B 80.

I'll try running the latest version of Hydrogenate to see what it does and let you know.

[russell-taylor]

Trying with mmtbx.hydrogenate from my current build was also missing them. Doing a new pull and build and then redoing just now using the master branch of cctbx_project:

python bootstrap.py --builder=phenix --cciuser=taylorr --use-conda --python=310
mmtbx.hydrogenate D:\data\Richardsons\4fen.pdb

@dcliebschner This still does not add the two hydrogens on C5' C B 80. I attach the hydrogenate PDB and an image showing the centered residue.

4fen_hydrogenate.zip

[dcliebschner]

Thanks, will check.

[dcliebschner]

I still cannot reproduce this. Your attached file has the following atoms for residue name C, residue number 80 in chain B ATOM 2083 P C B 80 -6.055 -3.171 8.370 1.00 45.01 P ATOM 2084 OP1 C B 80 -7.139 -3.998 7.781 1.00 45.23 O ATOM 2085 OP2 C B 80 -6.400 -2.060 9.293 1.00 44.51 O ATOM 2086 O5' C B 80 -5.036 -4.139 9.119 1.00 47.34 O ATOM 2087 C5' C B 80 -4.571 -5.334 8.496 1.00 51.64 C ATOM 2088 C4' C B 80 -3.537 -6.011 9.365 1.00 54.68 C ATOM 2089 O4' C B 80 -2.376 -5.150 9.485 1.00 55.24 O ATOM 2090 C3' C B 80 -3.956 -6.272 10.803 1.00 56.57 C ATOM 2091 O3' C B 80 -4.673 -7.498 10.902 1.00 59.54 O ATOM 2092 C2' C B 80 -2.611 -6.370 11.515 1.00 56.43 C ATOM 2093 O2' C B 80 -2.014 -7.645 11.390 1.00 56.52 O ATOM 2094 C1' C B 80 -1.785 -5.324 10.762 1.00 55.98 C ATOM 2095 N1 C B 80 -1.751 -4.018 11.439 1.00 56.02 N ATOM 2096 C2 C B 80 -0.737 -3.769 12.368 1.00 55.99 C ATOM 2097 O2 C B 80 0.103 -4.654 12.590 1.00 56.26 O ATOM 2098 N3 C B 80 -0.698 -2.574 12.999 1.00 55.93 N ATOM 2099 C4 C B 80 -1.621 -1.647 12.731 1.00 55.90 C ATOM 2100 N4 C B 80 -1.543 -0.482 13.378 1.00 55.65 N ATOM 2101 C5 C B 80 -2.664 -1.875 11.787 1.00 56.04 C ATOM 2102 C6 C B 80 -2.691 -3.063 11.170 1.00 56.02 C ATOM 2103 H4 C B 80 -3.270 -6.850 8.958 1.00 54.68 H ATOM 2104 H3 C B 80 -4.469 -5.523 11.144 1.00 56.57 H ATOM 2105 H2 C B 80 -2.699 -6.139 12.453 1.00 56.43 H ATOM 2106 HO2 C B 80 -1.319 -7.577 10.924 1.00 56.52 H ATOM 2107 H1 C B 80 -0.877 -5.652 10.667 1.00 55.98 H ATOM 2108 H41 C B 80 -0.912 -0.347 13.947 1.00 55.65 H ATOM 2109 H42 C B 80 -2.124 0.134 13.226 1.00 55.65 H ATOM 2110 H5 C B 80 -3.302 -1.223 11.606 1.00 56.04 H ATOM 2111 H51 C B 80 -4.177 -5.116 7.637 1.00 51.64 H ATOM 2112 H5*2 C B 80 -5.319 -5.936 8.357 1.00 51.64 H ATOM 2113 H6 C B 80 -3.360 -3.241 10.549 1.00 56.02 H

Notably, there are atoms H51 and H52, which are attached to C5'.

Could it be a naming issue? Reduce calls the newly placed H atoms H5' and H5''. Are you using King for the display? Possibly it does not display H atoms with * in it?

[dcliebschner]

Markup changed a bit the lines which stars.

[russell-taylor]

Wow! Sure enough, when I rename them to H5' and H5* they show up in KiNG. Sorry for sending you on this wild goose chase!

[russell-taylor]

Per Jane, the names given by Hydrogenate are very old and no longer valid. Reopening so that the naming issue can be dealt with.