How to generate submodels in a mol2 file in Chimera?
Dear friends, Hello! I'm wondering how many models and submodels in all can Chimera save into one single mol2 file? Right now I can have models only 0-9 into one single mol2 file. I think I'm going to use submodels, but how can I generate them? For instance, if I have a brunch of pdb files which contain one molecule each, I'd like to combine them into one mol2 file, which has a submodel corresponding to each molecule. (If this statement of the problem is not clear enough, please let me know). Thank you for your help and sorry to bother the others. Best wishes. Sincerely yours CHIU,YEUNG
Hi Yeung, You can save as many models/submodels as you want into one mol2 file. Choose File.... Save Mol2. In that dialog there is an option to "Save multiple models in": a single file [individual @MOLECULE sections] multiple files [appending model number] a single file [combined @MOLECULE section] If you choose "individual @MOLECULE sections", that means that when you read the file back into Chimera, all the models/submodels that you have now will be submodels in that newly opened model. If you choose "combined @MOLECULE sections" that means when you read the file back into Chimera, all the models you have now will be one giant model. It sounds like you want "individual". http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#mol2 Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Dec 1, 2008, at 4:34 AM, CHIU,YEUNG wrote:
Dear friends,
Hello! I'm wondering how many models and submodels in all can Chimera save into one single mol2 file? Right now I can have models only 0-9 into one single mol2 file. I think I'm going to use submodels, but how can I generate them? For instance, if I have a brunch of pdb files which contain one molecule each, I'd like to combine them into one mol2 file, which has a submodel corresponding to each molecule. (If this statement of the problem is not clear enough, please let me know).
Thank you for your help and sorry to bother the others. Best wishes.
Sincerely yours CHIU,YEUNG
To supplement Elaine's answer: you can have model numbers higher than 9. The command line interface only shows buttons for models 0-9, but you can have models 10+, there just aren't buttons for them. They can still be referenced in commands (e.g. #13) and will show up in the Model Panel. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Dec 1, 2008, at 10:16 AM, Elaine Meng wrote:
Hi Yeung, You can save as many models/submodels as you want into one mol2 file. Choose File.... Save Mol2. In that dialog there is an option to "Save multiple models in": a single file [individual @MOLECULE sections] multiple files [appending model number] a single file [combined @MOLECULE section]
If you choose "individual @MOLECULE sections", that means that when you read the file back into Chimera, all the models/submodels that you have now will be submodels in that newly opened model. If you choose "combined @MOLECULE sections" that means when you read the file back into Chimera, all the models you have now will be one giant model. It sounds like you want "individual". http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#mol2
Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
On Dec 1, 2008, at 4:34 AM, CHIU,YEUNG wrote:
Dear friends,
Hello! I'm wondering how many models and submodels in all can Chimera save into one single mol2 file? Right now I can have models only 0-9 into one single mol2 file. I think I'm going to use submodels, but how can I generate them? For instance, if I have a brunch of pdb files which contain one molecule each, I'd like to combine them into one mol2 file, which has a submodel corresponding to each molecule. (If this statement of the problem is not clear enough, please let me know).
Thank you for your help and sorry to bother the others. Best wishes.
Sincerely yours CHIU,YEUNG
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participants (3)
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CHIU,YEUNG -
Elaine Meng -
Eric Pettersen