Hi, I've docked a ligand with a receptor and I get a pdb with1 chain (chain A) I'd like to separate recpetor-ligand in two different chians (chain A e chain B). How can I do that in Chimera? regards
Hi Francesco, If they are already called chain A and B, you can split the chains in one model to make separate models using the command "split": <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/split.html> For example, if your structure with chains A and B is open as model 0, command: split #0 ... will make two models, model #0.1 with chain A and #0.2 with chain B. Even though they are still both #0 you can refer to them separately as #0.1 and #0.2, move them separately, etc. However, if they are currently both chain A, that will not do anything. To make separate models, you would have to open the receptor+ligand structure two times and in one copy, delete the ligand, and in the other copy, delete the receptor. Alternatively, you could manually text-edit the PDB file so make the ligand chain B before opening it in Chimera, and then use the "split" method. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Apr 29, 2011, at 3:55 AM, Francesco Burresi wrote:
Hi, I've docked a ligand with a receptor and I get a pdb with1 chain (chain A) I'd like to separate recpetor-ligand in two different chians (chain A e chain B). How can I do that in Chimera? regards
Just to be more clear, there isn't a simple way to change chain ID using Chimera. If that is all you wanted to do, you could text-edit the PDB file yourself, or this web server may be able to do it: <http://www.igs.cnrs-mrs.fr/Caspr2/magicPDB.cgi> Elaine On Apr 29, 2011, at 9:49 AM, Elaine Meng wrote:
Hi Francesco, If they are already called chain A and B, you can split the chains in one model to make separate models using the command "split": <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/split.html>
For example, if your structure with chains A and B is open as model 0, command:
split #0
... will make two models, model #0.1 with chain A and #0.2 with chain B. Even though they are still both #0 you can refer to them separately as #0.1 and #0.2, move them separately, etc.
However, if they are currently both chain A, that will not do anything. To make separate models, you would have to open the receptor+ligand structure two times and in one copy, delete the ligand, and in the other copy, delete the receptor. Alternatively, you could manually text-edit the PDB file so make the ligand chain B before opening it in Chimera, and then use the "split" method.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 29, 2011, at 3:55 AM, Francesco Burresi wrote:
Hi, I've docked a ligand with a receptor and I get a pdb with1 chain (chain A) I'd like to separate recpetor-ligand in two different chians (chain A e chain B). How can I do that in Chimera? regards
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Pdb files are text files so you can probably use a text editor. If you use windows I suggest to use vim www.vim.org and not word, to avoid extra characteres. ciao, Marco Def. Quota "Francesco Burresi" <francesco.burresi@gmail.com>:
Hi, I've docked a ligand with a receptor and I get a pdb with1 chain (chain A) I'd like to separate recpetor-ligand in two different chians (chain A e chain B). How can I do that in Chimera?
regards
Dr.Marco Sette, Ph.D. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette@uniroma2.it e-mail: m77it@yahoo.it Tel.: +39-0672594424 Fax: +39-0672594328 ---------------------------------------------------------------- Invito da parte dell'Ateneo: Il tuo futuro e quello della Ricerca Scientifica hanno bisogno del tuo aiuto. Dona il 5 x mille all'Universita' di Roma Tor Vergata codice fiscale: 80213750583 http://5x1000.uniroma2.it
hello, i know that this is a chimera forum, but for the purpose of changing the chain id you can use 2 software packages: 1. vmd. in vmd console you do a selection like: set sel [atomselect top "chain A"] $sel set chain B given that your initial chain id was A and the desired is B if you don't have a initial chain id, then you can specify a residue range: set sel [atomselect top "resid 1 to 24"] $set sel chain B mind you that top specifies the top molecule that is selected in vmd main window. 2. coot. in coot it's simpler: calculate -> change chain ids. in both cases you need to save your file for the changes to take effect best, jean-paul
participants (4)
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Elaine Meng -
Francesco Burresi -
Jean-Paul Armache -
sette＠uniroma2.it