error: unable to read input file: *.pdb

Calculation of SAXS and SANS profiles (CRYSOL, CRYSON), superposition of models (SUPCOMB, DAMAVER, DAMCLUST), database DARA
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2107086a
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error: unable to read input file: *.pdb

#1 Post by 2107086a » 2016.05.04 11:17

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?

ckerr
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Location: EMBL Hamburg

Re: error: unable to read input file: *.pdb

#2 Post by ckerr » 2016.05.04 13:06

Which OS are you using, and what exact command line are you typing?

2107086a
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Posts: 11
Joined: 2016.04.14 12:57

Re: error: unable to read input file: *.pdb

#3 Post by 2107086a » 2016.05.04 17:01

OS 10.10.5 and the command I'm using is

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

ckerr
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Posts: 86
Joined: 2015.03.25 09:03
Location: EMBL Hamburg

Re: error: unable to read input file: *.pdb

#4 Post by ckerr » 2016.05.09 08:17

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

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$ /Applications/ATSAS/bin/crysol *.pdb bd1971.dat -sm 0.3
(without the quotation marks)

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*.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

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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

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*.pdb
in quote marks (

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"*.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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