Dear sir/madam,
I am doing research at IIT Kharagpur on modeling retrotransposable genes. I faced severe problem while running Widows based modeller version. The steps I had followed for running modeller is
1) generated alignment file as .ali file
2) generated pdb display file and structure file as pdb format.
3) Model-default
4) Then I run the modeller from the command prompt but after giving mod.bat model-default.top it was showing error Len,string: D:\sh\modeller6v2\bin\sg\
5) The folder containing the modeller is sh and sg is folder in which we are working.
Please let me know how to work out this problem.
We will be greatly thankful for your kind cooperation.
Thanking you.
Yahoo! India Careers: Over 65,000 jobsonline.
On Wed, Jul 14, 2004 at 07:16:24AM +0100, shantanu gautam wrote: > I am doing research at IIT Kharagpur on modeling retrotransposable genes. > I faced severe problem while running Widows based modeller version. The > steps I had followed for running modeller is > > 1) generated alignment file as .ali file > > 2) generated pdb display file and structure file as pdb format. > > 3) Model-default > > 4) Then I run the modeller from the command prompt but after giving > mod.bat model-default.top it was showing error Len,string: > D:\sh\modeller6v2\bin\sg\ > > 5) The folder containing the modeller is sh and sg is folder in > which we are working.
1. Run modeller with 'mod.bat model-default.top > model-default.log'. 2. Send me model-default.top, model-default.log, and any other input files you used (i.e. .ali file and PDB file).
Without seeing your input files, it's extremely hard to diagnose your problem.
Ben Webb, Modeller Caretaker
Summarizing for the list:
On Wed, Jul 14, 2004 at 07:16:24AM +0100, shantanu gautam wrote: > I faced severe problem while running Widows based modeller version. ... > 4) Then I run the modeller from the command prompt but after giving > mod.bat model-default.top it was showing error > Len,string: D:\sh\modeller6v2\bin\sg\
The actual error Modeller was giving was the (admittedly somewhat cryptic) str_sn2_E> # of ' <> even: (i.e. 'uneven number of single quotes') when processing the following: SET ATOM_FILES_DIRECTORY = 'D:\sh\modeller6v2\bin\sg'
Modeller treats the \ character as an escape character in standard Unix fashion, and as such doesn't see the closing quote on this string. Additionally, the : character is used as a directory separator, so cannot be used to specify the D: drive.
The solution: use Unix-style path names, i.e. SET ATOM_FILES_DIRECTORY = '/sh/modeller6v2/bin/sg/'
Modeller is unable, however, to read files from a drive different to that you're running it from.
Ben Webb, Modeller Caretaker
participants (2)
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Modeller Caretaker -
shantanu gautam