Help saving models as .pdb file
I have constructed model of pentameric protein by exchanging one of the chains with a very closely related chain from other variant of such pentameric protein. Chimera recognizes that my model consists of parts of two proteins. I would like to save it as a single protein file. When I attempt to save model as a single file (option in save dialog) a PDB file is produced. However, when I open this file in other application (such as Cresset Flare) to explore molecular dynamics or docking in this newly constructed hybrid system - it opens as two different proteins. Is it possible to “merge” the parts to become a single pentameric protein, that would behave as single entity during docking or MD computations? Jacek Jagodzinski PS. I am not computational chemist, I am medicinal chemist by training and long career.
Hi Jacek, From your description, the atoms are in two different "models" in Chimera, i.e. when you show the Model Panel (e.g. from the Favorites menu) it shows them as two separate entries with different model numbers. So when you save as a single PDB file, they are still in two different models (in the PDB file, there will be MODEL and ENDMDL around each) and opening that file just gives the same situation you had before. Instead you want to first combine them into a single model, and then save the single model. To combine models without changing the relative positions of the atoms, you can use the "combine" command, e.g. combine #0,1 name mynewmodel modelId #2 see <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html> ...or if you prefer a GUI, in the Model Panel (under Favorites in the menu) you can choose both models on the left side of that tool and then the "copy/combine" function on the right. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html#combine> Then save your new single model (#2 in the command example above) to PDB. Make sure that you save only the new combined model and not also the original separate models. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 3, 2024, at 10:35 AM, Jacek Jagodzinski via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
I have constructed model of pentameric protein by exchanging one of the chains with a very closely related chain from other variant of such pentameric protein. Chimera recognizes that my model consists of parts of two proteins. I would like to save it as a single protein file. When I attempt to save model as a single file (option in save dialog) a PDB file is produced. However, when I open this file in other application (such as Cresset Flare) to explore molecular dynamics or docking in this newly constructed hybrid system - it opens as two different proteins. Is it possible to “merge” the parts to become a single pentameric protein, that would behave as single entity during docking or MD computations?
Jacek Jagodzinski
PS. I am not computational chemist, I am medicinal chemist by training and long career.
EWlaine, thanks, it worked! Jacek
On Jun 3, 2024, at 10:50 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Jacek, From your description, the atoms are in two different "models" in Chimera, i.e. when you show the Model Panel (e.g. from the Favorites menu) it shows them as two separate entries with different model numbers. So when you save as a single PDB file, they are still in two different models (in the PDB file, there will be MODEL and ENDMDL around each) and opening that file just gives the same situation you had before.
Instead you want to first combine them into a single model, and then save the single model. To combine models without changing the relative positions of the atoms, you can use the "combine" command, e.g.
combine #0,1 name mynewmodel modelId #2
see <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html>
...or if you prefer a GUI, in the Model Panel (under Favorites in the menu) you can choose both models on the left side of that tool and then the "copy/combine" function on the right. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html#combine>
Then save your new single model (#2 in the command example above) to PDB. Make sure that you save only the new combined model and not also the original separate models.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 3, 2024, at 10:35 AM, Jacek Jagodzinski via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
I have constructed model of pentameric protein by exchanging one of the chains with a very closely related chain from other variant of such pentameric protein. Chimera recognizes that my model consists of parts of two proteins. I would like to save it as a single protein file. When I attempt to save model as a single file (option in save dialog) a PDB file is produced. However, when I open this file in other application (such as Cresset Flare) to explore molecular dynamics or docking in this newly constructed hybrid system - it opens as two different proteins. Is it possible to “merge” the parts to become a single pentameric protein, that would behave as single entity during docking or MD computations?
Jacek Jagodzinski
PS. I am not computational chemist, I am medicinal chemist by training and long career.
participants (2)
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Elaine Meng -
Jacek Jagodzinski