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Frequency of amino acids from 'ATOM ' of PDB

by RRK
on Aug 10, 2012 at 09:05 UTC ( #986694=perlquestion: print w/ replies, xml ) Need Help??
RRK has asked for the wisdom of the Perl Monks concerning the following question:

Hi,I am masters student of Bioinformatics,and as a part of my masters project I need to write a program to count the frequency of each amino acids present in the ATOM section of PDB file.I tried to write the program but due to partial occupancies some residues are repeating which made me so confused.Any perl experts please help me.I need only perl scripting for the project.somebody told me that I can use Bioperl or some modules.But for my project I need to write a fresh program to parse the information.Please do help me.

Comment on Frequency of amino acids from 'ATOM ' of PDB
Re: Frequency of amino acids from 'ATOM ' of PDB
by Anonymous Monk on Aug 10, 2012 at 09:07 UTC

      hi,thank you all,the books and links suggested by perl monks have been useful.I could write code.I will uplaod the code if somebody needs it.I need one more help form monks. The problem is,I want to calculate the distance between x,y,z coordinate,from HOH to all other molecules.Then I have to make a table or something like that .The table headings are Serial number of HOH,Serial number of other atoms,Atom name,How many atoms are close to each HOH within 5 angstroms distance. Till now I have calculated the distance and found out all atoms within 5 Angstroms distance.But I unable to format the out put required.Please help me.

        But I unable to format the out put required.Please help me.

        Sure, show your code

Re: Frequency of amino acids from 'ATOM ' of PDB
by marto (Chancellor) on Aug 10, 2012 at 09:12 UTC

    This isn't a code writing service. If you need to use Perl to do this I suggest you learn Perl (http://learn.perl.org, tutorials etc) and use the BioPerl framework if that makes your task easier. I'm pretty sure questions very similar to this have been asked here before Super Search should turn up some results.

Re: Frequency of amino acids from 'ATOM ' of PDB
by BrowserUk (Pope) on Aug 10, 2012 at 09:24 UTC
    I tried to write the program but due to partial occupancies some residues are repeating which made me so confused.

    You couldn't write the program because the data confused you. Did you get confused after writing the first line of your program? Or the second?

    I can use Bioperl or some modules.But for my project I need to write a fresh program to parse the information.

    How do you judge the "freshness"? Smell, taste, touch?

    The program I wrote for another guy last week to do pretty much the same thing wouldn't be any good to you? It would be stale?


    With the rise and rise of 'Social' network sites: 'Computers are making people easier to use everyday'
    Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.
    "Science is about questioning the status quo. Questioning authority".
    In the absence of evidence, opinion is indistinguishable from prejudice.

    The start of some sanity?

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