Trying to install Data Warrior on Mac (MacOs 11.1)

[lindapatio]

Hi I'm Linda, a final year MPharm student doing my 3 month masters project with Prof Todd. I need to install Datawarrior but I'm having issues with opening the software, the popup (shown below) keeps showing whenever I try to open the app. Would anyone be able to help please? @drc007 @edwintse @mattodd

[drc007]

Hi,

Open “settings” and go to Security and Privacy.

Under “Apps downloaded from” you should see an option open anyway.

This often happens with software not downloaded from the AppStore.

Cheers

Chris

On 11 Nov 2021, at 14:41, Linda Patio @.***> wrote:

Hi I'm Linda, a final year MPharm student doing my 3 month masters project with Prof Todd. I need to install Datawarrior but I'm having issues with opening the software, the popup (shown below) keeps showing whenever I try to open the app. Would anyone be able to help please? @drc007 https://github.com/drc007 @edwintse https://github.com/edwintse @mattodd https://github.com/mattodd https://user-images.githubusercontent.com/92246733/141315726-e6a894ea-0472-4216-aee3-7f9d599ed82a.png — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/StructuralGenomicsConsortium/CNP4-Nsp13-C-terminus-B/issues/7, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABWAURCGYE2QGVNGSSHGQ4TULPIZJANCNFSM5H2T3SXQ. Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

[mattodd]

@lindapatio give @drc007 a harder problem next time :)

[lindapatio]

@drc007 Ohhh it worked thank you so much!

@mattodd I'll keep a note of that for future references hahaha

[lindapatio]

Hi! I have another question, which unfortunately isn't complicated (I hope). @drc007 would you be able to help me with setting up the Jupyter Notebook please? I think I'm missing the "notebook for docking" in my home page. My username is UCNVLC8

Thanks for your help!

[drc007]

@lindapatio This looks like you are running on the UCL cluster? If so you will need to talk to the cluster admin who I think is Frank Otto? @mattodd will probably know.

They will also need to install RDKit and SMINA etc.

[lindapatio]

@drc007 thank you for your help! I'll send an email to Frank Otto

[lindapatio]

Hi Prof Chris @drc007, I've been trying to begin my molecular docking experiment but need a file to be optimised. Would you be able to optimise this PDB file please? The lab manual mentioned that you'd be able to use MOE to help with these issues.

Protein_and_ligand5rm3.cif.zip

[drc007]

Here you go, both tided up files in pdb format. Archive.zip

[lindapatio]

thank you very much sir!

[lindapatio]

@drc007 Hi Prof Swain, I've tried to dock but I'm getting errors on jupyter notebook (please see attached PDF), is there a way i can rectify these issues? Also, the SMINA cell disappeared after I ran it, but I'm not sure why. Hope you can help! Jupyter notebook issues (1).pdf

[drc007]

@lindapatio Are you running this locally or on the cluster?

[lindapatio]

@drc007 I think I'm running this on the cluster. I'm connected to VPN

[drc007]

@lindapatio @mattodd It looks like the environment is not set up correctly, can you check with Frank Otto?

[lindapatio]

@drc007 okay sure, I've emailed him.

[lindapatio]

Hi @mattodd Jupyter notebook works now! Prof Frank Otto sent me a modified version. I'm currently justifying one of the nature fragments: 5RMM. Please see the pymol session below for the unoptimised version of this analysis:

• unoptimsied 5RMM.pse.zip

• there are two potential conformations that bind the same way as the original 5RMM (state 37 and 73), however do I need to find the conformation that perfectly sits on the same position/active site of the original fragment? State 46 is similar to state 73, but binds more closely to nsp13

• Hi @drc007, would you be able to optimise this file for me please? 5RMM_and_NSP13.pdb.zip

[drc007]

@lindapatio Great news about the notebook, I wonder if we need to keep a copy somewhere for other users?

Here is the file 5RMM_and_NSP13updated.pdb.zip

[lindapatio]

@drc007 Apparently the jupyter notebook that was sent to me initially was a universal one that did not work on the UCL cluster. But the modified one from Frank Otto works and I have been in contact with Prof Kiappes who uses this in his programme, so he's aware of the differences for next term when students start using it!

Here's a copy of the notebook in case you need to put it somewhere on Github: ConformationGenerationDocking.ipynb.zip

And thank you very much for your help!