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Either by Python command, or via specific application (like Chimera) publicly available. Please provide example or link to one of.

I have to detect AA location within MAP (density) 3D matrix. And to verify with PDB format (which models same 3D structure). Each AA may have different rotamer (aka 3 angles usually used to describe AA exact position related to carbon C_alpha atom (the atom which AA side chain exits from). To justify inaccuracies - I need to show that (among other reasons) - inaccuracy is caused since not all possible rotamers existed in my training set (I use machine learning classification to decide what AA is it, and where it stands within cryo- EM scan).

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    $\begingroup$ sounds like a very specific question - you may want to give a little more detail to help others follow what you are asking - just my thougts $\endgroup$ – Vance L Albaugh Sep 8 '16 at 18:55
  • $\begingroup$ I clarified upon request, thanks for suggestion to improve chances for proper and and exact answers. $\endgroup$ – Leon Kigelman Sep 8 '16 at 19:06
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    $\begingroup$ As far as I am aware, Python commands are instructions you write on the command line to run individual lines of Python code. I presume it is a Python program you are after, but why do you specify this one language? $\endgroup$ – David Sep 8 '16 at 21:43
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    $\begingroup$ I am student at Computer Science department, and this post is about bioinformatic workshop I must proceed through. Teaching stuff guidelines require to implement in Python. Python is interpreter language where you can write single command. And you can build as well huge projects with many files - which call each other. $\endgroup$ – Leon Kigelman Sep 8 '16 at 22:10
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    $\begingroup$ I'm voting to close this question as off-topic because this site only accepts bioinformatics questions relating to the underlying biology of the computations, not how to do the computations themselves. If you have tried some code and need help, you may visit Stack Overflow, but they will not give package recommendations or write your code for you - you must show effort. You might also want to visit a bioinformatics forum such as Biostars for suggestions. $\endgroup$ – MattDMo Sep 9 '16 at 0:07
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I’m not sure if it is what you are after, but I have used Roland Dunbrack's dihedral perl script to get dihedral angles, the header of which is:

 RL_Dunbrack@fccc.edu

 usage 
 dihedral.pl filename [chain]

 dihedral.pl pdb2hla.ent 
     will print out all dihedrals from file pdb2hla.ent
 dihedral.pl pdb2hla.ent A
     will print out dihedrals only from chain A

I don’t know if it’s on his website as I got it from him personally. If not, or even if it’s not what you need, email him — he is likely to be able to help you.

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  • $\begingroup$ I downvoted this for several reasons. First, the question is off-topic. From How do I write a good answer? in the help center, Answer well-asked questions. Not all questions can or should be answered here. Next, the OP is specifically asking for a Python script, and you (sort of) gave them a Perl script. Python != Perl, most certainly. Finally, you didn't provide the actual script! You listed the header (which is useless), and basically said "Go find it yourself" even though you have it in your possession. $\endgroup$ – MattDMo Sep 9 '16 at 12:10
  • $\begingroup$ First @MattDMo, you've every right to vote down my answer (and suggest the closure of the question). I had thought the downvote might have been from the poster. In my defence, I couldn't make the script I had freely available as I had obtained it directly from Dunbrack when I needed a replacement or update for a previous program of his (for Silicon Graphics or something). It doesn't have a free distribution licence, so it would have been discourtious and illegal for me to distribute it to third parties. As for giving the header, that was a quick way to indicate what the program did. $\endgroup$ – David Sep 9 '16 at 13:00
  • $\begingroup$ The OP couldn't have downvoted, because they only have 1 rep. You need 125 rep to downvote. I understand why you can't distribute the program, perhaps my wording could have been a bit better. Overall, it just seems to me that you might have been better off just not answering, or leaving a comment suggesting the OP get in touch with Dr Dunbrack, since the answer itself isn't terribly helpful. Just my 2 cents, no hard feelings :) $\endgroup$ – MattDMo Sep 9 '16 at 14:16
  • $\begingroup$ @MattDMo — Fair enough. No hard feelings. $\endgroup$ – David Sep 9 '16 at 14:26

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