Hi Edward,
Have you tried just editing the short command script on a text editor so you keep the formatting. You could also try the full path for the executable and the lib files while you are at it.
I have a problem of a different nature. I get get the example data file to work but no other file seems to work. I have tried editing other pdb files to make them look more like the example pdb but none seems to work. I get an error message in the .lis file which reads;
Base atom C1* missing in strand 2 level 1 (Necessary for analysis). I have gotten the same error with a few files from the NDB and PDB as well as with mine. Any suggestions on how to solve this problem will be highly appreciated.
Raymond.
________________________________________
From: CCP4 bulletin board [[log in to unmask]] On Behalf Of KAMESH Narasimhan [[log in to unmask]]
Sent: Friday, February 04, 2011 4:44 AM
To: [log in to unmask]
Subject: Re: [ccp4bb] DNA analysis with Curves+
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
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