Hi, I need to use an own file as a template to modeling on Chimera (using Modeller).
When I try to blast my sequence only find the option to query structures available on PDB Web Site. Does someone know how to use an own structural template?
Thanks
You pre-load the local pdb file into Chimera using the "File/open" dialog rather than "fetch":
check here https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#approaches for step by step instructions for the different approaches:
"
Starting with a structure already known to be a suitable template:
- open the structure(s)
- if a single template structure, start Sequence to show its sequence
- if multiple template structures, use the Align Chain Sequences tool to generate a multiple alignment from their sequences
- add the target sequence to align it to the template sequence(s) (Edit... Add Sequence in the Multalign Viewer menu)
- if needed, realign the sequences to further improve the multiple alignment (Edit... Realign Sequences in the Multalign Viewer menu)
"
You pre-load the local pdb file into Chimera using the "File/open" dialog rather than "fetch":
check here https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#approaches for step by step instructions for the different approaches:
"
Starting with a structure already known to be a suitable template:
- open the structure(s)
- if a single template structure, start Sequence to show its sequence
- if multiple template structures, use the Align Chain Sequences tool to generate a multiple alignment from their sequences
- add the target sequence to align it to the template sequence(s) (Edit... Add Sequence in the Multalign Viewer menu)
- if needed, realign the sequences to further improve the multiple alignment (Edit... Realign Sequences in the Multalign Viewer menu)
"
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