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Topics - Phosphoserine

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DNA-protein interactions (SNAP) / Unrecognized interactions
« on: April 10, 2017, 10:24:59 am »
Dear Dr. Xiang-Jun,

I've recently compared the results of protein--DNA interaction analysis provided by 3DNA-SNAP to some (more primitive) analysis I did using my scripts. I've noticed that in some of the structures I was interested in the SNAP tool did not recognize some amino acid--nucleotide interactions, despite them containing inter-atomic distances shorter than the cut-off (4.5 A). See, for example, the structure 1TTU. Amino acids LYS 233, ARG 399, and VAL 403 are not mentioned in the .out file, despite each of them being involved in interactions with DNA residues in the 13-bp helix (there could also be others, I had used a shorter interaction cut-off in my analysis).

Is there any reason for omitting these interactions, or is it a bug ? Thought you might be interested in it.

Best regards,
David J.

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DNA-protein interactions (SNAP) / Segmentation fault
« on: May 21, 2016, 08:10:28 am »
Dear Dr. Xiang-Jun,

I have recently used the x64 Linux x3dna-snap binary to analyze the interactions in almost all available protein--DNA complexes, using the .pdb files as inputs. In over 3,700 of them, the program worked wonderfully, however, in four (PDB IDs 1LBG, 2VS7, 2VW9, 3T72) the program crashed with a segmentation fault. I was not able to observe any shared features in these complexes which could cause this unexpected behavior, nor do these complexes have any features which distinguish them from the structures for which the program worked (i.e., 1LBG is a C-alpha only structure, but the program did not crash for other CA structures).

This behavior was tested on Ubuntu 16.04 and Debian 8 machines and was reproduced under a Windows 10 environment with the .exe binary as well. Running the 32-bit Linux binary yields "program not found", so I can't test that. The web version of SNAP fails to process these structures as well.

It seems that it is beyond the scope of my knowledge to see what might be causing this behavior, but I thought you might appreciate this feedback and I hope it aids the development of this great tool.

Best regards,
David J.

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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.