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Questions and answers > General discussions (Q&As)
find_pair and HETATM
auffinger:
Dear Xiang-Jun,
Well, the .ana output does not apparently provide the column filed with | and x characters that is used for calculating stackings and other base pair step related infos (it seems to us). This results in an output from analyze in which some sections are just filled with zeros. At a later point we will probably need this info and forget our workaround. The workaround we wrote in perl converts the output from "find_pair -p" by placing indiscriminately | characters in this column. Not perfect indeed - its a workaround, but works at least for our purpose.
As for the RN9-YN1 and RC8-YC69 columns, you are right and we noticed that the info are correct, but the columns are misslabeled and that is something that might trouble other users. May be you would like to change at a later point the labeling of these columns to a lengthy text or something simpler with a note explaining what it means (much more coherent and satisfactory). Again, yes, the data are correct, no doubt about that.
pascal
auffinger:
Dear Xiang-Jun,
Just a few words to let you know that, still, with the -attach options, some HETATM remain attached to the base pair as in one bp of 1VBZ (barium atom) - see picture. We should be able to workaround this for now.
Kind regards,
Pascal
xiangjun:
Hi Pascal,
Could you provide a step-by-step reproducible example? At the bare minimum, please attach the PDB file you used to generate the image. I checked 1VBZ, but failed to repeat the problem you reported -- I could not find any BA atom in file "allpairs.pdb".
If verified, it is certainly a bug and I won't hesitate to fix it.
Best regards,
Xiang-Jun
auffinger:
Hi Xiang-Jun,
I was a little bit quick on this. We had a selection issue with pymol that for unknown reasons takes sometimes connectity cards into cosideration leading to the picture I sent to the forum. Our scripts start to become quite complex,and even after the recent pdb file updates (cleaning), there are a lot of special issues to deal with that complicate our work. I can remove this and my preceding post from the file since it might not be too useful to the community. By curiosity, do you take into account connectivity cards in 3DNA? Anyway, your programs don't need to be modified.
Cheers,
Pascal
xiangjun:
Hi Pascal,
Thanks for your verification. We all learn from mistakes, and our change of views serves as another example of the ever-refining process (kaizen; improve; 改善) that is required to keep a (software) product alive. As a general rule, I have never deleted or changed posts from users. I lock a thread when I believe the topic is finished.
3DNA does not read CONECT records from PDB, which is incomplete (by design), inconsistent, and unreliable. Instead, 3DNA implements an algorithm to decide if two atoms are covalently connected based on pure geometrical criteria. If you want to discuss this topic further, please start a new thread.
Best regards,
Xiang-Jun
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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.
