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select polymer not working properly on PDB entry 1a2c #317

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Stefano-Trapani opened this issue Oct 2, 2023 · 0 comments
Open

select polymer not working properly on PDB entry 1a2c #317

Stefano-Trapani opened this issue Oct 2, 2023 · 0 comments

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@Stefano-Trapani
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PyMOL 2.5.0 Open-Source, 2022-03-17

Tested on PDB entry 1a2c.
Tested on both PDB and mmCIF files (with connect_mode either 0 or 4).

select polymer leaves out 2 out of 4 residues from chain J (which contains non-standard amino acids).

fetch 1a2c, async=0
show lines
hide everything, (not (c. J and not solvent))
zoom visible
set seq_view
select 1a2c_J , 1a2c and c. J and not solvent
select 1a2c_J_poly , 1a2c and c. J and not solvent and polymer

1a2c_J


1a2c_J_poly


speleo3 added a commit to speleo3/pymol-open-source that referenced this issue Dec 19, 2023
Use mmCIF polypeptide information for atom classification if
`preserve_classified` setting is on.

Limitations: Bypasses auto_show_classified

Related to schrodinger#317
speleo3 added a commit to speleo3/pymol-open-source that referenced this issue Jan 15, 2024
Use mmCIF polypeptide information for atom classification if
`preserve_classified` setting is on.

Limitations: Bypasses auto_show_classified

Related to schrodinger#317
speleo3 added a commit to speleo3/pymol-open-source that referenced this issue Jan 31, 2024
Use mmCIF polypeptide information for atom classification if
`preserve_classified` setting is on.

Limitations: Bypasses auto_show_classified

Related to schrodinger#317
speleo3 added a commit to speleo3/pymol-open-source that referenced this issue Jan 31, 2024
Use mmCIF polypeptide information for atom classification if
`preserve_classified` setting is on.

Limitations: Bypasses auto_show_classified

Related to schrodinger#317
speleo3 added a commit to speleo3/pymol-open-source that referenced this issue Feb 1, 2024
Use mmCIF polypeptide information for atom classification if
`preserve_classified` setting is on.

Limitations: Bypasses auto_show_classified

Related to schrodinger#317
speleo3 added a commit to speleo3/pymol-open-source that referenced this issue Feb 29, 2024
Use mmCIF polypeptide information for atom classification if
`preserve_classified` setting is on.

Limitations: Bypasses auto_show_classified

Related to schrodinger#317
speleo3 added a commit to speleo3/pymol-open-source that referenced this issue Mar 15, 2024
Use mmCIF polypeptide information for atom classification if
`preserve_classified` setting is on.

Limitations: Bypasses auto_show_classified

Related to schrodinger#317
speleo3 added a commit to speleo3/pymol-open-source that referenced this issue May 6, 2024
Use mmCIF polypeptide information for atom classification if
`preserve_classified` setting is on.

Limitations: Bypasses auto_show_classified

Related to schrodinger#317
speleo3 added a commit to speleo3/pymol-open-source that referenced this issue Jun 10, 2024
Use mmCIF polypeptide information for atom classification if
`preserve_classified` setting is on.

Limitations: Bypasses auto_show_classified

Related to schrodinger#317
speleo3 added a commit to speleo3/pymol-open-source that referenced this issue Jun 10, 2024
Use mmCIF polypeptide information for atom classification if
`preserve_classified` setting is on.

Limitations: Bypasses auto_show_classified

Related to schrodinger#317
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