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PostPosted: 2016.05.04 11:17 
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Joined: 2016.04.14 12:57
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Hi,

I'm trying to run multiple pdbs in CRYSOL but I keep on getting messages 'error: unable to read input file: *.pdb'. I also have the CRYSOL3 option in my ATSAS package but I'm not sure if it runs teh same as CRYSOL..Any ideas as to why this happens?


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PostPosted: 2016.05.04 13:06 
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Joined: 2015.03.25 09:03
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Location: EMBL Hamburg
Which OS are you using, and what exact command line are you typing?


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PostPosted: 2016.05.04 17:01 
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OS 10.10.5 and the command I'm using is

$ "/Applications/ATSAS/bin/crysol *.pdb bd1971.dat -sm 0.3"


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PostPosted: 2016.05.09 08:17 
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Joined: 2015.03.25 09:03
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Location: EMBL Hamburg
2107086a wrote:
OS 10.10.5 and the command I'm using is

$ "/Applications/ATSAS/bin/crysol *.pdb bd1971.dat -sm 0.3"


I'm assuming you mean
Code:
$ /Applications/ATSAS/bin/crysol *.pdb bd1971.dat -sm 0.3

(without the quotation marks)

Code:
*.pdb
means "all files with names ending in '.pdb' in the current directory". This so-called 'glob expansion' is done by the command shell and not by crysol itself - the command line that crysol sees will be something like
Code:
crysol A.pdb B.pdb C.pdb bd1971.dat -sm 0.3
. If there are no files ending in .pdb, or if you put the
Code:
*.pdb
in quote marks (
Code:
"*.pdb"
), the glob expansion will not be done and crysol will try to open a file called '*.pdb', but this file does not exist.

In short, you need to run the command from the folder where the pdb files are stored.


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