<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">It looks like some of your file names have non-alphanumeric characters in them, which is causing the “wildcard matching” of file names to throw an error. In the script, instead of:<div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><i class="">rc(“open “ + fn)</i></div><div class=""><br class=""></div><div class="">try:</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><i class="">rc(“open nowildcard “ + fn)</i></div><div class=""><i class=""><br class=""></i></div><div class="">If that still doesn’t work, try:</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><i class="">rc(“open ‘“ + fn + “‘“)</i></div><div class=""><i class=""><br class=""></i></div><div class="">(i.e. single quote just before the double quote that ends the first string, and single quote between two double quotes in the second string).</div><div class=""><br class=""></div><div class="">—Eric</div><div class=""><br class=""><div class="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>Eric Pettersen</div><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>UCSF Computer Graphics Lab</div></div><br class="Apple-interchange-newline">
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<br class=""><div><blockquote type="cite" class=""><div class="">On Jun 7, 2017, at 9:42 AM, Nikolaos Bismpikos <<a href="mailto:nikolaosbismpikos@gmail.com" class="">nikolaosbismpikos@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class="">Hello, I am having a problem with trying to open a .pdb file using a python script.<br class=""><br class=""></div>The file opens and the protein structure is displayed properly when I open the file using the Chimera GUI. However, when I try to run the code from a python script, using the demo script for looping through .pdb files I get the following error:<br class=""><div class=""><div class=""><br class="">----------------------------------------------------------------------<br class=""><br class="">File "/home/nick/.local/UCSF-Chimera64-1.11.2/lib/python2.7/re.py", line 251, in _compile<br class=""> raise error, v # invalid expression<br class=""><br class="">----------------------------------------------------------------------</div><div class="">This is the code I am trying to run:<br class="">----------------------------------------------------------------------<br class=""><br class="">import sys<br class="">import os<br class="">from chimera import runCommand as rc # use 'rc' as shorthand for runCommand<br class="">from chimera import replyobj # for emitting status messages<br class=""><br class=""># change to folder with data files<br class="">os.chdir("/home/nick/Python/pdb")<br class="">print >> sys.stdout, retval<br class=""><br class=""># gather the names of .pdb files in the folder<br class="">file_names = [fn for fn in os.listdir(".") if fn.endswith(".pdb")]<br class=""><br class=""># loop through the files, opening, processing, and closing each in turn<br class="">for fn in file_names:<br class=""> replyobj.status("Processing " + fn) # show what file we're working on<br class=""> rc("open " + fn)<br class=""> replyobj.status("Opened " + fn) # show what file we're working on<br class=""> rc("align ligand ~ligand") # put ligand in front of remainder of molecule<br class=""> rc("focus ligand") # center/zoom ligand<br class=""> rc("surf") # surface receptor<br class=""> rc("preset apply publication 1") # make everything look nice<br class=""> rc("surftransp 15") # make the surface a little bit see-through<br class=""> # save image to a file that ends in .png rather than .pdb<br class=""> png_name = fn[:-3] + "png"<br class=""> rc("copy file " + png_name + " supersample 3")<br class=""> rc("close all")<br class=""></div><div class=""><br class="">----------------------------------------------------------------------<br class=""><br class="">The error in more detail, including the traceback from the terminal is the following:<br class=""><br class="">----------------------------------------------------------------------<br class=""><br class="">Processing prediction[NoEnergy-K:0-BS:0.00]-21(20.310186).pdb<br class=""><br class="">Traceback (most recent call last):<br class=""> File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimeraInit.py", line 683, in init<br class=""> chimera.openModels.open(a, prefixableType=1)<br class=""> File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimera/__init__.py", line 1929, in open<br class=""> models = func(filename, *args, **kw)<br class=""> File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimera/__init__.py", line 1299, in _openPython<br class=""> loadFunc(sandboxName, fileName, f)<br class=""> File "test1.py", line 23, in <module><br class=""> rc("open " + fn)<br class=""> File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimera/__init__.py", line 2747, in runCommand<br class=""> makeCommand(*args, **kw)<br class=""> File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/Midas/midas_text.py", line 69, in makeCommand<br class=""> f(c, args)<br class=""> File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/Midas/midas_text.py", line 1552, in doOpen<br class=""> paths = testPath(text, wildcarding)<br class=""> File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/Midas/midas_text.py", line 1538, in testPath<br class=""> return glob(expanded)<br class=""> File "/home/nick/.local/UCSF-Chimera64-1.11.2/lib/python2.7/glob.py", line 27, in glob<br class=""> return list(iglob(pathname))<br class=""> File "/home/nick/.local/UCSF-Chimera64-1.11.2/lib/python2.7/glob.py", line 49, in iglob<br class=""> for name in glob1(os.curdir, basename):<br class=""> File "/home/nick/.local/UCSF-Chimera64-1.11.2/lib/python2.7/glob.py", line 83, in glob1<br class=""> return fnmatch.filter(names, pattern)<br class=""> File "/home/nick/.local/UCSF-Chimera64-1.11.2/lib/python2.7/fnmatch.py", line 56, in filter<br class=""> _cache[pat] = re_pat = re.compile(res)<br class=""> File "/home/nick/.local/UCSF-Chimera64-1.11.2/lib/python2.7/re.py", line 194, in compile<br class=""> return _compile(pattern, flags)<br class=""> File "/home/nick/.local/UCSF-Chimera64-1.11.2/lib/python2.7/re.py", line 251, in _compile<br class=""> raise error, v # invalid expression<br class="">error: bad character range<br class=""><br class="">Error while processing test1.py:<br class="">error: bad character range<br class=""><br class=""> File "/home/nick/.local/UCSF-Chimera64-1.11.2/lib/python2.7/re.py", line 251, in _compile<br class=""> raise error, v # invalid expression<br class=""><br class="">See reply log for Python traceback.<br class=""><br class=""><br class="">----------------------------------------------------------------------<br class=""></div><div class="">The error obviously appears at the 2nd line of the for loop ( rc("open " + fn) ) <br class=""></div><div class=""><br class=""></div><div class="">Any tips on why this might happen? I am using Ubuntu 14.04 LTS and the Chimera version I installed is chimera-1.11.2-linux_x86_64.bin<br class=""><br class=""><br class=""></div></div></div>
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