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

[Eric Pettersen]

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 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
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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