Splitting an pdb with multiple proteins
Hi, I´m frequently looking at pdb´s that contain multiple chains, like ribosomes or preribosomes (e.g. Pdb 3JCT). Is there a way to import the information from the pdb database, which tells you the name of the chains? Chain A = rpl2 Chain B = Rpl4 etc. Cool would be to split the pdb into multiple models that have the name from the pdb database. (It is quite annoying to have a pdb with nearly 60 different chains and you have to spend half a day to rename the chains or to create individual models, before analyzing the structure) Thanks for suggestions and solutions Best wishes Jochen
Hi Jochen, This information is already imported, and when you mouse over the chain, it is shown in the “status message” area across the bottom of the Chimera window. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/chimerawindow.html> I tested just now, and the information is retained and can be shown in the same way after “split” is used. However, it is not automatically used as the model names. 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 Jun 9, 2016, at 4:05 AM, Jochen Baßler <jochen.bassler@bzh.uni-heidelberg.de> wrote:
Hi,
I´m frequently looking at pdb´s that contain multiple chains, like ribosomes or preribosomes (e.g. Pdb 3JCT). Is there a way to import the information from the pdb database, which tells you the name of the chains? Chain A = rpl2 Chain B = Rpl4 etc. Cool would be to split the pdb into multiple models that have the name from the pdb database. (It is quite annoying to have a pdb with nearly 60 different chains and you have to spend half a day to rename the chains or to create individual models, before analyzing the structure)
Thanks for suggestions and solutions
Best wishes
Jochen
It is also listed in the reply log as the structure is opened. —Eric Eric Pettersen UCSF Computer Graphics Lab
On Jun 9, 2016, at 4:49 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Jochen, This information is already imported, and when you mouse over the chain, it is shown in the “status message” area across the bottom of the Chimera window. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/chimerawindow.html>
I tested just now, and the information is retained and can be shown in the same way after “split” is used. However, it is not automatically used as the model names. 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 Jun 9, 2016, at 4:05 AM, Jochen Baßler <jochen.bassler@bzh.uni-heidelberg.de> wrote:
Hi,
I´m frequently looking at pdb´s that contain multiple chains, like ribosomes or preribosomes (e.g. Pdb 3JCT). Is there a way to import the information from the pdb database, which tells you the name of the chains? Chain A = rpl2 Chain B = Rpl4 etc. Cool would be to split the pdb into multiple models that have the name from the pdb database. (It is quite annoying to have a pdb with nearly 60 different chains and you have to spend half a day to rename the chains or to create individual models, before analyzing the structure)
Thanks for suggestions and solutions
Best wishes
Jochen
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participants (3)
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Elaine Meng -
Eric Pettersen -
Jochen Baßler