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Topics - bala

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1
General discussions (Q&As) / irregular structure
« on: August 30, 2007, 09:24:44 am »
I want to calculate the struc.parameters for a irregular structure. The structure contains mismatche and bulge region.  We want to calculate  all parameters especially for these two regions but when i tried in 3DNA, it calculates parameters only for those pairs it for which it detects HYD bond.  I dnt know how to get aroud of this problem. Can anyone pls share your experience of using 3DNA for structures which are having bulges and folds etc.

I have uploaded the structure in the link provided the announcement section of 3DNA forum. The structure name is "structur.pdb".

thanks
Bala

2
General discussions (Q&As) / using 3DNA for irregular nuc. structure
« on: April 16, 2007, 09:22:52 am »
Hello,

I have a RNA duplex with a bulge on one strand.   I want to calculate the helicoidal parameters by excluding the bulge part.  When i run the find_pair followed by analyze, it takes the whole structure and analyze.  To be precise, is there any way that i can do the analysis only on a specific portion of my interest.  

It would be highly helpful if someone could wite me your experience (some ref's) on using 3DNA for irregular nuc. acid structure.

regards,
Bala

3
General discussions (Q&As) / extracting best representative from NMR
« on: April 09, 2007, 10:53:23 am »
Hello,

I want to extract the best structure from a NMR ensemble. When i run the command as below,

ex_str -nmrb  qd_nmr.pdb best.pdb

I got the following message
------------------------------------------------------------------------------------------
No best representative conformer assigned: set to 1
Model selected #1
------------------------------------------------------------------------------------------

I think the program selects model 1 by default if it cant find a best representative.  Kindly write 1) what may be wrong 2) What is the criteria based on which this program selects the best representative.

thanks in advance,
Bala

4
General discussions (Q&As) / broken O3'[i] to P[i+1] linkages
« on: April 05, 2007, 08:29:07 am »
Hello all,

I am getting a message as pasted below when i run find_pair.  I would like to know whether it is an information or an error.  When i view the structure, i dnt find any missing linkage. Kindly write me why this message comes and how i can rectify it.

 ...... /home/souvik/X3DNA/BASEPARS/ ......
 ...... reading file: misc_3dna.par ......
This structure has broken O3' to P[i+1] linkages

Bala

5
General discussions (Q&As) / using 3dna to analyze quadruplex
« on: February 13, 2007, 04:30:21 am »
Hello,

I am using 3DNA to analyze a quadruplex structure.  I gave the command as follows,

find_pair -pt quad.pdb quad.bps | anyhelix.  

It created the following files
mulbp.inp, mref_frames.dat, allpairs.pdb, ref_frames.dat etc.

I want to calculate the backbone torsions and pucker.  But i am not finding these informations in any file. I doubt whether it is possible to calculate these values for quadruplex using X3DNA.

Bala

6
General discussions (Q&As) / setting path for 3DNA in linux
« on: February 13, 2007, 03:59:51 am »
Hello,

First of all, i would like to thank the authors for such a useful program.  

I am using 3DNA in Red hat enterprise Linux 3.0.  I downloaded the software and installed in /usr/local.  When i unzip and untar the file, it created a directory called X3DNA.

so my path is /usr/local/X3DNA.  Then i set an enviroment variable as follows in my .bashrc file.

export X3DNA=/usr/local/X3DNA/
export PATH=$PATH:$X3DNA/bin

Howver, when i run  any executable, say find_pair, it says command not found and hence every time i am copying my pdb file /usr/local/X3DNA and run the program. Why is it so.  Kindly suggest me something.  Is is because the environmental variable name and the directory name are the same.

Bala

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Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University