Try and copy this on your command line and see if it works. The trick is to shift first 3 lines by one space.

[xxxxx@zeus ~/curves]$ Cur+ <<!

&inp file=data/1bna, lis=r+bdna,
 lib=standard, &end
 2 1 -1 0 0
 1:12
 24:13
!

Curves is very handy once you get a hang of how to submit the input. Alternatively, I use “3DNA to generate the curves input” --- which is less cryptic.

-----Original Message-----
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Eddie Pryor
Sent: Friday, February 04, 2011 4:05 AM
To: [log in to unmask]
Subject: [ccp4bb] DNA analysis with Curves+

Hi, All,

I am trying to analyze DNA from a recent structure with the program Curves+ (R. Lavery et al, Nuc. Acids. Res (2009) 37:17 5917; http://gbio-pbil.ibcp.fr/Curves_plus/Curves+.html).  I have downloaded the files, and untarred them to a directory "curves" on my machine.  Running the Make command on these files yielded no errors, and I have the executable file Cur+ in this directory.  I am trying to run this program, first using the example data that is provided (the Drew-Dickerson Dodecamer), but am having some difficulties.  The resource for Curves gives the following command to run the program:

/Users/RL/Code/Cur+ <<!
   &inp file=str/1bna, lis=r+bdna,
   lib=/Users/RL/Code/standard,
   &end
2 1 -1 0 0
1: 12
24:13
!

On my machine, the directory structure is slightly different:
   - the executable Cur+ is in a folder named "curves"
   - the files standard_b.lib and standard_s.lib are also in this folder
   - the pdb file 1bna.pdb is in the subfolder "data"

I have tried to run the program by doing the following:

[xxxxx@zeus ~/curves]$ Cur+ <<!
? &inp file=data/1bna, lis=r+bdna,
? lib=standard, &end
? 2 1 -1 0 0
? 1:12
? 24:13
? !

The question mark prompts appear upon hitting enter after each line.

The only error message I get when I try to run this is:

   ---- Error in namelist input for  ----


I have even tried the following (entering all if the input files on the same line):

[xxxxx@zeus ~/curves]$ Cur+ <<! &inp file=data/1bna, lis=r+bdna, lib=standard, &end
? 2 1 -1 0 0
? 1:12
? 24:13
? !

Which gives the following errors:
  inp: Command not found
  end: Not in while/foreach
  At line 28 of file nml.f
  Fortran runtime error: End of file

I am hoping that some of you have had success with running this program and can offer any advice.  I would really appreciate it!

Thanks!

Edward Pryor
Ph.D. Candidate
Tom Hollis Lab
Department of Biochemistry
Center for Structural Biology
Wake Forest University School of Medicine