Messages

1

General discussions (Q&As) / Re: local helical axis

« on: April 20, 2012, 11:06:07 am »

I understand now. I think, I can do in two ways: (1) I can rebuild an atomic structure, then analyze the structure to obtain the local helical axis,  (2) I can use matlab to compute a local helical axis with the algorithm introduced in the manual.

Thanks,

Fei

2

General discussions (Q&As) / Re: local helical axis

« on: April 19, 2012, 04:44:42 pm »

Hi! Xiangjun:
I created a file containing the values of step parameters like this:

8 # base-pairs
   0 # ***local base-pair & step parameters***
  #   Shear Stretch Stagger  Buckle Prop-Tw Opening   Shift   Slide    Rise    Tilt    Roll   Twist
A-T     0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
A-T     0.00    0.00    0.00    0.00    0.00    0.00   -2.67    0.52    3.25  -13.51    6.10 -101.59
A-T     0.00    0.00    0.00    0.00    0.00    0.00   -2.67    0.52    3.25  -13.51    6.10 -101.59
A-T     0.00    0.00    0.00    0.00    0.00    0.00   -2.67    0.52    3.25  -13.51    6.10 -101.59
........
Then I used 'rebuild' command. The output file was ref_frames.dat and an .alc file. The ref_frames.dat is as below:

8 base-pairs
...     1 A-T ...
    0.0000    0.0000    0.0000
    1.0000    0.0000    0.0000
    0.0000    1.0000    0.0000
    0.0000    0.0000    1.0000
...     2 A-T ...
   -0.8746    2.5068    3.3034
   -0.1866   -0.9758    0.1141
    0.9508   -0.2086   -0.2290
    0.2472    0.0658    0.9667
...     3 A-T ...
    2.4889    3.0548    5.8231
   -0.8648    0.3931    0.3125
   -0.4323   -0.8994   -0.0651
    0.2554   -0.1914    0.9477
(....base pair 4-5)
...     7 A-T ...
    5.0245    0.8174   17.2665
   -0.2431    0.9359    0.2549
   -0.9621   -0.2662    0.0597
    0.1237   -0.2307    0.9651
...     8 A-T ...
    3.2341   -1.4303   20.3816
    0.9983    0.0588    0.0043
   -0.0588    0.9982    0.0089
   -0.0038   -0.0091    1.0000
~                             

I guess, the first line for each base pair is a origin and the other three lines are a middle frame. I used the repeating values of step parameters so the vector of local helical axis of each step should be the same. I wonder where is the vectors of the local helical axis. I also attach a sample figure I made. I need to know the local helical axis and rotate it to a perpendicular position.

Best,

Fei

3

General discussions (Q&As) / local helical axis

« on: April 19, 2012, 12:23:34 pm »

HI!
I am building a uniform helix with repeating values of step parameters. In this way, the local helical axis is the same for every step. I want to put the local helical axis in  at the center and perpendicular to the bottom of my figure. Where can I find the vectors of the local helical axis? Are they contained in the ref_frames.dat generated by the 'rebuild' command?

Thanks a lot!

Fei

4

General discussions (Q&As) / Re: 3DNA on 64 bit Linux (Ubuntu)

« on: October 17, 2011, 04:13:19 pm »

Hi! Xiang-jun:
Thanks a lot! It works smoothly.

Fei

5

General discussions (Q&As) / 3DNA on 64 bit Linux (Ubuntu)

« on: September 09, 2011, 04:52:36 pm »

I have to work at 64 bit Linux (Ubuntu) system. Now I can't run X3DNA (32 bit Linux version) at 64 bit Linux system.
Do we have any solution to avoid this problem or we need to compile 3DNA at 64 bit Linux (Ubuntu)?
Thanks a lot!

Fei

6

General discussions (Q&As) / 3DNA setup at Linux

« on: August 19, 2011, 04:06:23 pm »

HI! Xiangjun:
I downloaded and unzipped 3DNA in Linux version. I went to /X3DNA/bin/ and run x3dna_setup, it gave me error message

feixu@homestar:~/X3DNA/bin$ x3dna_setup
x3dna_setup: command not found

I checked the mode of the directories. They are executable.
feixu@homestar:~/X3DNA$ ls -l
total 24
drwx------  2 feixu feixu 4096 2008-08-06 18:56 bin
drwx------  5 feixu feixu 4096 2008-08-06 18:56 config
drwx------  2 feixu feixu 4096 2008-10-14 01:39 doc
drwx------  7 feixu feixu 4096 2008-08-06 18:20 examples
drwx------ 58 feixu feixu 4096 2008-08-06 18:20 fiber
drwx------  9 feixu feixu 4096 2008-08-06 18:20 NP_Recipes

And the OS system is UBUNTU 11.04

Could you please think of the solution?

Thanks a lot!

Fei