Messages

1

General discussions (Q&As) / Re: This structure has broken O3' to P[i+1] linkages

« on: May 25, 2012, 08:20:39 am »

Thankyou, I shall try the same again.


Regards
Vandana.R

2

General discussions (Q&As) / This structure has broken O3' to P[i+1] linkages

« on: May 24, 2012, 01:58:05 am »

Hello dr Lu and other users,
I am new to 3DNA. I ran a pdb file with find_pair followed by analyze. I got this msg "This structure has broken O3' to P[i+1] linkages.". could any one help me in understanding what this means?? Also i need to know the major groove and minor groove which application do i run for the same. I have attached the pdb file i have used.

Regards
Vandana.R

3

General discussions (Q&As) / Re: Problems with installing 3DNA on MinGW/MSYS

« on: April 19, 2012, 07:37:16 am »

As mentioned in my previous post the setup file did not run but the applications ran like find_pair etc. I have installed the  3DNA v2.1beta version on my systems. below is the out put that i got when i ran your command.
Microsoft Windows [Version 6.1.7600]
Copyright (c) 2009 Microsoft Corporation.  All rights reserved.

C:\Users\triindia>cd C:\X3DNA\3DNA bin

C:\X3DNA\3DNA bin>cd $X3DNA/bin
The system cannot find the path specified.

C:\X3DNA\3DNA bin> ls -al
'ls' is not recognized as an internal or external command,
operable program or batch file.

Regards
Vandana.R

4

General discussions (Q&As) / Re: Problems with installing 3DNA on MinGW/MSYS

« on: April 17, 2012, 10:24:40 am »

Thankyou for the reply .I have installed MinGW/MSYS on my system. Apart from this i have also installed raster3d , pymol and Rasmol. The error msg that i get is " 'blocview' is not recognized as an internal or external command,operable program or batch file ". I have followed the steps as that given in the nature protocol paper. Will installing perl solve my problem to some extent ??

Regards
Vandana.R

5

General discussions (Q&As) / Re: Problems with installing 3DNA on MinGW/MSYS

« on: April 16, 2012, 12:15:12 pm »

Hi,

I have installed 3DNA on a windows platform. I can run all applications but have problem in running files like blocview etc. an error as 'blocview' is not recognized as an internal or external command,operable program or batch file keeps poping up. Could plz help me resolve the problem

Regards
Vandana.R

6

General discussions (Q&As) / Re: Problems with installing 3DNA on MinGW/MSYS

« on: April 04, 2012, 11:32:30 am »

Thankyou 

7

General discussions (Q&As) / Re: Problems with installing 3DNA on MinGW/MSYS

« on: April 04, 2012, 01:44:17 am »

I just tried to run the find_pair command and it did display a detailed command-line help then i tried the example given in the nature protocol paper and a PDB coordinate file  named 'multiplets.pdb was created. 
 

8

General discussions (Q&As) / Re: Problems with installing 3DNA on MinGW/MSYS

« on: April 04, 2012, 01:17:56 am »

thankyou. I did execute the commands you posted
1. changed the bin to 3DNA bin
2. the pwd showed the following result 'pwd' is not recognized as an internal or external command,
operable program or batch file.
3. ruby -v showed ruby 1.9.3p125 (2012-02-16) [i386-mingw32]
4. ruby x3dna_setup showed : Unknown shell: not-set -- you've to set X3DNA and PATH manually:
             o set up the X3DNA environment variable
             o add $X3DNA/bin to your command search path
Regards
Vandana

9

General discussions (Q&As) / Re: Problems with installing 3DNA on MinGW/MSYS

« on: April 03, 2012, 12:49:40 pm »

I have installed the 3DNA v2.1beta MinGW/MSYS on windows 7. I have also installed ruby and MinGW as given in your previous post. I have extracted till bin. I have a problem with the x3dna_setup  command. It keeps showing an error as not recognized as internal or external command operable program or file. Can you tell me how to compile this and I also tried setting the environment variable from the control panel but it didn't work.
Thanking you

Vandana