Index error/ List Index out of range in the Display 3D structure

[yudanshi]

Expected Behavior

I am trying to use my own template (single PDB in a mmcif format) with single_sequence (msa_mode).

I get the following error in the Display 3D Structure cell:

IndexError Traceback (most recent call last) in () 46 47 ---> 48 show_pdb(rank_num,show_sidechains, show_mainchains, color).show() 49 50

in show_pdb(rank_num, show_sidechains, show_mainchains, color) 19 modelname = f"rank{rank_num}" 20 view = py3Dmol.view(js='https://3dmol.org/build/3Dmol.js',) ---> 21 view.addModel(open(pdb_file[0],'r').read(),'pdb') 22 23 if color == "lDDT":

IndexError: list index out of range

Steps to Reproduce (for bugs)

Seq: PHSMRYFETAVSRPGLEEPRYISVGYVDNKEFVRFDSDAENPRYEPRAPWMEQEGPEYWERETQKAKGQEQWFRVSLRNLLGYYNQSAGGSHTLQQMSGCDLGSDWRLLRGYLQFAYEGRDYIALNEDLKTWTAADMAAQITRRKWEQSGAAEHYKAYLEGECVEWLHRYLKNGN:FAPGVFPYM

job_name: test template mode: custom Upload the template: 1bz9.cif (downloaded in PDB)

msa_mode: single_sequence pair Mode: Unpaired+Paired

model_type : auto

Context

Trying to set this PDB as initial guess.

Can you please help resolve this? Thanks!

[yudanshi]

Some screenshots:

[martin-steinegger]

This should be fixed now. If you still encounter the issue please share you input sequence and mmcif file.

[yudanshi]

Hi Martin,

Thanks for your quick reply! But it still doesn't work. Same error popped up when I tried again this morning. Input sequence: PHSMRYFETAVSRPGLEEPRYISVGYVDNKEFVRFDSDAENPRYEPRAPWMEQEGPEYWERETQKAKGQEQWFRVSLRNLLGYYNQSAGGSHTLQQMSGCDLGSDWRLLRGYLQFAYEGRDYIALNEDLKTWTAADMAAQITRRKWEQSGAAEHYKAYLEGECVEWLHRYLKNGNATLLRTDSPKAHVTHHPRSKGEVTLRCWALGFYPADITLTWQLNGEELTQDMELVETRPAGDGTFQKWASVVVPLGKEQNYTCRVYHEGLPEPLTLRWERWE:MIQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDWSFYILAHTEFTPTETDTYACRVKHDSMAEPKTVYWDRDM:FAPGVFPYM Template in mmcif: (please find the attached file)

(The template is same as the sequence I am trying to model, both are 1BZ9)

Thanks! 1bz9.cif.zip

On Sat, Apr 16, 2022 at 2:49 AM Martin Steinegger @.***> wrote:

This should be fixed now. If you still encounter the issue please share you input sequence and mmcif file.

— Reply to this email directly, view it on GitHub https://github.com/sokrypton/ColabFold/issues/206#issuecomment-1100588550, or unsubscribe https://github.com/notifications/unsubscribe-auth/AXUOAZ4K4UNKFGZXELW2Y7TVFJPGTANCNFSM5TRA73LQ . You are receiving this because you authored the thread.Message ID: @.***>

[yudanshi]

[martin-steinegger]

This should be fixed now.

[yudanshi]

Thanks for your help! It works now!