pdb file from homology modeler not working ?
Closed this issue · 6 comments
Hello
I set the plugin in pymol (pymol via anaconda) on my RHEL8 station. Then I tested with our exemple and several pdb files imported from the pdb site; It s working well and I ll now explore our nice ring-pymol. The calculation was done on the web server.
However, I have 3 questions
a) I ve got a warning in the log file : RING path not found in current directory please set manually. what path ?
b) Within the configuration panel. Where do i find the ring executable ?
I havent clone the GIThub . All the plugin is set in /disk/prog/anaconda/envs/ring-pymol/
(Moreover when i tried in another attempt and git clone the repository I am still not sure what to select as executable)
C) Now the main concern. With a pdb file from the pdb site it s ok as t seems the .cif is used) . With my own .pdb (or .cif) it s not working . Some files are created into the /tmp dir but _ringEdges and _ringNodes files are empty ?
Ty if you may help
alain
Hello,
Many thanks for your work. To analyze our homology models and dynamic
trajectories we were using multiple tools from VMD/Discovery/Gmx. RING will
help us a lot.
From your answer and the test in // of the Ring’ website and the plugin, I
now understand that the Ring executable should perform the network analysis
and probably display the map contact (colored dots and links).
I’ll ask for this executable to be set on our linux station soon.
Yesterday :
a) We tried the website with a pdb file (https://ring.biocomputingup) (see cav21 file) and it was working well to obtain the network of connections + edges/nodes files.
b) When we did the same within pymol (on a linux station and on a PC too) using the plugin and via the web server=> we did not obtain any network map or results in pymol for our pdb file; (configuration = web serveur)
cav21 is a 1 chain protein and the same problem occurs with a multi chains protein
(see zip
cav_test_ring.zip
files)
c) with a pdb file from the pdb site within pymol/plugin => we obtained edges/nodes results in the pymol window (no connection map)
Ty for help
Alain
Hi Alain,
I've checked the files that you sent to the WS and I think the problem was related to the filename of the file that was uploaded. I have now changed the script that is responsible for checking the file and renaming it, now it should work.
Please try again and let me know if everything is ok. If not, as a simple test, try to rename the object on which you are running RING on to something like 'test' and see if it completes.
Alessio
Thank you very much!
I tested and It s working. All perfect !
Alain