Is there an option to open pdbqt as PDB format smoothly?
Hi Chimera team, I'm wondering if there is any chance that I can open a .pdbqt file smoothly (just like open a .pdb file ) through some strategies (for example, maybe modifying some source codes?). Since AutoDock (and vina) always gives a .pdbqt format file but not .pdb format, however the content of which is somewhat like pdb and we always want to open it in pdb format. This is not an important issue. But if so, the experience will be much better at least for me (Now, I have to choose the PDB format or rename the file suffix into .pdb). With Regards Qiancheng Xia 2022/12/23
Hi Qiancheng, You would need to modify <your Chimera installation>/share/chimera/__init__.py. On line 1436, change: _openPDBModel, (".pdb", ".pdb1", ".ent", ".pqr"), ("pdb",), to: _openPDBModel, (".pdb", ".pdb1", ".ent", ".pqr", ".pdbqt"), ("pdb",), keeping the indentation the same. On a Mac, <your Chimera installation> is Chimera.app/Contents/Resources. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Dec 23, 2022, at 5:20 AM, 夏前程 via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Chimera team,
I'm wondering if there is any chance that I can open a .pdbqt file smoothly (just like open a .pdb file ) through some strategies (for example, maybe modifying some source codes?).
Since AutoDock (and vina) always gives a .pdbqt format file but not .pdb format, however the content of which is somewhat like pdb and we always want to open it in pdb format.
This is not an important issue. But if so, the experience will be much better at least for me (Now, I have to choose the PDB format or rename the file suffix into .pdb).
With Regards
Qiancheng Xia
2022/12/23
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Thanks Eric, that's exactly what I need. -----原始邮件----- 发件人:"Eric Pettersen" <pett@cgl.ucsf.edu> 发送时间:2022-12-28 03:20:05 (星期三) 收件人: "夏前程" <xiaqiancheng@nibs.ac.cn> 抄送: Chimera <chimera-users@cgl.ucsf.edu> 主题: Re: [Chimera-users] Is there an option to open pdbqt as PDB format smoothly? Hi Qiancheng, You would need to modify <your Chimera installation>/share/chimera/__init__.py. On line 1436, change: _openPDBModel, (".pdb", ".pdb1", ".ent", ".pqr"), ("pdb",), to: _openPDBModel, (".pdb", ".pdb1", ".ent", ".pqr", ".pdbqt"), ("pdb",), keeping the indentation the same. On a Mac, <your Chimera installation> is Chimera.app/Contents/Resources. --Eric Eric Pettersen UCSF Computer Graphics Lab On Dec 23, 2022, at 5:20 AM, 夏前程 via Chimera-users <chimera-users@cgl.ucsf.edu> wrote: Hi Chimera team, I'm wondering if there is any chance that I can open a .pdbqt file smoothly (just like open a .pdb file ) through some strategies (for example, maybe modifying some source codes?). Since AutoDock (and vina) always gives a .pdbqt format file but not .pdb format, however the content of which is somewhat like pdb and we always want to open it in pdb format. This is not an important issue. But if so, the experience will be much better at least for me (Now, I have to choose the PDB format or rename the file suffix into .pdb). With Regards Qiancheng Xia 2022/12/23 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
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