Messages

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) /

« on: April 13, 2007, 01:17:47 am »

Hi, Xiang-Jun

Thank You.   But I am  not getting how i should extract it or why i am getting the message "NO BEST REPRESENTATIVE ASSIGNED".

Bala

4

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

5

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

6

General discussions (Q&As) /

« on: February 24, 2007, 01:21:28 am »

Hi,
Thank You.  I gave the commands one by one as you suggested and i have pasted below what i got.

echo $SHELL
/bin/bash

ls /usr/local/X3DNA/bin/find_pair
ls: /usr/local/X3DNA/bin/find_pair: Permission denied

export X3DNA=/usr/local/X3DNA
echo $X3DNA
/usr/local/X3DNA

ls $X3DNA/bin/find_pair
ls: /usr/local/X3DNA/bin/find_pair: Permission denied

export PATH=$PATH:$X3DNA/bin

which find_pair
alias find_pair='/usr/local/X3DNA/bin/find_pair'


Finally i gave "find_pair" in the shell prompt and it throwed following message.

bash: /usr/local/X3DNA/bin/find_pair: Permission denied

7

General discussions (Q&As) /

« on: February 22, 2007, 01:50:29 am »

Hello xiangjun,

Sorry for the delayed reply. I was on leave.

I have installed the sofware in /usr/local/X3DNA

I have set the following path in .bashrc file

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

When i give "which find_pair" as you suggestted, i got the following big message.


/usr/bin/which: no find_pair in (/usr/local/autodock/share/bin:/usr/local/autodock/i86Linux2/bin:
/usr/local/ifc/bin:/usr/local/autodock/share/bin:/usr/local/autodock/i86Linux2/bin:
/usr/local/ifc/bin:/usr/local/autodock/share/bin:/usr/local/autodock/i86Linux2/bin:
/usr/local/ifc/bin:/usr/kerberos/bin:/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:
/usr/local/amber8/exe:/usr/local/pass:/usr/local/nab-5.0/bin://usr/local/grace/bin:
/usr/local/mmtsb_toolset/perl:/usr/local/mmtsb_toolset/bin:/usr/local/X3DNA//bin:
/home/madhu/bin:/usr/local/amber8/exe:/usr/local/pass:/usr/local/nab-5.0/bin:
//usr/local/grace/bin:/usr/local/mmtsb_toolset/perl:/usr/local/mmtsb_toolset/bin:
/usr/local/X3DNA//bin:/usr/local/amber8/exe:/usr/local/pass:/usr/local/nab-5.0/bin:
//usr/local/grace/bin:/usr/local/mmtsb_toolset/perl:/usr/local/mmtsb_toolset/bin:
/usr/local/X3DNA//bin)

8

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

9

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