Recent Posts

1

RNA structures (DSSR) / Re: Analysis crashes: MD trajectory of abasic site in RNA

« Last post by xiangjun on September 06, 2018, 01:48:00 pm »

I've send you an email with a link to download the trajectory to xiangjun@x3dna.org

Got it -- thanks!

Just as a short note: I have to look deeper into it, but the output.json file has a size of 6.8G, while the do_x3dna files have combined only 992M.  Is the --json flag mandatory for trajectories or do the 'normal' output-files also contain frame informations?

The much larger output file from DSSR than that from do_x3dna is expected. DSSR produces far more RNA structural parameters than other tools I'm aware of. So the JSON output contains far more than you need (torsion angles) right now. However, other DSSR-derived features are of potential use in other projects, as DSSR is used more widely in the MD field.

The --json flag is not mandatory for trajectories, but only the JSON output contains a complete compilation of DSSR parameters. Otherwise, the torsion angles are not listed in 'normal' output file. Check the DSSR manual for more info.

In practice, you could use a tool like jq to filter the stream of JSON data produced by DSSR. This could produce a smaller output file than that from do_x3dna.

Best regards,

Xiang-Jun

2

Bug reports / Re: 5-hydroxy methyl cytosine

« Last post by shuxiang on September 06, 2018, 01:22:27 pm »

I have modified web 3DNA to deal with modified cytosine like 5HM.

3

RNA structures (DSSR) / Re: Analysis crashes: MD trajectory of abasic site in RNA

« Last post by Marcel Heinz on September 06, 2018, 11:42:33 am »

Indeed, it is much faster than do_x3dna. Great work!

I've send you an email with a link to download the trajectory to xiangjun@x3dna.org

Just as a short note: I have to look deeper into it, but the output.json file has a size of 6.8G, while the do_x3dna files have combined only 992M.  Is the --json flag mandatory for trajectories or do the 'normal' output-files also contain frame informations?

Best,

Marcel

4

RNA structures (DSSR) / Re: Analysis crashes: MD trajectory of abasic site in RNA

« Last post by xiangjun on September 06, 2018, 10:06:59 am »

Hi Marcel,

Glad to hear your encouraging feedback. I'm glad to hear that DSSR works for large NMR ensembles or MD trajectories -- 35m vs. 10 days for 100k structures! It is even faster than do_x3dna (2h) for the same dataset -- this is expected, based on your previous feedback that "DSSR and do_x3dna are approx. similar in analyzing the first ~1000 structures".

Are you still interested in a 10k structure trajectory?

It helps to have such a dataset for future tests. Please send me a ~1k (instead of 10k) sample structure trajectory.

Working together, we will make DSSR directly relevant in the active field of MD simulations.

Best regards,

Xiang-Jun

5

RNA structures (DSSR) / Re: Minimal required cif keys (cif files created with biopython not working)

« Last post by xiangjun on September 06, 2018, 09:54:01 am »

Thanks for your followups.

It is always a good idea to adhere to a standard format, as much as possible. That'd make downstream analysis simple.

I've revised the mmCIF parser in the DSSR v1.7.9-2018sep06 release. It is more tolerant of input mmCIF files than previous versions. As a result, DSSR now works with the Biopython-produced 333D_biopython.cif file you originally attached, without any modifications.

Please download DSSR v1.7.9-2018sep06. Have a try and report back how it works.

Best regards,

Xiang-Jun

6

RNA structures (DSSR) / Re: Analysis crashes: MD trajectory of abasic site in RNA

« Last post by Marcel Heinz on September 06, 2018, 09:46:54 am »

Hi Xiang-Jun,

Thank you so much for the DSSR update. I do apologize for the inconvenience of not having a trajectory, but I was traveling with an unexpectedly unstable internet connection.
Just arrived back and tested your latest DSSR version with my 100k structure trajectory.
Your update has a dramatic speed up in analyzing the trajectory. Great improvement!
 

Time used: 00:00:35:59

Are you still interested in a 10k structure trajectory?

Best regards,

Marcel

7

RNA structures (DSSR) / Re: Minimal required cif keys (cif files created with biopython not working)

« Last post by Bernhard10 on September 06, 2018, 07:50:15 am »

It seems that 'O5'' is actually correct.

The error was caused by using a non-integer model number.

8

RNA structures (DSSR) / Re: Minimal required cif keys (cif files created with biopython not working)

« Last post by Bernhard10 on September 06, 2018, 06:04:38 am »

Thanks for the help.

It seems there is a bug in biopython. I have submitted a bugreport and I'm testing the fix: https://github.com/biopython/biopython/issues/1784

9

RNA structures (DSSR) / Re: Minimal required cif keys (cif files created with biopython not working)

« Last post by xiangjun on September 05, 2018, 11:39:14 am »

I've performed a bit more investigation of your attached 333D_biopython.cif file. My findings are as follows:

In 333D_biopython.cif, the header together with the first atom reads:

loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_alt_id
_atom_site.label_comp_id
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.label_seq_id
_atom_site.pdbx_PDB_ins_code
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.auth_seq_id
_atom_site.auth_asym_id
_atom_site.pdbx_PDB_model_num
ATOM   1   O  'O5'' . C   A ? 1 ? 23.308 21.309 18.480 1.0 17.2  1  A ' ' 
### the above should be changed to the following:
ATOM   1   O  "O5'" . C   A ? 1 ? 23.308 21.309 18.480 1.0 17.2  1  A 1
......

The sugar atom name 'O5'' looks weird: it should be replaced with "O5'". The last item is pdbx_PDB_model_num, an integer. However, the ATOM record gives ' ' . The space character should be replaced with a number (e.g., 1). The revised version is shown above in bold green.

After these two fixes for all the ATOM/HETATM records, DSSR works as expected. I've attached the revised mmCIF file for your reference.

Best regards,

Xiang-Jum

10

RNA structures (DSSR) / Re: Minimal required cif keys (cif files created with biopython not working)

« Last post by xiangjun on September 05, 2018, 11:18:05 am »

Hi,

Thanks for using DSSR and for posting your questions on the Forum.

For parsing mmCIF, DSSR requires a minimal set of required keys. In principle, the Biopython output you have should suffice. Your attached example mmCIF file, however, cannot be read by Jmol or PyMOL. With Jmol 14.27.1 (2017-12-11 09:38), the error message is: "Error reading file at end of file -1". Loading into PyMOL open-source version 1.8.7.0, I cannot see any atoms showing up at all.

Are you sure your example file is valid in mmCIF format? Please verify.

Best regards,

Xiang-Jun