Error fetching pdb id 7BV2

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Error fetching pdb id 7BV2 #215

Open giagitom opened 2 years ago

giagitom commented 2 years ago

I'm having an error when fetching 7BV2 on PyMol 2.5.0. Below is the output:

TITLE     The nsp12-nsp7-nsp8 complex bound to the template-primer RNA and triphosphate form of Remdesivir(RTP)
 ExecutiveLoad-Detail: Detected mmCIF
 CmdLoad: "./7bv2.cif" loaded as "7bv2".
corrupted double-linked list
Aborted (core dumped)

giagitom commented 2 years ago

Spotted an other PDB id giving issues 7ACT

TITLE     The SARS-CoV-2 nucleocapsid phosphoprotein N-terminal domain in complex with 10mer ssRNA
 ExecutiveLoad-Detail: Detected mmCIF
 CmdLoad: "./7act.cif" loaded as "7act".
free(): invalid next size (normal)
Aborted (core dumped)

JarrettSJohnson commented 2 years ago

Hi, I can't seem to reproduce. Which OS are you using. Is this incentive 2.5.0 (if so have you tried 2.5.2?).

giagitom commented 2 years ago

Hi, I updated to pymol latest 2.6.0a0 (not incentive) but the issue is still present.

I'm on ubuntu 20.04 LTS

This happens also when loading from local 7n0b.cif Other formats are working fine instead.

giagitom commented 2 years ago

I noticed the problem seems to be related to retain_order setting on cif files only. If i set retain_order, 1 it works fine without crashing

tzok commented 1 year ago

This bug is still present a year later (January 2023) and @giagitom workaround with set retain_order, 1 helps. Thanks!