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Author Topic: 5-hydroxy methyl cytosine  (Read 164 times)

Offline rkareem

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5-hydroxy methyl cytosine
« 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

Offline xiangjun

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Re: 5-hydroxy methyl cytosine
« Reply #1 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
« Last Edit: September 05, 2018, 10:47:09 am by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline shuxiang

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Re: 5-hydroxy methyl cytosine
« Reply #2 on: September 06, 2018, 01:22:27 pm »
I have modified web 3DNA to deal with modified cytosine like 5HM. :)

 

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.