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Author Topic: Missing atoms  (Read 6183 times)

Offline Z3DNA2012

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Missing atoms
« on: March 08, 2012, 04:09:44 pm »
Dear Xiang-Jun,

Thank you for your 3DNA software and the 3DNA Webservice.
I generated a dsDNA fragment (18-mer) through your 3DNA Webserver. When I open the file with Swiss Pdb Viewer, I got a long list complaining missing atoms. I think that the atoms are there, but they have different names which Swiss Pdb Viewer can not recognize. Is there an easy way to fix this?

Thank you.

Xiao-Ping

Offline xiangjun

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Re: Missing atoms
« Reply #1 on: March 08, 2012, 04:49:28 pm »
Hi Xiao-Ping,

Thanks for using 3DNA. Your attached log file shows the atom-naming issue with w3DNA-generated PDB file in Swiss-PdbViewer. I can sort of see where the problem is: currently 3DNA-generated PDB files use O1P/O2P instead of OP1/OP2, and C5M instead of C7 for thymine. I do not know if PdbViewer insists on using DA/DC/DG/DT instead of A/C/G/T.

To verify, could you please test the following PDB files using PdbViewer? What message do you get? Raw PDB file generated directly with fiber is named fb-raw.pdb; renamed O1P/O2P/C5M to OP1/OP2/C7 is fb-new.pdb.

Here is how the files are generated using 3DNA v2.1beta:
fiber -seq=acgt fb-raw.pdb
cp -f fb-raw.pdb fb-new.pdb
ruby -i -pe 'sub(/O1P/, "OP1"); sub(/O2P/, "OP2"); sub(/C5M/, "C7 ")' fb-new.pdb

Xiang-Jun
« Last Edit: March 08, 2012, 04:53:07 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline Z3DNA2012

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Re: Missing atoms
« Reply #2 on: March 08, 2012, 05:10:42 pm »
Dear Xiang-Jun,

Thank you for your prompt reply. The two files linked to the message have the same name. Here I attach the message from Swiss pdb viewer when it open fb-raw.pdb. Could you please link the fb-new.pdb. I have not installed 3DNA locally yet.

Thank you for your help.

Xiao-Ping

Offline Z3DNA2012

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Re: Missing atoms
« Reply #3 on: March 08, 2012, 05:27:09 pm »
Dear Xiang-Jun,

The attached file is the message from Swiss pdb Viewer when open fb-new.pdb.

Thank you.

Xiao-Ping

Offline xiangjun

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Re: Missing atoms
« Reply #4 on: March 08, 2012, 05:27:37 pm »
Okay, I guess we were both online at the same time, and you accessed the draft version while I was revising my post.

Anyway, have a try of the following fb-pdbv3.pdb, generated with the quick written Ruby script cvt2pdbviewer.rb:

Code: [Select]
#!/usr/bin/env ruby

raise "$0 inppdb outpdb" unless ARGV.size == 2

File.open(ARGV.last, "w") do |aFile|
    File.open(ARGV.first).each_line do |line|
        if line =~ /^ATOM  /
            line.sub!(/ O1P/, " OP1")
            line.sub!(/ O2P/, " OP2")
            line.sub!(/ C5M/, " C7 ")
            line.sub!(/  A (\w)/, ' DA \1')
            line.sub!(/  C (\w)/, ' DC \1')
            line.sub!(/  G (\w)/, ' DG \1')
            line.sub!(/  T (\w)/, ' DT \1')
            line.sub!(/1\.00  0\.00/, "1.00  1.00")
        end
        aFile.puts line
    end
end

In addition to change atom names for O1P/O2P/C5M, the script converts A/C/G/T to DA/DC/DG/DT, and sets the temperature factor to 1.00 instead of 0.00 which PDBViewer is not happy with. The complains about missing atom O2' or O2* is likely due to the fact that PdbViewer takes A/C/G/T as RNA nucleotides, which the above conversion also takes care of. It seems PdbViewer is quick strict in following PDB format v3.x.

Unless I have missed something obvious, I believe fb-pdbv3.pdb should make PdbViewer happy. It helps if you could report back how it goes.

Xiang-Jun
« Last Edit: March 10, 2012, 05:55:51 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline Z3DNA2012

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Re: Missing atoms
« Reply #5 on: March 13, 2012, 04:56:22 pm »
Dear Xiang-Jun,

Swiss Pdb Viewer (4.0.4) is happy with the file fb-pdbv3.pdb. Thank you very much. Sorry for the late reply.

Xiao-Ping

Offline xiangjun

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Re: Missing atoms
« Reply #6 on: March 13, 2012, 06:12:02 pm »
Hi Xiao-Ping,

Thanks for reporting back, and I am glad to know that "Swiss Pdb Viewer (4.0.4) is happy with the file fb-pdbv3.pdb." You question prompted me to add a new option "-pdbv3" to make fiber/rebuild-generated structure files compliant with PDB format v3.x, which is apparently what PdbViewer likes. In connection with the option -three_letter_nts recently added to accomandate HADDOCK, 3DNA can now be directly connected with more third-party applications.

The "3DNA web server" is an interface to commonly used 3DNA functionality, and it is hosted and supported by the Olson laboratory at Rutgers University. Currently, w3DNA is based on 3DNA v2.0, thus not yet having the new features in v2.1beta. Your best bet is to download the v2.1beta I just compiled (2012mar13); then you can easily generate a fiber model that PdbViewer is happy with as follow (e.g. bDNA-pdbv3.pdb with sequence 'ACGTTTAA' -- case does not matter):

Code: [Select]
fiber -pdbv3 -seq=acgtttaa bDNA-pdbv3.pdb
Xiang-Jun
« Last Edit: March 13, 2012, 06:21:47 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline Z3DNA2012

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Re: Missing atoms
« Reply #7 on: March 13, 2012, 09:03:51 pm »
Dear Xiang-Jun,

That is nice update, good for all users. We appreciate your efforts very much. 

Best regards,

Xiao-Ping

 

Created and maintained by Dr. Xiang-Jun Lu[律祥俊]· Supported by the NIH grant R01GM096889 · Dr. Lu is currently a member of the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University. The project is in collabration with the Olson Laborarory at Rutgers where 3DNA got started.