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 [[email protected]] On Behalf Of KAMESH Narasimhan [[email protected]] Sent: Friday, February 04, 2011 4:44 AM To: [email protected] 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:[email protected]] On Behalf Of Eddie Pryor Sent: Friday, February 04, 2011 4:05 AM To: [email protected] 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
