ReadMolFile-Error: bad coordinate

janlittletwinstar commented 3 years ago

Hi,

When I opened a .mol2 file with Pymol, I had an error: "ReadMolFile-Error: bad coordinate." I could not read all the compounds that should be present in the file. I am using MacOS ver. 10.14.6. How to fix the issue?

janlittletwinstar commented 3 years ago

speleo3 commented 3 years ago

Can you attach your .sdf file here?

janlittletwinstar commented 3 years ago

The forum does not support this file format. Please see the file attached. There should be 100 compounds instead of 5. Thanks.

On Tue, 12 Jan 2021 at 12:23, Thomas Holder notifications@github.com wrote:

Can you attach your .sdf file here?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/schrodinger/pymol-open-source/issues/156#issuecomment-758813110, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASOCXDRSZMHRLSUCWWIPKFTSZSAQ3ANCNFSM4V7N4Y3Q .

JarrettSJohnson commented 3 years ago

Hi, I still haven't come across the file for us to take a look. Closing the ticket for now. If you do still have the file, feel free to email it to us at: pymol-dev-group@schrodinger.com and I'll reopen this ticket.

BJWiley233 commented 1 year ago

I have seen this as well on MacOS:


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  1 28  2  0
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  3  4  2  0
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M  END
$$$$

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 29 3

Stephenade commented 1 year ago

Dear All, Please how do I rectify this problem? I tried opening the output file from my production run of an array job.

schrodinger / pymol-open-source

ReadMolFile-Error: bad coordinate #156