Dear developers, I am a new user of ChimeraX. I need to create dimers in order to analyse adsorbate-adsorbant interactions for DFT calculation. I am able to create the image on the screen, but I don´t know how to save the atomic coordinates of the dimer in a single file. If I save a .pdb file in order to produce a .xyz file, just the information of one of the entities is kept. Can you please help me? [cid:image003.jpg@01DAA921.4F8EE270] Best regards, [Diapositiva1]
Hello, If both models are chosen in the bottom of the File... Save dialog, and you choose File type PDB, then it does save both of them in a single PDB file. However, they are still in separate MODEL parts of the PDB file and maybe whatever you are using to convert PDB -> xyz only looks at the first MODEL. So instead of just saving your two models to PDB, you may need to first combine these two models into a single model. You can do it with the "combine" command, <https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html> ...e.g. if your models are #1,2: combine #1,2 model #3 name combined ...then in the File... Save dialog to save the PDB file, choose only the new model #3 "combined" to save to the file. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On May 18, 2024, at 3:45 AM, GOTZONE BARANDIKA via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear developers, I am a new user of ChimeraX. I need to create dimers in order to analyse adsorbate-adsorbant interactions for DFT calculation. I am able to create the image on the screen, but I don´t know how to save the atomic coordinates of the dimer in a single file. If I save a .pdb file in order to produce a .xyz file, just the information of one of the entities is kept. Can you please help me?
<image003.jpg> Best regards,
<image004.png>
Thanks a lot!!!! Enviado de Samsung Mobile Enviado desde Outlook para Android<https://aka.ms/AAb9ysg> ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Sunday, May 19, 2024 6:05:38 PM To: GOTZONE BARANDIKA <gotzone.barandika@ehu.eus> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: combine the models Hello, If both models are chosen in the bottom of the File... Save dialog, and you choose File type PDB, then it does save both of them in a single PDB file. However, they are still in separate MODEL parts of the PDB file and maybe whatever you are using to convert PDB -> xyz only looks at the first MODEL. So instead of just saving your two models to PDB, you may need to first combine these two models into a single model. You can do it with the "combine" command, <https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html> ...e.g. if your models are #1,2: combine #1,2 model #3 name combined ...then in the File... Save dialog to save the PDB file, choose only the new model #3 "combined" to save to the file. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On May 18, 2024, at 3:45 AM, GOTZONE BARANDIKA via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear developers, I am a new user of ChimeraX. I need to create dimers in order to analyse adsorbate-adsorbant interactions for DFT calculation. I am able to create the image on the screen, but I don´t know how to save the atomic coordinates of the dimer in a single file. If I save a .pdb file in order to produce a .xyz file, just the information of one of the entities is kept. Can you please help me?
<image003.jpg> Best regards,
<image004.png>
participants (2)
-
Elaine Meng -
GOTZONE BARANDIKA