Hi, Currently it is only possible to select a template from PDB based on the PDB code. Would it be possible to have an option to use one of the currently open PDB files in Chimera? Thanks! Dina
Hi Dina! It will work if your structure is associated with your sequence alignment. Then in the dialog where you choose template, it will list the name of the associated sequence. So pick that one. Then, when you execute there may be a message “could not discern PDB ID” or something like that, but it will still run the calculation. It is only trying to find the PDB ID to be able to show more information in the template-choosing area of the dialog. I tried it just now on some structure that was not opened from the PDB, and it worked to produce a model from that template, so hopefully it will work for you too. You can check that the job is running in the Task Panel (opened by clicking the small “i” button near the lower right corner of the Chiemra window). 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 Nov 16, 2016, at 12:48 AM, Dina Schneidman <dina.schneidman@mail.huji.ac.il> wrote:
Hi,
Currently it is only possible to select a template from PDB based on the PDB code. Would it be possible to have an option to use one of the currently open PDB files in Chimera?
Thanks! Dina
Dear Elaine, It is me and not Dina who is trying to use Chimera Modeller interface and I am having several problems. I tried to do what you suggested and it does not work. The error message is “could not determine structure to load for selected template” and the modeller does not run the calculation. I am sending you my pdb file and the sequence alignment file. Could you look at it and tell me what is wrong? Also, I was having trouble with two chains being in the file. I would like to model one chain, but in the presence of the second chain. I do not 100% understand what should be in the comments in the .ali file and if I inserted them correctly: Here: structureX:5C7Jcut: 520 :A: 75 :C:::: sequence:llama: 520 :A: 75 :C:::: I would be very grateful for you if you could solve me these problems. Julia Dr. Julia Shifman Department of Biological Chemistry Hebrew University of Jerusalem Phone: 972-2-658-4078 WEB: www.bio.huji.ac.il/shifman
On Nov 16, 2016, at 10:25 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear Elaine, I was able to get over the first bug and not to download the file form the pDB. However, I am experiencing another problem with modeling two chains. For some reason my models come out with one chain correctly folded and the second chain fused to the C-terminus of the first chain and unfolded. I am sending you the output file together with the alignment file. Could you tell me what the problem is? Thanks, Julia Dr. Julia Shifman Department of Biological Chemistry Hebrew University of Jerusalem Phone: 972-2-658-4078 WEB: www.bio.huji.ac.il/shifman
On Nov 16, 2016, at 10:25 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Dina! It will work if your structure is associated with your sequence alignment. Then in the dialog where you choose template, it will list the name of the associated sequence. So pick that one. Then, when you execute there may be a message “could not discern PDB ID” or something like that, but it will still run the calculation. It is only trying to find the PDB ID to be able to show more information in the template-choosing area of the dialog.
I tried it just now on some structure that was not opened from the PDB, and it worked to produce a model from that template, so hopefully it will work for you too. You can check that the job is running in the Task Panel (opened by clicking the small “i” button near the lower right corner of the Chiemra window). 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 Nov 16, 2016, at 12:48 AM, Dina Schneidman <dina.schneidman@mail.huji.ac.il> wrote:
Hi,
Currently it is only possible to select a template from PDB based on the PDB code. Would it be possible to have an option to use one of the currently open PDB files in Chimera?
Thanks! Dina
Hi Julia, You cannot model multichain structures using the simple Modeller interface in Chimera. To do that you would have to run Modeller “manually” outside of Chimera. Even though the template may have additional chains, they will be ignored in the modeling process. This is described in the documentation: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html#comparative> The “/“ character in the sequence alignment to mean chain break is notation specific to Modeller, and not understood by Chimera (or other programs as far as I know, since it is not in the official alignment format definitions). Chimera interprets each sequence as only a single chain, which is why when you use this interface, you get additional residues stuck on the end of the other chain. So, none of these things are bugs, just limitations of what you can do with the simple Modeller interface in Chimera. Sorry, you may need to use Modeller the “hard way.” Regards, 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 Nov 17, 2016, at 5:14 AM, Julia Shifman <jshifman@mail.huji.ac.il> wrote:
Dear Elaine,
I was able to get over the first bug and not to download the file form the pDB. However, I am experiencing another problem with modeling two chains. For some reason my models come out with one chain correctly folded and the second chain fused to the C-terminus of the first chain and unfolded. I am sending you the output file together with the alignment file. Could you tell me what the problem is? Thanks,
Julia
<5C7_model.pdb><5C7Jcut.pdb><5C7Jchainc-fill.ali> Dr. Julia Shifman Department of Biological Chemistry Hebrew University of Jerusalem Phone: 972-2-658-4078
WEB: www.bio.huji.ac.il/shifman
On Nov 16, 2016, at 10:25 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Dina! It will work if your structure is associated with your sequence alignment. Then in the dialog where you choose template, it will list the name of the associated sequence. So pick that one. Then, when you execute there may be a message “could not discern PDB ID” or something like that, but it will still run the calculation. It is only trying to find the PDB ID to be able to show more information in the template-choosing area of the dialog.
I tried it just now on some structure that was not opened from the PDB, and it worked to produce a model from that template, so hopefully it will work for you too. You can check that the job is running in the Task Panel (opened by clicking the small “i” button near the lower right corner of the Chiemra window). 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 Nov 16, 2016, at 12:48 AM, Dina Schneidman <dina.schneidman@mail.huji.ac.il> wrote:
Hi,
Currently it is only possible to select a template from PDB based on the PDB code. Would it be possible to have an option to use one of the currently open PDB files in Chimera?
Thanks! Dina
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participants (3)
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Dina Schneidman -
Elaine Meng -
Julia Shifman