Re: [cctbxbb] cctbx versions causing indentation crash?

Thanks for your suggestions, Markus. I should have mentioned that I did a tab/space check & also tried indenting like you suggest. I installed the old version of Coot (vers 0.8) and now it works. I guess they’ve changed the way commands are called slightly between versions. Cheers, Magnus

On 09 Nov 2017, at 22:27, wrote:

Dear Magnus,

I suspect that the error is unrelated to all those things and instead a change in your code. An IndentationError happens in parsing a python file, and all python files contained in cctbx are syntax checked. The python syntax has not changed within 2.7.

I suggest searching the problematic file for tab characters and if you find any, replace them with spaces. Otherwise I can take a look at the file if you upload it somewhere (github.com/pastebin.com/email)

Does the IndentationError happen inside coot? If I parse the code correctly it should be approximately equivalent to:

from dials.util.procrunner import run_process coot_input = ''' (handle-read-draw-molecule-with-recentre "{inf}" 1) (set-refinement-immediate-replacement 1) (set-refine-max-residues 40) (regularize-zone 0 " " {res1minus} {res3}" ") (accept-regularizement) (regularize-zone 0 " " {res3} {res2plus}" ") (accept-regularizement) (write-pdb-file 0 "{outf}") (coot-real-exit 0) '''.format(inf=inf, outf=outf, res1minus=res1-2, res3=res3, res2plus=res2+2) run_process(['coot', '--no-graphics'], stdin=coot_input)

Does coot allow space in front of commands? (And I'm not sure about coot console commands. but some of the "-pairs look a bit strange to me)

-Markus

________________________________________ From: [email protected] [[email protected]] on behalf of Magnus Andersson [[email protected]] Sent: Thursday, November 09, 2017 20:15 To: cctbx mailing list Subject: [cctbxbb] cctbx versions causing indentation crash?

Hi all,

I have a script that runs fine on my old computer, but crashes on my new computer with the error message:

IndentationError: unexpected indent

This script is (amongst other things) calling the softwatre Coot such as:

subprocess.call(["""coot --no-graphics<

which is ok on my old system. I am trying to find the most likely source of this error. Here are the differences:

- OLD cctbx = uses Python 2.7.10, NEW cctbx 2.7.14 - OLD OSX = 10.10.5 (i.e. Yosemite), NEW OSX = 10.11.5 (i.e. El Capitan) - OLD Coot = vers 0.8, NEW Coot = vers 0.8.8 [old Coot install was from Fink but this shouldn’t matter I think]

Perhaps someone has encountered something similar or has an educated guess on whether different cctbx versions can cause such errors?

Thanks,

Magnus

#### Magnus Andersson, Docent, Ph.D.

Email: [email protected] Phone: 0769469872

Mailing address: Science For Life Laboratory Alpha 6 Box 1031 171 21 Solna

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#### Magnus Andersson, Docent, Ph.D. Email: [email protected] Phone: 0769469872 Mailing address: Science For Life Laboratory Alpha 6 Box 1031 171 21 Solna Visiting address: Tomtebodavägen 23A 171 65 Solna