<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">If you have a large number of PDBs then you might want to use Python, where you have access to loops and variables. Say you had the PDBs listed in a file, one per line, named "mypdbs". Then you might use a Python script like this:<DIV><BR class="khtml-block-placeholder"></DIV><DIV>--------------------------------------</DIV><DIV>import chimera</DIV><DIV>from chimera import runCommand</DIV><DIV>f = open("mypdbs", "r")</DIV><DIV>for line in f:</DIV><DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>pdbID = line.strip()</DIV><DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>runCommand("open " + pdbID)</DIV><DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>runCommand("scale 1.5; ~disp; ribbon; ribrepr smooth; rainbow")</DIV><DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>runCommand("copy file %s.png png supersample 5" % pdbID)</DIV><DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>runCommand("close all")</DIV><DIV>--------------------------------------</DIV><DIV>Note that the "runCommand" function allows you to do things that you know the Chimera command for without knowing what the Python equivalent is. Assuming you name the script file with a ".py" ending so that Chimera can recognize it as Python, then you can run the script with any of the ways that Chimera opens files (File...Open dialog, "open" command, startup shell command argument).</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Also, Chimera needs the graphics window to be showing and not obscured by other windows in order to render the images. If you are doing a lot of images you may have to turn off your screen saver so that it doesn't hide the Chimera window.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>--Eric</DIV><DIV><BR><DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT face="Helvetica" size="5" style="font: 16.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN>Eric Pettersen</FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT face="Helvetica" size="5" style="font: 16.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN>UCSF Computer Graphics Lab</FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT face="Helvetica" size="5" style="font: 16.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN><A href="mailto:pett@cgl.ucsf.edu">pett@cgl.ucsf.edu</A></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 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></DIV> <BR class="Apple-interchange-newline"> </DIV><BR><DIV><DIV>On Sep 28, 2006, at 9:14 AM, Elaine Meng wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite">Hi Vishal,<DIV>Actually you can do this with a Chimera command script, as opposed to programming in Python. A command script just contains the same commands you would enter in the Command Line. I'm not sure of what type of saving you had in mind, " but the "copy" command can be used to save an image file, "save" to save a session, and "write" to save a PDB file.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>This page links to all the command man pages, plus it discusses command scripts (at the bottom):</DIV><DIV><A href="http://www.cgl.ucsf.edu/chimera/1.2199/docs/UsersGuide/framecommand.html">http://www.cgl.ucsf.edu/chimera/1.2199/docs/UsersGuide/framecommand.html</A></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Just opening the command file will execute the commands.</DIV><DIV>Here are links to a couple of example command files:</DIV><DIV><A href="http://www.cgl.ucsf.edu/chimera/1.2199/docs/UsersGuide/tutorials/setup.com">http://www.cgl.ucsf.edu/chimera/1.2199/docs/UsersGuide/tutorials/setup.com</A></DIV><DIV><A href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/recorder/1gfl.com">http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/recorder/1gfl.com</A></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>And here is another, between the dashed lines:</DIV><DIV>-----------------------------------------------------------------</DIV><DIV>open 1hxx</DIV><DIV>open 1pho</DIV><DIV>modelcolor coral #0</DIV><DIV>modelcolor cornflower blue #1</DIV><DIV>~disp; rep bs; ribbon; ribrepr smooth</DIV><DIV>matchmaker #0 #1</DIV><DIV>-----------------------------------------------------------------</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>I guess the main difficulty if you are saving images is how to get a good view of the structures. Usually some rotation, scaling, etc. is done interactively to make a better picture.</DIV><DIV>I hope this helps,</DIV><DIV>Elaine</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR><DIV><DIV>On Sep 27, 2006, at 7:29 PM, Vishal Pua wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"> <DIV><FONT face="Arial" size="2">Hi, I was wondering if there was a way to create a script, that would open pdb files, render them to look a certain way ex. wire or ribbon, then save, automatically? this would have to work for a number of pdb files? I have little programming experience, and wonder if there was an easy way to do this, thanks</FONT></DIV> <DIV><FONT face="Arial" size="2"></FONT> </DIV> <DIV><FONT face="Arial" size="2">Vishal Pua</FONT></DIV><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-dev mailing list</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="mailto:Chimera-dev@cgl.ucsf.edu">Chimera-dev@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-dev">http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev</A></DIV> </BLOCKQUOTE></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: 12px; 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; "><DIV>-----</DIV><DIV>Elaine C. Meng, Ph.D. <A href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</A></DIV><DIV>UCSF Computer Graphics Lab and Babbitt Lab</DIV><DIV>Department of Pharmaceutical Chemistry</DIV><DIV>University of California, San Francisco</DIV><DIV> <A href="http://www.cgl.ucsf.edu/home/meng/index.html">http://www.cgl.ucsf.edu/home/meng/index.html</A></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><BR class="Apple-interchange-newline"></SPAN> </DIV><BR></DIV><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-dev mailing list</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="mailto:Chimera-dev@cgl.ucsf.edu">Chimera-dev@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-dev">http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev</A></DIV> </BLOCKQUOTE></DIV><BR></DIV><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-dev mailing list</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="mailto:Chimera-dev@cgl.ucsf.edu">Chimera-dev@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-dev">http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev</A></DIV> </BODY></HTML>