Eric Pettersen
UCSF Computer Graphics Lab
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