Show Posts
1
Bug reports / 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
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