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Author Topic: O1P_O2P program  (Read 8363 times)

Offline auffinger

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O1P_O2P program
« on: November 08, 2010, 11:10:00 am »
Dear Xiang-Jun,

We are using the O1P_O2P program that s quite useful. Yet, this program removes part of the header and we would like to keep it as it is. Is there an option to keep the entire header or remove it entirely ?

Thanks for your reply,
best regards,

Pascal
pascal auffinger
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Offline xiangjun

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Re: O1P_O2P program
« Reply #1 on: November 08, 2010, 10:24:15 pm »
Hi Pascal,

First, some background information: the utility program [mono:2uhtgbv8]o1p_o2p[/mono:2uhtgbv8] was written for a simple, specific purpose: long time ago, while calculating the RMSD value between the A-DNA NDB entry [mono:2uhtgbv8]adh026[/mono:2uhtgbv8] and the corresponding 3DNA rebuilt structure (with sugar-phosphate backbone), I noticed this RMSD was much larger than expected. Further inspection revealed that the issue was due to a mislabeling of O1P and O2P atoms for this specific NDB entry at that time (still available in directory [mono:2uhtgbv8]X3DNA/examples/analyze_rebuild[/mono:2uhtgbv8]). So [mono:2uhtgbv8]o1p_o2p[/mono:2uhtgbv8] was designed to check for proper O1P/O2P labeling, and to swap them if necessary, given a PDB file. Overall, the utility program works for its purpose, and has been released as part of 3DNA from the very beginning.

As a side note, current PDB/NDB entries have changed O1P/O2P to OP1/OP2. The mislabeling of O1P/O2P for [mono:2uhtgbv8]adh026[/mono:2uhtgbv8] has been corrected. Also, 3DNA v2.0 identifies OP1/OP2 labeling internally, but I still prefer to use O1P/O2P in 3DNA output.

[hr:2uhtgbv8][/hr:2uhtgbv8]
Now back to your question: I am glad that you've found [mono:2uhtgbv8]o1p_o2p[/mono:2uhtgbv8] useful. I know the problem you refer to, regarding header removal from [mono:2uhtgbv8]o1p_o2p[/mono:2uhtgbv8] output PDB file. However, current version of [mono:2uhtgbv8]o1p_o2p[/mono:2uhtgbv8] does not have an option to keep header as is. Conceivably, it should be feasible to add such functionality. I'll consider to put this point in my to-do list for future release of 3DNA (I am busy for my job until the following couple of weeks  8) ). In the meantime, you may prefer to write a script to extract the header from original PDB file, combined with "corrected" O1P/O2P coordinates.

HTH,

Xiang-Jun

Offline auffinger

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Re: O1P_O2P program
« Reply #2 on: November 09, 2010, 06:25:57 am »
Hi Xiang-Jun,

Thanks for your reply. Wrote a script for that purpose. It is just that at a first glance, I didn't realize that the header was shortened. This is a problem when one wants to generate symmetry related images. In fact, shortening the header is probably not very useful here and it would be nice to put at least a note in your program description for other eventual users  8)

Best,

Pascal
pascal auffinger
ibmc-cnrs
15, rue rené descartes
67084 strasbourg cedex
france

web sites:
http://www-ibmc.u-strasbg.fr/arn/Westho ... er_pub.HTM
http://www-ibmc.u-

Offline auffinger

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Re: O1P_O2P program
« Reply #3 on: November 15, 2010, 02:09:54 pm »
Hi again Xiang-Jun,

Read your most recent blog page and found it quite interesting. The question I am asking now is: given the recent PDB changes, is the O1P_O2P still interesting to use? I noted that this program still finds mislabelled O1P/O2P atoms and corrects them. Yet, after checking some of them, I noted that these changes occur mostly for terminal residues and I am not sure that everything is OK at this level (you could eventually like to check file 10MH). On my side, I will continue to check the files, it might well be that some modified residues are also mislabeled in original files. A bunch of O1P/O2P atoms can still be found in PDB files (HETATM lines; see 1RZR).

Best,

Pascal
pascal auffinger
ibmc-cnrs
15, rue rené descartes
67084 strasbourg cedex
france

web sites:
http://www-ibmc.u-strasbg.fr/arn/Westho ... er_pub.HTM
http://www-ibmc.u-

Offline xiangjun

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Re: O1P_O2P program
« Reply #4 on: November 15, 2010, 07:42:00 pm »
Hi Pascal,

Thanks for reading my recent blog post on O1P/O2P labeling, which was inspired by your above question!

Quote
given the recent PDB changes, is the O1P_O2P still interesting to use? Yet, after checking some of them, I noted that these changes occur mostly for terminal residues and I am not sure that everything is OK at this level (you could eventually like to check file 10MH).
The mislabeling issue should not have happened in PDB/NDB in the first place. The very fact that such error did happen, as shown for [mono:3dv13ht8]adh026[/mono:3dv13ht8], prompted the creation of the [mono:3dv13ht8]o1p_o2p[/mono:3dv13ht8] utility program. I am not surprised at all if you still find mislabeled O1P/O2P atoms in the currently "remediated" PDB files. I have quickly checked [mono:3dv13ht8]10MH[/mono:3dv13ht8] --  the two terminal phosphate groups (DC-402  on chain B and DG-422  on chain C) apparently still have O1P/O2P mislabeled.

Quote
On my side, I will continue to check the files, it might well be that some modified residues are also mislabeled in original files.
I think it is certainly a good idea to continue to check the files you care about. The command-line driven [mono:3dv13ht8]o1p_o2p[/mono:3dv13ht8] utility can be applied to any compliant PDB file, not just the one from PDB/NDB. Please report back if meet further issues, or have a request for added functionality :wink:.  Hopefully, I'd be able to "spare" more time to address 3DNA-related questions in the future  8) .

Xiang-Jun

 

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.