Saving multiple identical PDB in a single file with unique chain ID
Hello, I'm building a tubulin lattice. I want to save the structure as a single model, however, the chain ID for each monomer should be different from the other ones. If I copy/combine my alpha-beta tubulin monomer, I get another structure with A and B chains. What I want is different chain letters. How can I do it? Regards.
Hi Ahmad, The “copy/combine” dialog has a choice “If original moleculea have duplicate single-letter chain IDs, then: rename them uniquely” which is the default. Make sure that that option is chosen (or if you are using the “combine” command, it also has “newchainids true” by default). Also make sure you choose with the mouse in that dialog all the models you want to combine (highlight all the rows for those models). Maybe it is confusing that your original models are still open at the same time as the new combined model. If you look only at the new combined model, it should not have any duplicate chain IDs if the default option mentioned above is used. Your question confuses me because if the starting structure is a monomer, it would only contain A (not B). However, even if your original structure is a dimer (A and B) if you combine multiples of either one, you should end up with only one A and only one B, etc. in the single combined model. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 19, 2018, at 8:34 AM, Ahmad Abdelzaher <underoath006@gmail.com> wrote:
Hello,
I'm building a tubulin lattice. I want to save the structure as a single model, however, the chain ID for each monomer should be different from the other ones. If I copy/combine my alpha-beta tubulin monomer, I get another structure with A and B chains. What I want is different chain letters.
How can I do it?
Regards.
Sorry for the confusion. By tubulin monomer I mean an alpha-beta dimer. A tubulin trimer would be three tubulins of six chains A-B-A-B-A-B, each two belonging to a tubulin monomer. My question is, if the first monomer has chains A and B, I want the copy/combine model to have different chain ID letters from A and B, for example C and D, and so on for the third, and fourth, etc. How can I do that? Regards.
Hi Ahmad, See the previous reply: the combined single model will not have any two chains with the same ID if you use the option I described, which is the default. Make sure you are looking only at the final combined model, not the other starting models which may still be open. Elaine
On Apr 19, 2018, at 12:40 PM, Ahmad Abdelzaher <underoath006@gmail.com> wrote:
Sorry for the confusion. By tubulin monomer I mean an alpha-beta dimer. A tubulin trimer would be three tubulins of six chains A-B-A-B-A-B, each two belonging to a tubulin monomer.
My question is, if the first monomer has chains A and B, I want the copy/combine model to have different chain ID letters from A and B, for example C and D, and so on for the third, and fourth, etc.
How can I do that?
Regards.
Thanks a lot for trying to help. I did exactly just that, the option you described renames duplicate chains in the structure, however, in my structure, there are no duplicate chains. There's an A and a B chain. When I copy combine, I get another structure with A and B as well. I want the second structure to have C and D instead, i.e. a unique chain ID that is different from the original model's chain. On Thu, Apr 19, 2018 at 6:43 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Ahmad, See the previous reply: the combined single model will not have any two chains with the same ID if you use the option I described, which is the default. Make sure you are looking only at the final combined model, not the other starting models which may still be open.
Elaine
On Apr 19, 2018, at 12:40 PM, Ahmad Abdelzaher <underoath006@gmail.com> wrote:
Sorry for the confusion. By tubulin monomer I mean an alpha-beta dimer. A tubulin trimer would be three tubulins of six chains A-B-A-B-A-B, each two belonging to a tubulin monomer.
My question is, if the first monomer has chains A and B, I want the copy/combine model to have different chain ID letters from A and B, for example C and D, and so on for the third, and fourth, etc.
How can I do that?
Regards.
That is exactly what the option does: it would make a combined single model with A B C D, not AB AB. The “duplicate” refers to the output single model, not your input models. All I can say is that you must be doing something wrong, or you have not closed the input models (which are still AB AB) and they are causing confusion. If you are trying to combining two models, you have to choose BOTH models in the Model Panel and then click “copy/combine” and then make sure BOTH models are also chosen in the copy/combine dialog. Choose “rename them uniquely” and maybe you should also choose “Close source models” (get rid of your two starting models) so that they will not confuse you. Elaine
On Apr 19, 2018, at 6:18 PM, Ahmad Abdelzaher <underoath006@gmail.com> wrote:
Thanks a lot for trying to help. I did exactly just that, the option you described renames duplicate chains in the structure, however, in my structure, there are no duplicate chains. There's an A and a B chain. When I copy combine, I get another structure with A and B as well. I want the second structure to have C and D instead, i.e. a unique chain ID that is different from the original model's chain.
On Thu, Apr 19, 2018 at 6:43 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Ahmad, See the previous reply: the combined single model will not have any two chains with the same ID if you use the option I described, which is the default. Make sure you are looking only at the final combined model, not the other starting models which may still be open.
Elaine
On Apr 19, 2018, at 12:40 PM, Ahmad Abdelzaher <underoath006@gmail.com> wrote:
Sorry for the confusion. By tubulin monomer I mean an alpha-beta dimer. A tubulin trimer would be three tubulins of six chains A-B-A-B-A-B, each two belonging to a tubulin monomer.
My question is, if the first monomer has chains A and B, I want the copy/combine model to have different chain ID letters from A and B, for example C and D, and so on for the third, and fourth, etc.
How can I do that?
Regards.
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Ahmad Abdelzaher -
Elaine Meng