Dear all,
I am trying to make figures of a peptide nucleic acid, that is, a molecule with protein-like backbone but nucleic acid-like side chain, meaning nucleobases.
I cannot get Pymol to recognize the nucleobase rings as rings fo the cartoon_ring_mode, likely due to a rather unusual nomenclature. I copy a representative segment below. I tried changing the residue names to G and C, but still, no planar rings.
So, what does pymol recognize as a ring, how must I rename the atoms/residues to get the ring representation?
Is it a names problem or rather due to the absence of phophates and riboses?
Any clever fix?
Thanks a lot,
Jose Antonio Cuesta-Seijo.
HETATM 246 N LHC B 24 -5.629 -7.774 0.171 1.00 20.95 N
ANISOU 246 N LHC B 24 1731 3490 2741 -2 -37 9 N
HETATM 247 CA LHC B 24 -4.892 -6.518 0.132 1.00 20.73 C
ANISOU 247 CA LHC B 24 1840 3412 2624 -29 -7 -179 C
HETATM 248 CB LHC B 24 -5.778 -5.347 -0.318 1.00 20.88 C
ANISOU 248 CB LHC B 24 1902 3628 2405 -185 -101 240 C
HETATM 249 CG LHC B 24 -5.093 -4.057 -0.194 1.00 20.00 C
ANISOU 249 CG LHC B 24 1772 3495 2333 -12 43 138 C
HETATM 250 N1 LHC B 24 -5.696 -2.848 -0.740 1.00 20.11 N
ANISOU 250 N1 LHC B 24 1621 3684 2335 -153 47 421 N
HETATM 251 C6 LHC B 24 -5.132 -2.217 -1.840 1.00 20.59 C
ANISOU 251 C6 LHC B 24 1580 4104 2138 -245 -26 397 C
HETATM 252 C5 LHC B 24 -5.630 -1.087 -2.329 1.00 20.07 C
ANISOU 252 C5 LHC B 24 1653 3744 2230 -412 63 269 C
HETATM 253 C4 LHC B 24 -6.809 -0.569 -1.672 1.00 17.97 C
ANISOU 253 C4 LHC B 24 1634 3417 1776 -485 -191 98 C
HETATM 254 N4 LHC B 24 -7.342 0.587 -2.067 1.00 18.12 N
ANISOU 254 N4 LHC B 24 1798 3419 1666 -457 -36 78 N
HETATM 255 N3 LHC B 24 -7.372 -1.211 -0.629 1.00 17.35 N
ANISOU 255 N3 LHC B 24 1768 3212 1612 -266 -122 -10 N
HETATM 256 C2 LHC B 24 -6.857 -2.356 -0.170 1.00 18.28 C
ANISOU 256 C2 LHC B 24 1845 3239 1860 -108 -37 53 C
HETATM 257 O2 LHC B 24 -7.355 -2.975 0.798 1.00 18.97 O
ANISOU 257 O2 LHC B 24 2035 3431 1743 -114 7 133 O
HETATM 258 C LHC B 24 -4.302 -6.233 1.506 1.00 19.85 C
ANISOU 258 C LHC B 24 1718 3434 2392 -211 88 285 C
HETATM 259 O LHC B 24 -5.036 -6.292 2.492 1.00 21.96 O
ANISOU 259 O LHC B 24 1904 3911 2527 -328 143 436 O
HETATM 260 HA LHC B 24 -4.155 -6.611 -0.507 1.00 24.87 H
HETATM 261 HB LHC B 24 -6.585 -5.332 0.220 1.00 25.06 H
HETATM 262 HBA LHC B 24 -6.039 -5.482 -1.242 1.00 25.06 H
HETATM 263 HG LHC B 24 -4.942 -3.902 0.752 1.00 24.00 H
HETATM 264 HGA LHC B 24 -4.220 -4.155 -0.606 1.00 24.00 H
HETATM 265 H6 LHC B 24 -4.385 -2.596 -2.246 1.00 24.71 H
HETATM 266 H5 LHC B 24 -5.242 -0.652 -3.053 1.00 24.09 H
HETATM 267 HN4 LHC B 24 -8.028 0.906 -1.659 1.00 21.74 H
HETATM 268 HN4A LHC B 24 -6.999 1.014 -2.730 1.00 21.74 H
HETATM 269 HNA LHC B 24 -6.476 -7.793 0.022 1.00 25.15 H
HETATM 270 C2 AGD B 25 -4.413 -1.616 2.817 1.00 22.60 C
ANISOU 270 C2 AGD B 25 2289 3641 2658 -451 22 566 C
HETATM 271 C4 AGD B 25 -2.649 -2.627 1.930 1.00 22.75 C
ANISOU 271 C4 AGD B 25 2143 3407 3095 -565 -74 371 C
HETATM 272 C5 AGD B 25 -2.544 -1.756 0.860 1.00 24.10 C
ANISOU 272 C5 AGD B 25 2364 3730 3063 -380 91 437 C
HETATM 273 C6 AGD B 25 -3.467 -0.671 0.750 1.00 21.73 C
ANISOU 273 C6 AGD B 25 2234 3311 2711 -675 149 318 C
HETATM 274 N AGD B 25 -3.000 -6.010 1.593 1.00 20.45 N
ANISOU 274 N AGD B 25 1760 3287 2723 -163 9 185 N
HETATM 275 CA AGD B 25 -2.364 -5.643 2.816 1.00 21.59 C
ANISOU 275 CA AGD B 25 1827 3205 3170 6 -200 -112 C
HETATM 276 CB AGD B 25 -1.233 -4.647 2.552 1.00 24.95 C
ANISOU 276 CB AGD B 25 2284 3592 3604 -450 -539 316 C
HETATM 277 N9 AGD B 25 -1.632 -3.508 1.763 1.00 25.03 N
ANISOU 277 N9 AGD B 25 1914 3979 3616 -403 -155 595 N
HETATM 278 N3 AGD B 25 -3.551 -2.621 2.947 1.00 22.65 N
ANISOU 278 N3 AGD B 25 2462 3463 2681 -535 -179 209 N
HETATM 279 N2 AGD B 25 -5.444 -1.453 3.613 1.00 24.26 N
ANISOU 279 N2 AGD B 25 3376 3608 2234 -254 395 188 N
HETATM 280 N1 AGD B 25 -4.412 -0.772 1.721 1.00 21.97 N
ANISOU 280 N1 AGD B 25 2288 3443 2615 -728 156 374 N
HETATM 281 O6 AGD B 25 -3.465 0.189 -0.153 1.00 23.61 O
ANISOU 281 O6 AGD B 25 2546 3637 2788 -475 394 465 O
HETATM 282 N7 AGD B 25 -1.502 -2.087 0.011 1.00 28.78 N
ANISOU 282 N7 AGD B 25 2421 4424 4092 -59 683 1001 N
HETATM 283 C8 AGD B 25 -1.018 -3.149 0.595 1.00 25.13 C
ANISOU 283 C8 AGD B 25 2037 3648 3863 -566 247 407 C
HETATM 284 C AGD B 25 -1.826 -6.837 3.594 1.00 22.53 C
ANISOU 284 C AGD B 25 2663 3466 2432 -91 -109 113 C
HETATM 285 O AGD B 25 -1.180 -6.753 4.659 1.00 31.42 O
ANISOU 285 O AGD B 25 3852 4252 3833 711 -1533 -505 O
HETATM 286 HN1 AGD B 25 -5.090 -0.248 1.645 1.00 26.36 H
HETATM 287 HA AGD B 25 -3.031 -5.195 3.378 1.00 25.90 H
HETATM 288 HB AGD B 25 -0.888 -4.333 3.402 1.00 29.94 H
HETATM 289 HBA AGD B 25 -0.512 -5.108 2.094 1.00 29.94 H
HETATM 290 HN2 AGD B 25 -5.978 -0.790 3.496 1.00 29.11 H
HETATM 291 HN2A AGD B 25 -5.585 -2.011 4.253 1.00 29.11 H
HETATM 292 H8 AGD B 25 -0.304 -3.628 0.241 1.00 30.16 H
HETATM 293 HNA AGD B 25 -2.519 -6.089 0.885 1.00 24.54 H
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