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Hi Chao,<div><span class="Apple-tab-span" style="white-space:pre"> </span>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:</div><div><br class="webkit-block-placeholder"></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>outFile.close()</div><div><br class="webkit-block-placeholder"></div><div>to:</div><div><div><br class="webkit-block-placeholder"></div></div><div><div><span class="Apple-tab-span" style="white-space:pre"> </span>import sys</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>if fileName != sys.stdout:</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>outFile.close()</div><div><br class="webkit-block-placeholder"></div><div>--Eric</div><div><br class="webkit-block-placeholder"></div></div><div><br><div> <span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>Eric Pettersen</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>UCSF Computer Graphics Lab</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> </span><a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></p><br class="Apple-interchange-newline"></span> </div><br><div><div>On Feb 25, 2008, at 5:23 AM, 吴超 wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hi, folks!<br>I came across with a problem when using <br>chimera --nogui file.cmd > data.log<br><br>the file.cmd is as follows:<br><br>open /home/lynn/project/hivrt_pdb/holo_without_mutation/1C1C.pdb<br>findclash :.het@C1 overlap -1 hbond 0 ignoreIntraRes true log true<br> findclash :.het@C2 overlap -1 hbond 0 ignoreIntraRes true log true<br>findclash :.het@C3 overlap -1 hbond 0 ignoreIntraRes true log true<br>findclash :.het@C4 overlap -1 hbond 0 ignoreIntraRes true log true<br>findclash :.het@C5 overlap -1 hbond 0 ignoreIntraRes true log true<br> findclash :.het@C6 overlap -1 hbond 0 ignoreIntraRes true log true<br>findclash :.het@S overlap -1 hbond 0 ignoreIntraRes true log true<br>findclash :.het@C7 overlap -1 hbond 0 ignoreIntraRes true log true<br>findclash :.het@C12 overlap -1 hbond 0 ignoreIntraRes true log true<br> findclash :.het@CF overlap -1 hbond 0 ignoreIntraRes true log true<br>findclash :.het@CH overlap -1 hbond 0 ignoreIntraRes true log true<br>findclash :.het@CI overlap -1 hbond 0 ignoreIntraRes true log true<br>findclash :.het@C11 overlap -1 hbond 0 ignoreIntraRes true log true<br> findclash :.het@O11 overlap -1 hbond 0 ignoreIntraRes true log true<br>findclash :.het@N8 overlap -1 hbond 0 ignoreIntraRes true log true<br>findclash :.het@C9 overlap -1 hbond 0 ignoreIntraRes true log true<br>findclash :.het@O9 overlap -1 hbond 0 ignoreIntraRes true log true<br> findclash :.het@N10 overlap -1 hbond 0 ignoreIntraRes true log true<br>findclash :.het@CA overlap -1 hbond 0 ignoreIntraRes true log true<br>findclash :.het@OB overlap -1 hbond 0 ignoreIntraRes true log true<br>findclash :.het@CC overlap -1 hbond 0 ignoreIntraRes true log true<br> findclash :.het@CD overlap -1 hbond 0 ignoreIntraRes true log true<br><br><br>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.<br>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 <br> <br>open /home/lynn/project/hivrt_pdb/holo_without_mutation/1C1C.pdb<br>findclash :.het@C1 overlap -1 hbond 0 ignoreIntraRes true log true<br><br><br>Results are: <br>Opening 1C1C.pdb...<br>1 model opened<br>Opened 1C1C.pdb containing 1 model, 7997 atoms, and 1096 residues<br> Allowed overlap: -1<br>H-bond overlap reduction: 0<br>Ignore overlap between atoms separated by 4 bonds or less<br>Ignore intra-residue overlaps<br><br>5 overlaps<br>atom1 atom2 overlap distance<br>#0:999.het@C1 #0:100.A@CD1 -0.352 4.112<br> #0:999.het@C1 #0:100.A@CD2 -0.643 4.403<br>#0:999.het@C1 #0:188.A@CD2 -0.723 4.363<br>#0:999.het@C1 #0:188.A@CB -0.883 4.643<br>#0:999.het@C1 #0:188.A@CG -0.989 4.479<br><br><br><br><br><br><br><br><br><br>Error in the shell is as follows:<br> <br>$ /usr/local/chimera/bin/chimera --nogui /home/lynn/cmd/1C1C.cmd > /home/lynn/project/data/distance/1C1C.dist<br>Traceback (most recent call last):<br> File "/usr/local/chimera/share/__main__.py", line 65, in ?<br> value = chimeraInit.init(sys.argv)<br> File "/usr/local/chimera/share/chimeraInit.py", line 358, in init<br> replyobj.reportException(<br> File "CHIMERA/share/chimera/replyobj.py", line 610, in reportException<br> File "CHIMERA/share/chimera/replyobj.py", line 438, in nogui_message<br>ValueError: I/O operation on closed file<br>$ <br><br><br><br><br><br><br><br><br><br>Could anyone give me hand? I am really frustrated! Thanks in advance...<br> <br><br><br clear="all"><br>-- <br>Chao Wu<br><br>Currently:<br>National Institute of Biological Sciences, Beijing<br>Huang Niu's Lab<br><a href="http://www.nibs.ac.cn/" target="_blank">http://www.nibs.ac.cn/</a><br>Tel: 80726688-8572<br> Address: Beijing ZhongGuanCun Life Science Park, NO.7 Science Park East Road, NIBS B427<br> Postcode: 102206<br><br><br><br>Life Science Honors Program, China Agricultural University<br>PO.1055, NO.2 YuanMingYuan west road, Beingjing, 100094<br>P.R. China<br>Tel: 86-10-62812484<br>E-mail: <a href="mailto:lynnwuchao@gmail.com" target="_blank">lynnwuchao@gmail.com</a><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">_______________________________________________</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Chimera-users mailing list</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><a href="http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users">http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users</a></div> </blockquote></div><br></div></body></html>