pdb file from homology modeler not working ?

[Alain-chavanieu]

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

[AlessioDelConte]

Hi, The warning is related you by the fact that the plugin does not find the path to the RING executable, it is not a problem if you are using the web server APIs. In the configuration tab you can set the path to RING executable, you can request it on https://biocomputingup.it/services . It is not included with the plugin. Regarding your own file this can be hard to debug without having the file, could you possibly attach it? RING only works with standard PDB files, as described by the wwwPDB consortium, maybe your file is not compliant with that, but I can take a look at that.

Best, Alessio

Il Mer 15 Mar 2023, 15:16 Alain-chavanieu @.***> ha scritto:

Hello I set the plugin in pymol (pymol via anaonda) 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 int the /tmp dir but _ringEdges and _ringNodes files are empty ?

Ty if you mau help

alain

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[Alain-chavanieu]

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

[AlessioDelConte]

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

[Alain-chavanieu]

Hello

I ll try in days coming from pymol + web server.

Many thanks

We run also in local mode as we have now the ring executable (TY for that); Very useful for us !

Alain

From: Alessio Del Conte @.> Sent: Tuesday, March 21, 2023 5:11 PM To: BioComputingUP/ring-pymol @.> Cc: Alain-chavanieu @.>; State change @.> Subject: Re: [BioComputingUP/ring-pymol] pdb file from homology modeler not working ? (Issue #2)

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

— Reply to this email directly, view it on GitHub https://github.com/BioComputingUP/ring-pymol/issues/2#issuecomment-1478137730 , or unsubscribe https://github.com/notifications/unsubscribe-auth/AYV2FUV7CNX4VBQVSVKXALDW5HHJTANCNFSM6AAAAAAV34OGPE . You are receiving this because you modified the open/close state. https://github.com/notifications/beacon/AYV2FUQSBSJTJQOMAK3C2K3W5HHJTA5CNFSM6AAAAAAV34OGPGWGG33NNVSW45C7OR4XAZNMJFZXG5LFINXW23LFNZ2KUY3PNVWWK3TUL5UWJTSYDKLYE.gif Message ID: @. @.> >

[AlessioDelConte]

Thank you very much!

[Alain-chavanieu]

I tested and It s working. All perfect ! Alain