search

ncbi / icn3d

web-based protein structure viewer and analysis tool interactively or in batch mode
https://www.ncbi.nlm.nih.gov/Structure/icn3d
Other
154 stars 42 forks source link

View RNA pdb files #36

Closed namratasp20 closed 3 years ago

namratasp20 commented 3 years ago

I have few pdb files generated for RNA using rnacomposer (http://rnacomposer.cs.put.poznan.pl/)

When I try to load these files in the viewer, 3D structure is not available

Thus, wanted to understand icn3d can visualize PDB files of proteins only ?

Following is the first of few lines of pdb file obtained through above site for input RNA sequence MODEL 1 ATOM 1 HO5' G A 1 -0.154 -0.520 0.011 1.00 0.00 H
ATOM 2 O5' G A 1 0.395 -0.651 -0.766 1.00 0.00 O
ATOM 3 C5' G A 1 1.734 -0.303 -0.401 1.00 0.00 C
ATOM 4 H5' G A 1 1.995 0.660 -0.843 1.00 0.00 H
ATOM 5 H5'' G A 1 2.423 -1.059 -0.773 1.00 0.00 H
ATOM 6 C4' G A 1 1.874 -0.213 1.100 1.00 0.00 C
ATOM 7 H4' G A 1 2.937 -0.120 1.327 1.00 0.00 H
ATOM 8 O4' G A 1 1.077 0.908 1.575 1.00 0.00 O
ATOM 9 C1' G A 1 0.348 0.524 2.727 1.00 0.00 C
ATOM 10 H1' G A 1 0.480 1.314 3.467 1.00 0.00 H
ATOM 11 N9 G A 1 -1.067 0.463 2.376 1.00 0.00 N
ATOM 12 C4 G A 1 -2.077 -0.059 3.147 1.00 0.00 C
ATOM 13 N3 G A 1 -1.937 -0.607 4.371 1.00 0.00 N
ATOM 14 C2 G A 1 -3.090 -1.019 4.862 1.00 0.00 C
ATOM 15 N2 G A 1 -3.129 -1.581 6.073 1.00 0.00 N
ATOM 16 H21 G A 1 -2.267 -1.680 6.592 1.00 0.00 H
ATOM 17 H22 G A 1 -4.003 -1.883 6.471 1.00 0.00 H
ATOM 18 N1 G A 1 -4.289 -0.910 4.205 1.00 0.00 N
ATOM 19 H1 G A 1 -5.118 -1.258 4.659 1.00 0.00 H
ATOM 20 C6 G A 1 -4.459 -0.350 2.944 1.00 0.00 C
ATOM 21 O6 G A 1 -5.587 -0.299 2.442 1.00 0.00 O
ATOM 22 C5 G A 1 -3.227 0.103 2.403 1.00 0.00 C
ATOM 23 N7 G A 1 -2.946 0.716 1.189 1.00 0.00 N
ATOM 24 C8 G A 1 -1.657 0.910 1.218 1.00 0.00 C
ATOM 25 H8 G A 1 -1.107 1.376 0.414 1.00 0.00 H
ATOM 26 C2' G A 1 0.924 -0.809 3.199 1.00 0.00 C
ATOM 27 H2' G A 1 0.164 -1.430 3.679 1.00 0.00 H
ATOM 28 O2' G A 1 2.033 -0.551 4.040 1.00 0.00 O
ATOM 29 HO2' G A 1 2.677 -1.238 3.870 1.00 0.00 H
ATOM 30 C3' G A 1 1.362 -1.422 1.875 1.00 0.00 C

jiywang3 commented 3 years ago

I just released iCn3D 3.2.2. It should be working. After loading your PDB file of nucleotides, you may need to change the style from "Style > Nucleotides > cartoon" to "Style > Nucleotides > Stick" if the nucleotides have no cartoon display.

namratasp20 commented 3 years ago

Thank you for the update. I am able to view to PDB file of nucleotides in cartoon as well as stick styles