Hi Shengyou, Currently there is no command to save a Mol2 file - the only way is with File... Save Mol2 in the Chimera menu. There is a "write" command for saving coordinates, but it only saves PDB format. In the future, it may be improved to also save Mol2 format. Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jan 16, 2007, at 8:19 PM, Huang, Shengyou wrote:

Hi,

Does anybody know a COMMAND which can save a mol2 format file in Chimera? Thanks!

Shengyou Huang

_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

Hi, Eric, hi, Elaine, It works great for me with the Python script file. Thanks so much for your help! Shengyou ________________________________ From: Eric Pettersen [mailto:pett@cgl.ucsf.edu] Sent: Fri 1/19/2007 6:22 PM To: Huang, Shengyou Cc: Chimera BB Subject: Re: [Chimera-users] save mol2 command Hi Shengyou, As Elaine says, there is no command yet. It is pretty easy to do with a Python script though. If you put the following lines in a file: import chimera from WriteMol2 import writeMol2 writeMol2(chimera.openModels.list(modelTypes=[chimera.Molecule]), "models.mol2") into a file ending in ".py" (e.g. "writeMol2.py"), then if you open that file in Chimera (using File->Open... or the "open" command), then a Mol2 file named models.mol2 containing your current structures will be written into the same folder where the Python script is. --Eric Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu <http://www.cgl.ucsf.edu/> On Jan 19, 2007, at 10:36 AM, Elaine Meng wrote: Hi Shengyou, Currently there is no command to save a Mol2 file - the only way is with File... Save Mol2 in the Chimera menu. There is a "write" command for saving coordinates, but it only saves PDB format. In the future, it may be improved to also save Mol2 format. Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jan 16, 2007, at 8:19 PM, Huang, Shengyou wrote: Hi, Does anybody know a COMMAND which can save a mol2 format file in Chimera? Thanks! Shengyou Huang _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users