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Questions and answers => General discussions (Q&As) => Topic started by: Auffinger on June 18, 2012, 04:39:07 am

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Title: O1P_O2P still needed ?
Post by: Auffinger on June 18, 2012, 04:39:07 am
Hi Xiang_Jun,

Just wondering, is currently, with the new version of 3DNA, O1P_O2P still needed ?

Thanks for the reply,

Pascal
Title: Re: O1P_O2P still needed ?
Post by: xiangjun on June 18, 2012, 07:51:05 am
Hi Pascal,

As you know, o1p_o2p is a tiny utility program to check if O1P and O2P atoms of a phosphate group are labelled properly. The program is as useful as before, so still distributed as part of 3DNA v2.1. In my experience, whenever I check a feature consistently throughout nucleic acid containing structures in wwPDB, I (nearly) always find some inconsistency. As a test, you may run o1p_o2p on all entries of the current NDB, and see what you get.

I am sure you are aware that O1P/O2P have been labelled OP1/OP2 respectively as of PDB format v3. The o1p_o2p program recognizes the new naming convention internally, and the output can be written accordingly with option -pdbv3.

In the v2.x series, I've been trying to keep 3DNA backward compatible, with added features/programs and improved functionality for each new release. It is imaginable that in 3DNA v3.x (in the not-too-distant future), among other things, I will reorganize/consolidate program structure, unify command-line options and configuration file formats. At that time, I am sure o1p_o2p as a stand-alone program will be gone, but its functionality would be integrated into a more versatile program.

HTH,

Xiang-Jun
Title: Re: O1P_O2P still needed ?
Post by: Auffinger on June 19, 2012, 01:36:49 pm
Hi Xiang-Jun,

I tried several times to use the -pdbv3 option with the find_pair and analyze programs. Unfortunately, this option seem to work only with the O1P_O2P program. Is that because I am using a very early release of the 2.1 version of 3DNA ?

Best,

Pascal
Title: Re: O1P_O2P still needed ?
Post by: xiangjun on June 19, 2012, 01:50:01 pm
Then install the latest release dated 2012jun06 and have a try again. Report back how it goes.

Xiang-Jun
Title: Re: O1P_O2P still needed ?
Post by: Auffinger on June 20, 2012, 05:42:44 am
Xiang-Jun,

Yes, the latest version works fine with the -pdbv3 option (find_pair and analyze)
BTW, I discovered the -torsion option for analyze that is really cool although it needs to run analyze twice to get all the outputs.

A small comment, in order to parse efficiently the output, it would be nice to have a separate column for BI/BII.
Same for Syn/anti.

Best,

Pascal
Title: Re: O1P_O2P still needed ?
Post by: xiangjun on June 20, 2012, 07:43:33 am
Hi Pascal,

I am glad you found the current version of 3DNA v2.1beta works for your purpose.

Quote
BTW, I discovered the -torsion option for analyze that is really cool although it needs to run analyze twice to get all the outputs.
Yes, the -torsion was designed to be a handy tool for calculating the commonly used DNA/RNA backbone torsion angles. Since 3DNA is a command-line driven toolset and is efficient, I hope running analyze twice is not that a hassle. As mentioned previously, I'd like to reorganize/consolidate the various 3DNA components in future v3.x series. I welcome user feedback in any aspect, including how to name the programs consistently and logically.

Quote
A small comment, in order to parse efficiently the output, it would be nice to have a separate column for BI/BII.
Same for Syn/anti.
Message heard. Will update x3dna_ensemble shortly -- so stay tuned!

What would you suggest the header for the BI/BII and syn/anti columns called?

Best regards,

Xiang-Jun
Title: Re: O1P_O2P still needed ?
Post by: Auffinger on June 20, 2012, 09:31:38 am
Cannot think about something better than "Anti/Syn" or eventually "A/S" and "BI/BII".

Hope it helps,

Pascal
Title: Re: O1P_O2P still needed ?
Post by: xiangjun on June 20, 2012, 10:00:38 am
Quote
Cannot think about something better than "Anti/Syn" or eventually "A/S" and "BI/BII".
Advice taken and appreciated!

Xiang-Jun
Title: Re: O1P_O2P still needed ?
Post by: xiangjun on June 20, 2012, 01:11:19 pm
Hi Pascal,

I've just updated 3DNA v2.1beta to 2012jun20. There are currently separate columns for chi and A/S, e-z and BI/BII, as you suggested. Moreover, the -pdbv3 option is now on by default, so you do not have to bother with adding it in every 3DNA program. The previous behavior is still available by setting explicitly -pdbv3=no.

As always, let me know if you have any problems or suggestions.

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.