Re:pdb problem in 3DNA

[rparkesh]

I was trying to use 3DNA web server for analyzing of the RNA double stranded   (CCGCUGCGG)2 but the server seems not to recognize the file.
 I am not able to figure out the error source. I think it might be some atom types are not recognized. I will appreciate if you can give me any insight into how I can modify the files for proper format for  3DNA. I have attached the pdb file.
Help will be highly appreciated.
Regards
Raman

[xiangjun]

Dear Raman,

I was trying to use 3DNA web server for analyzing of the RNA double stranded (CCGCUGCGG)2 but the server seems not to recognize the file.

w3DNA works (or should work) for the most common/standard cases, but it is not that sophisticated yet. Technically, I am not involved in supporting w3DNA per se. See the section "w3DNA web server topics".

I am not able to figure out the error source. I think it might be some atom types are not recognized. I will appreciate if you can give me any insight into how I can modify the files for proper format for 3DNA. I have attached the pdb file.

Thanks for your attached file, the issue becomes clear: it is related to the 'non-standard' PDB format you use -- read carefully the "Coordinate Section" of the standard PDB documentation. For illustration purpose, here is an comparison of two ATOM records, one from your file, another in standard PDB format:

Code: [Select]

# 1st from your file; 2nd in standard format
ATOM     40  O3' C A    2      -6.273 -12.136   8.883  1.00  0.00           O  
ATOM     47  O3'  DC A   3      24.468  20.110  19.126  1.00 15.21           O  
What software package did you use to generate the pseudo-'PDB' file? There should be a utility for converting it to standard PDB format. It is easy to write an ad hoc script for converting as well, see the following Ruby script (note while it works in this case, it serves only as a starting point for further refinement):

Code: [Select]

File.open('cug_new_3_3_ok.pdb', 'w') do |aFile|
    File.open('cug_new_3_3.pdb').each_line do |line|
        if line =~ /^(ATOM|HETATM)/
            sb = line[0, 17] # upto atom name plus alt-loc
            resname, chain_id, resnum = line[17, 8].split
            se = line[26..-1]
            aFile.puts "%17s%3s %1s%4s %s" % [sb, resname, chain_id, resnum, se]
        else
            aFile.puts line
        end
    end
end
With the above script, [mono:2x0a5suh]find_pair[/mono:2x0a5suh] will get the following base-pairing info

Code: [Select]

   1   18  0 #    1 | ....>A:...1_:[..C]C-----G[..G]:..24_:B<....  0.58  0.24 21.25  8.84 -2.88
    2   17  0 #    2 | ....>A:...2_:[..C]C-----G[..G]:..23_:B<....  1.20  0.86 31.10  8.66 -0.52
    3   16  0 #    3 | ....>A:...3_:[..G]G-----C[..C]:..22_:B<....  1.54  1.27 25.83  8.63  0.37
    4   15  0 #    4 | ....>A:...4_:[..C]C-----G[..G]:..21_:B<....  0.21  0.06 44.98  8.77 -2.42
    5   14  0 #    5 | ....>A:...5_:[..U]U-*---U[..U]:..20_:B<....  2.89  1.60 22.74  8.20  6.22
    6   13  0 #    6 | ....>A:...6_:[..G]G-----C[..C]:..19_:B<....  0.84  0.67 23.53  8.88 -1.66
    7   12  0 #    7 | ....>A:...7_:[..C]C-----G[..G]:..18_:B<....  0.65  0.46 35.94  8.95 -1.64
    8   11  0 #    8 | ....>A:...8_:[..G]G-----C[..C]:..17_:B<....  0.21  0.14 25.89  8.78 -3.22
    9   10  0 #    9 | ....>A:...9_:[..G]G-----C[..C]:..16_:B<....  0.84  0.69 25.34  8.83 -1.50HTH,

Xiang-Jun

[rparkesh]

Thanks Xiang for your help. You are right that it is the format issue problem. I generated these files using CYANA. I was looking for various program for converting to the right format but I came to conclusion using script in sed, vim or the one you did in ruby are the best solutions. Does anyone know any webserver or any other program for generating proper pdb format files?

Regards
raman