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Questions and answers > General discussions (Q&As)
find_pair and HETATM
auffinger:
Dear Xiang-Jun,
Just found out that for some base pairs, find_pair extracts some additional atoms (CA, K, TL, MG among others) and also complete modified residues like in 1MO5 (bp 12) and 2PIS (bp 9) (see attached files). Is that how it should be. Did we miss an option or misunderstand something ? This does not occur with the -a option, yet info related to modified residues are then lost.
Thanks for your help,
Pascal
xiangjun:
Dear Pascal,
Over the years, I have always been surprised by your sharp observations of some fine details of undocumented 3DNA features, through our extensive email communications (mostly before the 3DNA forum was set up) and your posts in the forum.
--- Quote from: "Pascal" ---Just found out that for some base pairs, find_pair extracts some additional atoms (CA, K, TL, MG among others) and also complete modified residues like in 1MO5 (bp 12) and 2PIS (bp 9) (see attached files). Is that how it should be. Did we miss an option or misunderstand something ? This does not occur with the -a option, yet info related to modified residues are then lost.
--- End quote ---
Yes, the attached HETATM moieties (including metals, and modified nucleotides) you observed are expected, thus you did not miss any option or misunderstand something. Based on my experience with PDB format 2.x, I checked for possible linkage between a hetero group (e.g., a drug molecule) and the base residue, and added the HETATM group to the output coordinates file if it is connected to the nucleotide.
Obviously, the extra-mileage I took seems too far for your purpose. So I am considering to add a new command line option to “find_pair” that, if specified explicitly, would exclude such HETATM groups (metals, or modified residues). I am pretty busy for my job right now, but I would keep your request in mind. Hopefully, I would be able to get a working solution for you in a week (by the end of this month).
Xiang-Jun
auffinger:
Dear Xiang-Jun,
Thanks for your reply. I understand better what you intended to do. This is, as you wrote, undocumented and therefore puzzling when one discovers it, although probably very useful when one is aware of the bias you chose. Indeed, an option in find_pair, related to this issue would be really welcome and add more flexibility to 3DNA. Getting an updated version is great news for us and we are waiting for it.
Regarding our last post, we would also really appreciate if you could at one point consider providing an output for "find_pair -p" (using the -p option) that could be run through analyze (its not the case right now). This would be also more than helpful for us. Yet, I understand that you are really busy combining several jobs.
Thanks for being so reactive,
Kind regards,
Pascal
xiangjun:
Dear Pascal,
--- Quote from: "Pascal" ---Regarding our last post, we would also really appreciate if you could at one point consider providing an output for "find_pair -p" (using the -p option) that could be run through analyze (its not the case right now). This would be also more than helpful for us.
--- End quote ---
I may consider adding a new output file from "find_pair -p" that can be fed directly into "analyze" when I turn into "programming mode" to address your HETATM request. In the meantime, it should be straightforward to write a script that parses the output file from "find_pair -p" to feed into "analyze". More generally, as demonstrated in the 2008 Nature Protocols paper, 3DNA should be taken as a toolset that, when combined with other programs, can be explored with command line scripts to fulfill specific needs.
--- Quote from: "Pascal" ---Yet, I understand that you are really busy combining several jobs.
--- End quote ---
As mentioned several times in the forum and on the 3DNA websites, and made clear in my blog post titled "On maintaining the 3DNA forum", my supporting of 3DNA and the forum is purely on a voluntary basis, not a "job" duty at all:
--- Quote ---Over the past few years, maintaining the 3DNA forum (i.e., answering questions, performing administrative tasks) has taken up a significant amount of my spare time. Sometimes it could be quite demanding, especially because I need to pay great attention to details. Overall, though, it is a valuable experience, and I feel that the time is well-spent: 3DNA has been continuously refined and more widely used; my knowledge of nucleic acid structures (especially RNA) has been significantly sharpened; I have stayed aware of progress in related research fields and see more of the world; and I feel great pleasure in being of help to the community.
--- End quote ---
I do enjoy what I am doing with 3DNA and I have learned a lot, even from a negative comment on my effort (BTW, the thread is well worth reading):
[hr:1txo5elk][/hr:1txo5elk]
--- Quote ---You [Xiang-Jun] clearly have the ability to avoid answers to the questions. You lecture me how to pose a question, I recommend you learn how to answer a question. I read your answers to other questions and the pattern is the same: to give as little help as possible. Still I like your program better than the other programs, so please, try to be more helpful. Do you think Wilma knows how to use this program? Maybe I should write to her?
--- End quote ---
[hr:1txo5elk][/hr:1txo5elk]
Best regards,
Xiang-Jun
auffinger:
Dear Xiang-Jun,
Again, we appreciate your dedication to 3DNA and this program is a the ground on which a large part of our research evolves. As for "find_pair -p", we wrote a workaround (that is just a workaround) since we cannot translate everything (different info in both findpair outputs). If you do that, it would be certainly much nicer and accurate and benefit to ourselfs (certainly) and others (probably). Thanks.
Best regards,
Pascal
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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.
