Re: [Chimera-users] How to add change to multiple molecules

Hi Yang You mean adding "charge"? I think you can add charge to all of the models as long as you check the box referred to them at the bottom. If you want to add charge to some models only, you can ~disp all, then display one by one and add charge to them. I hope this would help. Good luck! On Sun Nov 02 20:32:46 EST 2008, zhouyang <zhouyang@mail.shcnc.ac.cn> wrote:
Sincerely yours CHIU,YEUNG

Hi Yang, Yeung Chiu is right that you simply choose the one or more (or all) models from the box in Add Charge. The lines for the models to affect will be highlighted, and in fact all of them were already highlighted when I started Add Charge in my test today. If you click one line, then only that model will be chosen, but you can drag to choose a whole range of models, or click the first line and then Shift-click the last to a choose a block of lines. Or, you can toggle each line between chosen and not chosen with Ctrl-click. It doesn't matter which ones are displayed in the Chimera window, however. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/addcharge...
A separate issue is that yes, there is an "addcharge" command: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/addcharge.html> It can also work on specified models or all models, for example addcharge all spec #0.1-5 addcharge all These would both bring up dialogs for verifying the estimated net charge of each nonstandard residue. If you didn't want any dialog interactions (for example using Chimera in nogui mode) you would have to give the net charge, and in that case you can only do one residue type at a time. That is probably one model in your case if each is a small molecule for docking: addcharge nonstd #0.2 -2 You can put a bunch of Chimera commands in a text file and then just open that file to execute it. That is different from a shell script or Python script, which I believe also could be used, but I don't use those myself. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#command> 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 Nov 3, 2008, at 3:51 AM, CHIU,YEUNG wrote:

On Nov 3, 2008, at 9:11 AM, Elaine Meng wrote:
One slight correction: in nogui mode, if you use "addcharge all" it will use estimated charges for any non-standard residues. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
participants (3)
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CHIU,YEUNG
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Elaine Meng
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Eric Pettersen