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
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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)
-
Elaine Meng -
Francesco Burresi -
Jean-Paul Armache -
sette＠uniroma2.it