[Chimera-users] [chimera-users] --nogui

[吴超]

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 at C1 overlap -1 hbond 0 ignoreIntraRes true log true
findclash :.het at C2 overlap -1 hbond 0 ignoreIntraRes true log true
findclash :.het at C3 overlap -1 hbond 0 ignoreIntraRes true log true
findclash :.het at C4 overlap -1 hbond 0 ignoreIntraRes true log true
findclash :.het at C5 overlap -1 hbond 0 ignoreIntraRes true log true
findclash :.het at C6 overlap -1 hbond 0 ignoreIntraRes true log true
findclash :.het at S overlap -1 hbond 0 ignoreIntraRes true log true
findclash :.het at C7 overlap -1 hbond 0 ignoreIntraRes true log true
findclash :.het at C12 overlap -1 hbond 0 ignoreIntraRes true log true
findclash :.het at CF overlap -1 hbond 0 ignoreIntraRes true log true
findclash :.het at CH overlap -1 hbond 0 ignoreIntraRes true log true
findclash :.het at CI overlap -1 hbond 0 ignoreIntraRes true log true
findclash :.het at C11 overlap -1 hbond 0 ignoreIntraRes true log true
findclash :.het at O11 overlap -1 hbond 0 ignoreIntraRes true log true
findclash :.het at N8 overlap -1 hbond 0 ignoreIntraRes true log true
findclash :.het at C9 overlap -1 hbond 0 ignoreIntraRes true log true
findclash :.het at O9 overlap -1 hbond 0 ignoreIntraRes true log true
findclash :.het at N10 overlap -1 hbond 0 ignoreIntraRes true log true
findclash :.het at CA overlap -1 hbond 0 ignoreIntraRes true log true
findclash :.het at OB overlap -1 hbond 0 ignoreIntraRes true log true
findclash :.het at CC overlap -1 hbond 0 ignoreIntraRes true log true
findclash :.het at 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 at 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 at C1  #0:100.A at CD1  -0.352  4.112
#0:999.het at C1  #0:100.A at CD2  -0.643  4.403
#0:999.het at C1  #0:188.A at CD2  -0.723  4.363
#0:999.het at C1  #0:188.A at CB   -0.883  4.643
#0:999.het at C1  #0:188.A at 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 at gmail.com
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