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21
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".

Quote
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
22
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
23
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!
 
Quote
Time used: 00:00:35:59

Are you still interested in a 10k structure trajectory?

Best regards,

Marcel
24
It seems that 'O5'' is actually correct.

The error was caused by using a non-integer model number.
25
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
26
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
27
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
28
Bug reports / Re: 5-hydroxy methyl cytosine
« Last post by xiangjun on September 05, 2018, 10:43:10 am »
Hi Kareem,

Thanks for using 3DNA and for posting your questions on the Forum.

Quote
I used web 3DNA for my structure which has 5- hydroxy methyl cytosine (5HM). When I used web 3 DNA and i got the error message "error in pdb.inp". Later, I used 4pw5 pdb file, which has 5HM (5hc different annotation) and I got the same message.

The web 3DNA error message for 5HM was due to unrecognized nucleotides (i.e., not in the list of baselist.dat) in early versions of 3DNA, up to v2.0 released 10 years ago. The limitation was fixed a long time ago, as of 3DNA v2.1, so an unrecognized nt such as 5HM is automatically matched to its canonical counterpart (cytosine for 5HM).

As far as I know, the web 3DNA server hosted by Rutgers is still using v2.0. As a result, PDB entries containing 5HM cannot be automatically processed. In principle, updating 3DNA v2.0 to the latest v2.3 release should fix the issue. In practice, there are maybe some technical implications. I've no idea when (or if) that update would happen. See the Section w3DNA -- web interface to 3DNA.

Assuming you 3DNA v2.3 installed on your computer, and the 5HM-containing PDB structure is named 5hm-str.pdb, the following command will solve your problem right away:

Code: [Select]
find_pair 5hm-str.pdb 5hm-str.inp
analyze 5hm-str.inp

The result is in file 5hm-str.out.

Quote
I used SNAP to identify DNA-protein interactions and I learned that we don't have reference to cite.

Can I mention like this in my paper citing SNAP.  ( "SNAP from 3DNA suite").

The suggested citation for SNAP is available by running x3dna-snap -h, and it reads as follows:

Quote
    CITATION: before a paper dedicated to SNAP is published, please
  cite the software as follows: *your specific usage* of SNAP, a new
  component of the 3DNA suite of programs [citing the 2003 NAR or the
  2008 Nature Protocols paper].

Inspired by your above question, I've added the --citation option to SNAP to make this point explicit.

Hope that helps.

Xiang-Jun
29
Hallo,

I noticed that the cif files created with biopython are not supported by DSSR.
Biopython `Bio.PDB.MMCIFIO' writes rather minimal cif files which ONLY contain the following loop:

Quote
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 ' '

When I analyze these biopython-generated cif files with DSSR, I get the following error: "no nucleotides found."

Could you tell me which dictionary keys of the cif format are essential for DSSR, so I can decide if I can extend biopython's cif writer to make it compatible with dssr.

(Attached is an example file. This is 333D.cif read with biopython and written to a new file. Tested with cif version v1.7.1-2017nov01)
30
Bug reports / 5-hydroxy methyl cytosine
« Last post by rkareem on September 05, 2018, 06:12:22 am »
Dear Xiang-Jun,

I would like to thank you for making 3DNA and other software's for the analysis of nucleic acid structures.

I used web 3DNA for my structure which has 5- hydroxy methyl cytosine (5HM). When I used web 3 DNA and i got the error message "error in pdb.inp". Later, I used 4pw5 pdb file, which has 5HM (5hc different annotation) and I got the same message.

When I edited my PDB file for 5HM to 5MC (5 methyl cytosine) it worked even keeping the 05 oxygen atom as such.
Therefore, i request you to tweak your web 3DNA software (very user friendly) to accept and process 5HM and other variant of modified cytosine.

I used SNAP to identify DNA-protein interactions and I learned that we don't have reference to cite.

Can I mention like this in my paper citing SNAP.  ( "SNAP from 3DNA suite").

Many thanks
Best regards
Kareem
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Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.