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:
Hi Recently I wanna add change to a series of molecules for DOCK6 which are stored in a single .mol2 file. It seems that the Chimera GUI can just add change for one molecules at one operation. I wonder how to add change to all of them? Alternatively I just suppose to use 'split' shell command to seperate these molecules to single files and then add change to them. Then the key point is whether Chimera can run in command-line mode so that I can achieve by writing a shell script? Thanks in advance Yang zhouyang@mail.shcnc.ac.cn
2008-11-03 ?????? ZHOU Yang Master Candidate Drug Discovery and Design Center Shanghai Institute of Meteria Medica China Academy of Sciences 555 Zu Chong Zhi Road , Zhang Jiang Hi-Tech Park, Shanghai, China (Postcode: 201203)
Mobile: 86-137-6430-7897 MSN: zhouyang_pku@hotmail.com _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
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:
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:
Hi Recently I wanna add change to a series of molecules for DOCK6 which are stored in a single .mol2 file. It seems that the Chimera GUI can just add change for one molecules at one operation. I wonder how to add change to all of them? Alternatively I just suppose to use 'split' shell command to seperate these molecules to single files and then add change to them. Then the key point is whether Chimera can run in command-line mode so that I can achieve by writing a shell script? Thanks in advance Yang zhouyang@mail.shcnc.ac.cn
Sincerely yours CHIU,YEUNG
On Nov 3, 2008, at 9:11 AM, Elaine Meng wrote:
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
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 -
Elaine Meng -
Eric Pettersen