[chimera-users] --nogui
Hi, folks! I came across with a problem when using chimera --nogui file.cmd > data.log the file.cmd is as follows: open /home/lynn/project/hivrt_pdb/holo_without_mutation/1C1C.pdb findclash :.het@C1 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@C2 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@C3 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@C4 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@C5 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@C6 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@S overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@C7 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@C12 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@CF overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@CH overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@CI overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@C11 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@O11 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@N8 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@C9 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@O9 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@N10 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@CA overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@OB overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@CC overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@CD overlap -1 hbond 0 ignoreIntraRes true log true If i use the graphic version and read the cmd file, it worked quite well and I can find all I need in the reply log. But when it came to the nogui version, the data file only contains the result of the first two lines of the cmd file. That is open /home/lynn/project/hivrt_pdb/holo_without_mutation/1C1C.pdb findclash :.het@C1 overlap -1 hbond 0 ignoreIntraRes true log true Results are: Opening 1C1C.pdb... 1 model opened Opened 1C1C.pdb containing 1 model, 7997 atoms, and 1096 residues Allowed overlap: -1 H-bond overlap reduction: 0 Ignore overlap between atoms separated by 4 bonds or less Ignore intra-residue overlaps 5 overlaps atom1 atom2 overlap distance #0:999.het@C1 #0:100.A@CD1 -0.352 4.112 #0:999.het@C1 #0:100.A@CD2 -0.643 4.403 #0:999.het@C1 #0:188.A@CD2 -0.723 4.363 #0:999.het@C1 #0:188.A@CB -0.883 4.643 #0:999.het@C1 #0:188.A@CG -0.989 4.479 Error in the shell is as follows: $ /usr/local/chimera/bin/chimera --nogui /home/lynn/cmd/1C1C.cmd > /home/lynn/project/data/distance/1C1C.dist Traceback (most recent call last): File "/usr/local/chimera/share/__main__.py", line 65, in ? value = chimeraInit.init(sys.argv) File "/usr/local/chimera/share/chimeraInit.py", line 358, in init replyobj.reportException( File "CHIMERA/share/chimera/replyobj.py", line 610, in reportException File "CHIMERA/share/chimera/replyobj.py", line 438, in nogui_message ValueError: I/O operation on closed file $ Could anyone give me hand? I am really frustrated! Thanks in advance... -- Chao Wu Currently: National Institute of Biological Sciences, Beijing Huang Niu's Lab http://www.nibs.ac.cn/ Tel: 80726688-8572 Address: Beijing ZhongGuanCun Life Science Park, NO.7 Science Park East Road, NIBS B427 Postcode: 102206 Life Science Honors Program, China Agricultural University PO.1055, NO.2 YuanMingYuan west road, Beingjing, 100094 P.R. China Tel: 86-10-62812484 E-mail: lynnwuchao@gmail.com
Hi Chao, It's a bug. The first findclash closes the output file (standard output) so all the subsequent findclashes fail. I've fixed it in the code now and the fix will be in tomorrow's daily build. It's not too big a change so you might want to just edit the file with the bug yourself. The file is : <your Chimera installation>/share/ DetectClash/__init__.py . On line 294 change: outFile.close() to: import sys if fileName != sys.stdout: outFile.close() --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Feb 25, 2008, at 5:23 AM, 吴超 wrote:
Hi, folks! I came across with a problem when using chimera --nogui file.cmd > data.log
the file.cmd is as follows:
open /home/lynn/project/hivrt_pdb/holo_without_mutation/1C1C.pdb findclash :.het@C1 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@C2 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@C3 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@C4 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@C5 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@C6 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@S overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@C7 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@C12 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@CF overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@CH overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@CI overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@C11 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@O11 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@N8 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@C9 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@O9 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@N10 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@CA overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@OB overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@CC overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@CD overlap -1 hbond 0 ignoreIntraRes true log true
If i use the graphic version and read the cmd file, it worked quite well and I can find all I need in the reply log. But when it came to the nogui version, the data file only contains the result of the first two lines of the cmd file. That is
open /home/lynn/project/hivrt_pdb/holo_without_mutation/1C1C.pdb findclash :.het@C1 overlap -1 hbond 0 ignoreIntraRes true log true
Results are: Opening 1C1C.pdb... 1 model opened Opened 1C1C.pdb containing 1 model, 7997 atoms, and 1096 residues Allowed overlap: -1 H-bond overlap reduction: 0 Ignore overlap between atoms separated by 4 bonds or less Ignore intra-residue overlaps
5 overlaps atom1 atom2 overlap distance #0:999.het@C1 #0:100.A@CD1 -0.352 4.112 #0:999.het@C1 #0:100.A@CD2 -0.643 4.403 #0:999.het@C1 #0:188.A@CD2 -0.723 4.363 #0:999.het@C1 #0:188.A@CB -0.883 4.643 #0:999.het@C1 #0:188.A@CG -0.989 4.479
Error in the shell is as follows:
$ /usr/local/chimera/bin/chimera --nogui /home/lynn/cmd/1C1C.cmd > / home/lynn/project/data/distance/1C1C.dist Traceback (most recent call last): File "/usr/local/chimera/share/__main__.py", line 65, in ? value = chimeraInit.init(sys.argv) File "/usr/local/chimera/share/chimeraInit.py", line 358, in init replyobj.reportException( File "CHIMERA/share/chimera/replyobj.py", line 610, in reportException File "CHIMERA/share/chimera/replyobj.py", line 438, in nogui_message ValueError: I/O operation on closed file $
Could anyone give me hand? I am really frustrated! Thanks in advance...
-- Chao Wu
Currently: National Institute of Biological Sciences, Beijing Huang Niu's Lab http://www.nibs.ac.cn/ Tel: 80726688-8572 Address: Beijing ZhongGuanCun Life Science Park, NO.7 Science Park East Road, NIBS B427 Postcode: 102206
Life Science Honors Program, China Agricultural University PO.1055, NO.2 YuanMingYuan west road, Beingjing, 100094 P.R. China Tel: 86-10-62812484 E-mail: lynnwuchao@gmail.com _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
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Eric Pettersen -
吴超