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Hi Xiangjun,
I'm trying to convert an xyz file to a pdb file to use it in 3dna (I got the xyz file from other program which can not provide pdb file directly). I have tried VESTA and OpenBabel but they failed to create a pdb file that can be used in 3dna (although VESTA can work normally with these files). After a quick search I have found other similar problems posted before in the forum (like Topic: PDB conversion on: May 29, 2017, 06:49:35 am), but I have not found a quick solution to my problem. So I'm here to ask if there is any tool that can do the job.
My xyz file is attached below.
Best regards,
Erik
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Hi Erik,
Thanks for using 3DNA and for posting your questions on the Forum.
There is no quick solution to your problem. 3DNA relies on proper naming of atoms in DNA and RNA, as a prerequisite. For example, the sugar atoms are all ended with a prime (e.g., C1'). With only C, O, N, P, H atomic symbols, as in the .xyz file you attached, it is practically impossible to know if an atom belongs to the base or the sugar moiety. The wwPDB is there to ensure the compliance of atom names to standard nomenclatures of biological macromolecular structures.
If VESTA or OpenBabel cannot do the job for you automatically, you've to come up with your own solution. Sorry for not being able to provide you a more encouraging answer.
Best regards,
Xiang-Jun
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Hello Xiangjun,
Thanks for replying. I think my situation is not that bad. You will find that softwares like OpenBabel are more powerful than you think. OpenBabel can actually identify an atom's pdb name from an xyz file (Although I don't know how it is done. Pretty cool as I think). I have attached the pdb file that OpenBabel generated from my xyz file DNA_TypeA_12bp_1.xyz. It can mark the C atoms as C5*, C4*, C8 etc, probably mean C5', C4', C8.
So I understand that I need to change symbols like C5* to C5', and do some other format changes. But do I need to add something like HEADER, TITLE, COMPND, SOURCE etc to the converted pdb file? I want to use 3dna to calculate some geometry attributes like diameter, rise and twist of the DNA segment, so I think maybe these things like "HEADER" are not necessary. So can I leave these parts empty or do I have to fake them to make the pdb file acceptable by 3dna? Is there anything besides the "ATOM" part that will be actually used in 3dna in my case?
Best,
Erik
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Hi Erik,
Thanks for your follow-up. 3DNA only needs the ATOM/HETATM coordinate records to its analysis and is generally tolerant of some variants of PDB format (e.g., C1* instead of C1'). As is often the case, please just try 3DNA (or other tools) and see what happens.
Glad to hear that OpenBabel can be of more help in your case. The PDB file you attached, however, is still not in good condition. As an example, the first residue (designated as A) has the following info, with ONLY hydrogen atoms.
ATOM 1 H5* A A 1 18.493 7.546 16.553 1.00 0.00 H
ATOM 2 H5*1 A A 1 18.971 5.507 14.623 1.00 0.00 H
ATOM 3 H5*2 A A 1 19.700 5.674 16.250 1.00 0.00 H
ATOM 4 H4* A A 1 21.435 6.259 14.778 1.00 0.00 H
ATOM 5 H3* A A 1 20.014 8.769 15.785 1.00 0.00 H
ATOM 6 H2*1 A A 1 21.745 10.136 14.663 1.00 0.00 H
ATOM 7 H2*2 A A 1 22.696 8.651 14.285 1.00 0.00 H
ATOM 8 H1* A A 1 21.349 8.823 12.282 1.00 0.00 H
ATOM 9 H2 A A 1 21.090 13.832 12.321 1.00 0.00 H
ATOM 10 H8 A A 1 18.005 8.213 13.369 1.00 0.00 H
ATOM 11 H61 A A 1 16.614 14.046 11.537 1.00 0.00 H
ATOM 12 H62 A A 1 16.008 12.397 11.886 1.00 0.00 H
You need further work on this file before 3DNA can handle it.
Best regards,
Xiang-Jun
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Hi Erik,
I dug a bit deeper into your attached PDB file and found it has a strange arrangement of the nucleotides. Instead of putting all atoms (base, sugar, and phosphate) of a nucleotide together, as is the case for a standard PDB entry (e.g., 355d), your PDB file has the atoms arranged by atom types: H, C, N, O, and P. An example is shown below, for A2 on chain A. As you can see clearly, it is separated into 5 segments.
The source of the issue may be due to the .xyz file which has atoms ordered that way. How was your .xyz generated? It is certainly the first time I see such a weird case for DNA structures.
ATOM 13 H2P A A 2 21.335 7.601 19.955 1.00 0.00 H
ATOM 14 H5*1 A A 2 23.439 9.452 17.299 1.00 0.00 H
ATOM 15 H5*2 A A 2 23.472 9.989 19.020 1.00 0.00 H
ATOM 16 H4* A A 2 24.470 11.663 17.626 1.00 0.00 H
ATOM 17 H3* A A 2 21.726 12.489 18.712 1.00 0.00 H
ATOM 18 H2*1 A A 2 22.286 14.772 17.743 1.00 0.00 H
ATOM 19 H2*2 A A 2 23.960 14.206 17.436 1.00 0.00 H
ATOM 20 H1* A A 2 22.953 13.709 15.302 1.00 0.00 H
ATOM 21 H2 A A 2 20.156 17.569 14.828 1.00 0.00 H
ATOM 22 H8 A A 2 20.392 11.254 16.304 1.00 0.00 H
ATOM 23 H61 A A 2 16.205 15.439 14.199 1.00 0.00 H
ATOM 24 H62 A A 2 16.535 13.725 14.562 1.00 0.00 H
ATOM 313 C5* A A 2 23.026 10.171 18.027 1.00 0.00 C
ATOM 314 C4* A A 2 23.361 11.581 17.596 1.00 0.00 C
ATOM 315 C3* A A 2 22.779 12.705 18.457 1.00 0.00 C
ATOM 316 C2* A A 2 22.902 13.896 17.502 1.00 0.00 C
ATOM 317 C1* A A 2 22.479 13.239 16.178 1.00 0.00 C
ATOM 318 C4 A A 2 20.345 14.424 15.560 1.00 0.00 C
ATOM 319 C2 A A 2 19.876 16.522 14.986 1.00 0.00 C
ATOM 320 C6 A A 2 18.108 14.968 14.888 1.00 0.00 C
ATOM 321 C5 A A 2 19.025 13.992 15.353 1.00 0.00 C
ATOM 322 C8 A A 2 20.101 12.255 15.998 1.00 0.00 C
ATOM 548 N9 A A 2 21.031 13.291 15.971 1.00 0.00 N
ATOM 549 N3 A A 2 20.841 15.678 15.407 1.00 0.00 N
ATOM 550 N1 A A 2 18.575 16.241 14.721 1.00 0.00 N
ATOM 551 N7 A A 2 18.882 12.639 15.633 1.00 0.00 N
ATOM 552 N6 A A 2 16.809 14.704 14.628 1.00 0.00 N
ATOM 630 O1P A A 2 19.542 8.422 18.155 1.00 0.00 O
ATOM 631 O2P A A 2 21.886 7.642 19.130 1.00 0.00 O
ATOM 632 O5* A A 2 21.577 10.009 18.124 1.00 0.00 O
ATOM 633 O4* A A 2 22.891 11.854 16.254 1.00 0.00 O
ATOM 634 O3* A A 2 23.577 12.788 19.672 1.00 0.00 O
ATOM 767 P A A 2 21.033 8.490 18.045 1.00 0.00 P
Knowing the issue, one can find a workaround for this special case as below. Note your attached PDB file is named DNA_TypeA_12bp_1.pdb. The resultant file duplex.pdb can be handled by 3DNA.
grep ' A A ' DNA_TypeA_12bp_1.pdb | sort -k 6n > chainA.pdb
grep ' T B ' DNA_TypeA_12bp_1.pdb | sort -k 6n > chainB.pdb
cat chainA.pdb chainB.pdb > duplex.pdb
Please have a try and report back how it goes.
Xiang-Jun
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Hello Xiangjun,
Sorry for replying late.
YES! You are right! It works! I haven't figured it out in a long time by myself, almost giving up.
I REALLY should have checked the forum earlier! You are a lifesaver, THANK YOU!
And to answer your question, my .xyz file was generated from a .cif file by VESTA. I have attached the .cif file below.
Best,
Erik
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Hi Erik,
Thanks for your confirmation that the proposed method works.
And to answer your question, my .xyz file was generated from a .cif file by VESTA. I have attached the .cif file below.
The so-called CIF file is nothing but a simple list of atom symbol and xyz coordinates. As shown below, it is just like the .xyz file you attached at the beginning of the thread. If you're interested in generating a starting DNA or RNA structure of generic sequence, you may find 3DNA itself helpful. Try the new "Web 3DNA 2.0 for the analysis, visualization, and modeling of 3D nucleic acid structures" at http://web.x3dna.org, especially the "Fiber (http://web.x3dna.org/index.php/fibermodel)" module.
Best regards,
Xiang-Jun
_data_test
audit_creation_method generated by ABACUS
_cell_length_a 31.7506
_cell_length_b 31.7506
_cell_length_c 84.6683
_cell_angle_alpha 90
_cell_angle_beta 90
_cell_angle_gamma 90
_symmetry_space_group_name_H-M
_symmetry_Int_Tables_number
loop_
_atom_site_label
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
H 0.58245 0.237665 0.195505
H 0.597501 0.173458 0.172704
H 0.620449 0.178712 0.191924
H 0.675105 0.197142 0.174543
H 0.630339 0.276193 0.186432
H 0.684881 0.319228 0.173178
H 0.714824 0.272464 0.168714
H 0.672394 0.277871 0.145056
H 0.664234 0.435631 0.145526
H 0.567061 0.258673 0.157903
......
P 0.25159 0.656626 0.15821
P 0.395947 0.720755 0.126839
P 0.551859 0.703742 0.0949896
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Hi Xiangjun,
I have noticed 3DNA can generate a starting DNA structure now. But, because I didn't know this when I was generating DNA structure, I chose another online tool to generate my structure, and used this structure to run a DFT calculation (with another software called ABACUS), which gave me the .cif file. Because of the DFT calculation, instead of generating a .pdb file from 3DNA, I have to find a method to convert this .cif file to a .pdb file. And because I thought .xyz file was easy to understand and edit, I chose to convert .cif file to .xyz file first, then convert .xyz file to .pdb file.
This is why I posted this topic, and I wish it may help others who have similar problems.
Best,
Erik
Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids
Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University