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Today's Topics:

1. file name problem (Starr Hazard) 2. Re: file name problem (Modeller Caretaker) 3. Re: To Model missing domains in the content of the rest (Shirley Li) 4. To use separate templates for different region of a protein (Shirley Li)

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Message: 1 Date: Thu, 08 Dec 2005 13:53:38 -0500 From: Starr Hazard Subject: [modeller_usage] file name problem To: modeller_usage@salilab.org Message-ID: Content-Type: text/plain; charset=us-ascii; format=flowed

Folks,

The following lines:

mdl.assess_dope(output='ENERGY_PROFILE NO_REPORT', file=code+'.profile', normalize_profile=True, smoothing_window=15)

are producing output files with a question mark in the name string.

ABC31_HUMAN.BL09950001.pdb?.profile

The question mark renders cp, mv and rename incapable of doing anything with the file. Is there a way to prevent modeller from appending the question mark to the created files?

Thanks,

Starr

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Message: 2 Date: Thu, 08 Dec 2005 11:17:16 -0800 From: Modeller Caretaker Subject: Re: [modeller_usage] file name problem To: Starr Hazard Cc: modeller_usage@salilab.org Message-ID: 439886BC.6050700@salilab.org Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Starr Hazard wrote: > mdl.assess_dope(output='ENERGY_PROFILE NO_REPORT', > file=code+'.profile', > normalize_profile=True, smoothing_window=15) > > are producing output files with a question mark in the name string. > > ABC31_HUMAN.BL09950001.pdb?.profile

If this is from your earlier script, you're getting 'code' from the following bit of Python: code = in_file.readline() Note that readline() does not remove the line-end character(s), and that's probably confusing Modeller. Try putting in code = code.rstrip('\r\n') after you read the line from your file.

> The question mark renders cp, mv and rename incapable of doing anything > with the file.

You can just quote the filename, or escape the ? with a \ character, to make cp, mv and friends work with it.

Ben Webb, Modeller Caretaker