Thanks, Carsten. I thought it would turn out to be something related to the
paths, but couldn't put my finger on it.
(I was able to run the script fine without either of those fixes on Incentive
PyMOL 1.5.0 32-bit on a Win XP VirtualBox VM guest on a Mac OS 10.8 host. Not
sure why that might be.)
Relatedly, I decided to try out Robert's align_allfiles.py (which is super
handy--it prints all the RMSDs in block form at the end, sorted both
alphabetically by filename AND by RMSD...very nice, Robert!), and found that
the regular expression for the extension doesn't compile as desired on Windows,
due to the same issue. For example, I was getting values for the `obj_name1`
variable with backslashes (e.g. "mut\3opl.pdb"), which turned into underscores
("mut_3opl") in the object names. The selections were wrong and the script
couldn't delete the objects, because the names didn't match, and it printed out
a list of rmsds of 0.000.
That line (line 36) should read as follows:
extension = re.compile( r'(^.*[\\/]|\.(pdb|ent|brk))' )
Note the raw string "r" as well as the double-backslash inside the brackets.
Robert, perhaps you could update the script on your website?
Cheers,
Jared
--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
550 First Avenue
New York, NY 10016
212-263-7898
http://kong.med.nyu.edu/
On Jan 9, 2014, at 2:33 PM, "Schubert, Carsten [JRDUS]"
<cschu...@its.jnj.com<mailto:cschu...@its.jnj.com>> wrote:
Hi Om,
asides from the usual list of suspects like access permissions try double
backslashes or a raw string in your path-filenames. Python on Windows is a bit
peculiar in that respect. Read up on raw strings in the Python docs.
Try
wt_file =
"D:\\STUDY\\STRUCTURE_PPT\\RMSD\\Pymol\\Original\\1APS.pdb<smb://STUDY//STRUCTURE_PPT//RMSD//Pymol//Original//1APS.pdb>"
or
wt_file = r"D:\STUDY\STRUCTURE_PPT\RMSD\Pymol\Original\1APS.pdb"
note the ‘r’ at the beginning of the string indicating a raw string.
HTH
Carsten
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