Dear All thanks to Thomas for the modfication on the plot_noe.py. It turns out that the CNS .tbl file can have different formats, the one I used only includes residue ID and atom name, but soemtimes it also inlcudes segment ID as well, see on the attached file. How do I have to modify the noe_regex pattern so that it is recognised?
Thanks in advance, regards, Krisztina --- On Mon, 10/29/12, Thomas Holder <spel...@users.sourceforge.net> wrote: From: Thomas Holder <spel...@users.sourceforge.net> Subject: Re: [PyMOL] visualise NOEs To: "Krisztina Feher" <feher_kriszt...@yahoo.com>, "pymol-users" <pymol-users@lists.sourceforge.net> Date: Monday, October 29, 2012, 4:23 PM Hi Krisztina, I slightly modified the script, see attachment. The regular expression is modified and I replaced "search" by "match". The script could be further optimized (exception handling etc.) but with your example file it works fine now. Cheers, Thomas On 10/29/2012 04:06 PM, Krisztina Feher wrote: > Sure, thanks for looking at it! > Krisztina > > --- On *Mon, 10/29/12, Thomas Holder wrote: > > From: Thomas Holder <spel...@users.sourceforge.net> > Subject: Re: [PyMOL] visualise NOEs > To: "Krisztina Feher" <feher_kriszt...@yahoo.com> > Date: Monday, October 29, 2012, 4:04 PM > > Hi Krisztina, > > can you send me the restraints file and PDB file as well? > > Cheers, > Thomas > > On 10/29/2012 04:00 PM, Krisztina Feher wrote: > > Hi Thomas, > > > > thanks a lot for your reply! Now I was running the script from > command > > line and executed it: it did not display anything on the structure. I > > inserted a couple of print statements into the script (attached), > but it > > seems that the "noe_regex" is not being found in the variable > "line" by > > the .search method (see the output below: match is None). The pdb > file > > does have residue 433 and all the listed atom names. The > noe_regex looks > > sort of complicated, I have no idea how to fix it. If anyone had > an idea > > how to fix it, I would very much appreciate it. > > > > Thanks, > > Krisztina > > > > ps. If this script works for on your system, please write me too! -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen
test_segid.tbl
Description: Binary data
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