search

harryjubb / arpeggio

Calculation of interatomic interactions in molecular structures
http://biosig.unimelb.edu.au/arpeggioweb/
GNU General Public License v3.0
69 stars 24 forks source link

pymol .pse for visualization #6

Closed diallobakary4 closed 6 years ago

diallobakary4 commented 6 years ago

Hello there

Please does the command line tool produces a pymol .pse for visualization?

Thanks

harryjubb commented 6 years ago

Hi, you can use the show_contacts.py script to generate a PyMOL script from Arpeggio output, which can then be saved to a .pse:

Having already run Arpeggio on your PDB file:

python show_contacts.py file.pdb -s

See python show_contacts.py -h for more options.

You can either manually run the .pml script in PyMOL through the GUI, or from the command line in PyMOL's batch mode (pymol -cq) and then save the .pse with an additional command (for example, using the -d command line flag with PyMOL to add a save command.

Please let me know if you have any issues.

diallobakary4 commented 6 years ago

Thank you

Very helpfull.

Le ven. 21 sept. 2018 à 14:30, Harry Jubb notifications@github.com a écrit :

Hi, you can use the show_contacts.py script to generate a PyMOL script from Arpeggio output, which can then be saved to a .pse:

Having already run Arpeggio on your PDB file:

python show_contacts.py file.pdb -s

See python show_contacts.py -h for more options.

You can either manually run the .pml script in PyMOL through the GUI, or from the command line in PyMOL's batch mode https://pymolwiki.org/index.php/Launching_PyMOL#Running_PyMOL_in_batch_mode (pymol -cq) and then save the .pse with an additional command (for example, using the -d command line flag with PyMOL to add a save command.

Please let me know if you have any issues.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/harryjubb/arpeggio/issues/6#issuecomment-423514845, or mute the thread https://github.com/notifications/unsubscribe-auth/AM6CFSWPfiHoI2DsM3LDaNspfIDq2bSHks5udNvMgaJpZM4Wz0uI .

--

Bakary N’tji DIALLO

Pharm. D. / M.Sc. Student in Bioinformatics https://www.linkedin.com/in/bakaryntjidiallo

Mail: diallobakary4@gmail.com | Skype: diallobakary4

Tel: ​+27798233845 | +223 74 56 57 22 | +223 97 39 77 14

harryjubb commented 6 years ago

No problem, let me know if you have any further questions 🙂