Dear Chimera developers： I have a problem in using Chimera！ I want to save a ligand-receptor complex file for further analysis，but I can not save a such PDB file！You can see the figure below！ The target was protein, and the atr_1 was the ligand, all files were saved from the dock results of Swissdock online tool (figure 2)! I hope you can help me, thank you very much! Best wish, Jianan Li Jianan Li-Harbin Medical University 364453372@qq.com
Dear Jianan Li, It is exactly what the error message says: if you choose to save "multiple models in multiple files" you must provide a file name that contains either $name or $number. You gave a file name "target_ab1.pdb" and this does not contain $name or $number. Do you really want two files for your two models? If so, you have to include $name or $number in the file name, for example, file name: target_ab1$number.pdb If you don't really want two files (one for ligand and one for receptor), i.e., you probably should combine ligand + receptor into one model before saving. You can combine models with the Model Panel (open from Favorites menu) function "copy/combine" or the command "combine" <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 14, 2023, at 10:05 PM, Jianan Li-Harbin Medical University via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Chimera developers： I have a problem in using Chimera！ I want to save a ligand-receptor complex file for further analysis，but I can not save a such PDB file！You can see the figure below！ The target was protein, and the atr_1 was the ligand, all files were saved from the dock results of Swissdock online tool (figure 2)! I hope you can help me, thank you very much!
Best wish, Jianan Li <3F942D54@A66BE50F.B897C363.jpg.jpg> <305B3130@608AEC4D.B897C363.jpg.jpg>
Thanks so much! Best wish! 发自我的iPhone ------------------ Original ------------------ From: Elaine Meng <meng@cgl.ucsf.edu> Date: Mon,Jan 16,2023 1:08 AM To: Jianan Li-Harbin Medical University <364453372@qq.com> Cc: chimera-users <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] problem Dear Jianan Li, It is exactly what the error message says: if you choose to save "multiple models in multiple files" you must provide a file name that contains either $name or $number. You gave a file name "target_ab1.pdb" and this does not contain $name or $number. Do you really want two files for your two models? If so, you have to include $name or $number in the file name, for example, file name: target_ab1$number.pdb If you don't really want two files (one for ligand and one for receptor), i.e., you probably should combine ligand + receptor into one model before saving. You can combine models with the Model Panel (open from Favorites menu) function "copy/combine" or the command "combine" <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html>; <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html>; I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Jan 14, 2023, at 10:05 PM, Jianan Li-Harbin Medical University via Chimera-users <chimera-users@cgl.ucsf.edu> wrote: > > Dear Chimera developers： > I have a problem in using Chimera！ > I want to save a ligand-receptor complex file for further analysis，but I can not save a such PDB file！You can see the figure below！ > The target was protein, and the atr_1 was the ligand, all files were saved from the dock results of Swissdock online tool (figure 2)! > I hope you can help me, thank you very much! > > Best wish, > Jianan Li > <3F942D54@A66BE50F.B897C363.jpg.jpg> > <305B3130@608AEC4D.B897C363.jpg.jpg>
participants (2)
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Elaine Meng -
Jianan Li-Harbin Medical University