Dear all,
I am testing Mr BUMP on vista and run into the following error message,
after it has performed fasta and clustal alignements, it downloads
several pdb files such as:
PDB Download log: Chain:1qyc_B
Download Log: Attempting to download the PDB file
for 1qyc from WWPDB site:
URL:
ftp://ftp.wwpdb.org/pub/pdb/data/structures/all/pdb/pdb1qyc.ent.gz
Download Log: This will be saved to:
C:/Users/Thierry/Desktop/LAR-NAP\search_7\PDB_files\1qyc.pdb
But the files which are saved in this directory are in fact:
C:/Users/Thierry/Desktop/LAR-NAP\search_7\PDB_files\1qyc.pdb.gz
and
C:/Users/Thierry/Desktop/LAR-NAP\search_7\PDB_files\pdb1qyc.ent
and afterwards, when executing PDBclip, I get the following message:
Processing PDB files (PDBclip):
-------------------------------
PDB Processing log: Model 1qyc_B - Could not find
the unprocessed PDB file for this model.
and afterwards:
-------------
Process PDBs
-------------
Processing file: 1qyc.pdb, chain: A
-----------------------------------------------
modifying with coord_format.....
Coord_format command line:
C:\CCP4-Packages\ccp4-6.1.1\bin\coord_format.exe
xyzin
C:/Users/Thierry/Desktop/LAR-NAP\search_7\PDB_files\1qyc.pdb
xyzout
C:/Users/Thierry/Desktop/LAR-NAP\search_7\data\1qyc_A\pdbclip\cf_1qyc_A.pdb
PDB download log: coord_format failed for 1qyc_A
PDB download log: log file can be found at:
C:/Users/Thierry/Desktop/LAR-NAP\search_7\data\1qyc_A\pdbclip\coord_format_1qyc_A.log
In this "coord_format_1qyc_A.log" file, I have the following:
File:
"C:/Users/Thierry/Desktop/LAR-NAP\search_7\PDB_files\1qyc.pdb"
Cannot be opened for reading
>>>>>> CCP4 library signal ccp4_general:Cannot
find input file (Error)
raised in ccp4setenv <<<<<<
It seems that the downloaded and uncompressed files are not the
apropriate ones.
How can I get around this problem?
thank you very much for your help
--
Thierry GRANIER
CNRS UMR 5248
CBMN
Bâtiment B8
Avenue des Facultés
Université Bordeaux 1
33405 Talence Cedex
FRANCE
Tél: 33 5 40 00 24 52
Fax: 33 5 40 00 22 00
email: t.gran...@cbmn.u-bordeaux.fr
