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Author Topic: exotic CIF format  (Read 2216 times)

Offline febos

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exotic CIF format
« on: September 06, 2015, 07:53:49 am »
Good Afternoon!

I'd like to draw Your attention to structure 5AJ0 (http://www.rcsb.org/pdb/files/5AJ0.cif).
Its mmCIF file contains exotic row orderings in its tables and DSSR is not capable to parse it in right way.
For instance, in its "_atom_site" table words "ATOM/HETATM" are not first words in line.

Best wishes
Eugene

Offline xiangjun

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Re: exotic CIF format
« Reply #1 on: September 06, 2015, 10:22:40 am »
Hi Eugene,

Thanks for reporting the DSSR parsing issue of 5aj0.cif (and the like). Quickly looking into 5aj0.cif and compared it with 355d.cif, I noticed that these two files indeed have different ordering of ATOM/HETATM fields. Nevertheless, both entries still follow the PDBx/mmCIF format guideline. So this is a bug in the current DSSR .cif parser. I'm working on it and will report back on this Forum shortly.

Best regards,

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline xiangjun

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Re: exotic CIF format
« Reply #2 on: September 06, 2015, 11:59:09 am »
Hi Eugene,

I've fixed the bug in DSSR's .cif parser, and updated the software to v1.3.4-2015sep06 on the download page. Please have a try and report back how it goes.

The originally DSSR .cif parser should have worked, since it did not expect a specific order of the .cif _atom_site fields. As it turned out, however, a negligence assumed ATOM/HETATM (_atom_site.group_PDB) to be the first field, instead of its actual position index in the .cif file. In this context (for RCSB PDB entry 5aj0), it is also interesting to note that the x-, y-, z-coordinates are now represented in the order of z, x, and y (colored red below).

loop_
_atom_site.type_symbol
_atom_site.pdbx_PDB_ins_code
_atom_site.label_seq_id
_atom_site.occupancy_esd
_atom_site.B_iso_or_equiv_esd
_atom_site.B_iso_or_equiv
_atom_site.auth_asym_id
_atom_site.label_asym_id
_atom_site.pdbx_formal_charge
_atom_site.label_entity_id
_atom_site.auth_seq_id
_atom_site.occupancy
_atom_site.id
_atom_site.pdbx_PDB_model_num
_atom_site.group_PDB
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.Cartn_y_esd
_atom_site.label_alt_id
_atom_site.Cartn_z_esd
_atom_site.auth_atom_id
_atom_site.auth_comp_id
_atom_site.Cartn_z
_atom_site.Cartn_x
_atom_site.Cartn_y
 
_atom_site.Cartn_x_esd
P  ? 1    ? ? 20.00  A3 A  ? 1  1    1.00 1      1 ATOM   P     C   ? . ? P     C   -54.864  60.295   10.209   ?
O  ? 1    ? ? 20.00  A3 A  ? 1  1    1.00 2      1 ATOM   OP1   C   ? . ? OP1   C   -53.786  61.291   9.998    ?

For the record, here is the output of running the updated command: x3dna-dssr -i=5aj0.cif -o=5aj0.out:

Code: [Select]
[i] '5aj0.cif' taken as in .cif format by file extension.

Processing file '5aj0.cif' [5aj0]

total number of base pairs: 2621
total number of multiplets: 309
total number of helices: 175
total number of stems: 347
total number of isolated WC/wobble pairs: 160
total number of atom-base capping interactions: 328
total number of hairpin loops: 118
total number of bulges: 80
total number of internal loops: 194
total number of junctions: 67
total number of non-loop single-stranded segments: 65
total number of kissing loops: 7
total number of A-minor (type I and II) motifs: 82
total number of ribose zippers: 46 (380)
total number of kink turns: 5
[w]  cross-paired segments in separate chains, be *careful* with .dbn

Time used: 00:00:07:35

Once again, thanks for reporting the bug -- it's users like you that help improving DSSR!

Xiang-Jun
« Last Edit: September 06, 2015, 12:03:14 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

 

Created and maintained by Dr. Xiang-Jun Lu[律祥俊]· Supported by the NIH grant R01GM096889 · Dr. Lu is currently a member of the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University. The project is in collabration with the Olson Laborarory at Rutgers where 3DNA got started.