Sequence based selections
Dear ChimeraX team, Two selection-related questions: 1. I'm looking for a way to combine multiple sequence based selections into one selection but I wasn't able to find a way to do this. The use case is, I have a lot of models that have these two proteins and I would like to use them together for superposition (via align command against Calphas). I would normally refer to them by chain ID, but here these are not consistently assigned so I need to use the sequence for selection. 1. Is it possible to have a named, sequence-based selection that, when called, would perform the selection? This would save a lot of pain when writing scripts for sequence based selections. Cheers, EP -- Esa-Pekka Kumpula, PhD Senior Postdoctoral Researcher Laboratory of Structural Biology Institute of Biotechnology Helsinki Institute of Life Science HiLIFE University of Helsinki www.helsinki.fi/lsb<http://www.helsinki.fi/lsb>
Hi EP - we're also interested in named selections for making things easier for people using Jalview with ChimeraX. If you need a quick workaround right now, and you aren't dealing with models linked to EM maps - or 100s of models per sequence, then I'd suggest trying out Jalview for this, since it handles 1 sequence -> many models naturally. The workflow we've found useful is to create sequence features in Jalview, open the linked models for each sequence in ChimeraX, and use the Jalview ChimeraX dropdown menu to write the features to ChimeraX as attributes. You can then construct expressions to select those regions from the ChimeraX command line. Hope this helps.. Jim. ________________________________ From: Kumpula, Esa-Pekka via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Sent: 26 June 2024 11:42 To: Kumpula, Esa-Pekka via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] Sequence based selections Dear ChimeraX team, Two selection-related questions: 1. I'm looking for a way to combine multiple sequence based selections into one selection but I wasn't able to find a way to do this. The use case is, I have a lot of models that have these two proteins and I would like to use them together for superposition (via align command against Calphas). I would normally refer to them by chain ID, but here these are not consistently assigned so I need to use the sequence for selection. 1. Is it possible to have a named, sequence-based selection that, when called, would perform the selection? This would save a lot of pain when writing scripts for sequence based selections. Cheers, EP -- Esa-Pekka Kumpula, PhD Senior Postdoctoral Researcher Laboratory of Structural Biology Institute of Biotechnology Helsinki Institute of Life Science HiLIFE University of Helsinki www.helsinki.fi/lsb<http://www.helsinki.fi/lsb> The University of Dundee is a registered Scottish Charity, No: SC015096
Hi EP, Using Jalview certainly could be the way to go. As for trying to do this directly in ChimeraX...
I'm looking for a way to combine multiple sequence based selections into one selection but I wasn't able to find a way to do this. The use case is, I have a lot of models that have these two proteins and I would like to use them together for superposition (via align command against Calphas). I would normally refer to them by chain ID, but here these are not consistently assigned so I need to use the sequence for selection.
If you are trying to specify all chains with the exact same sequence as a particular chain, say chain A in model 1, then the selector would be: //identity="#1/A" This 'identity' pseudo-attribute isn't restricted to a single sequence. You could use: //identity="#1/A,B" to select all chains with the exact same sequence as chains A or B in model 1.
Is it possible to have a named, sequence-based selection that, when called, would perform the selection? This would save a lot of pain when writing scripts for sequence based selections.
You could only use "frozen" selectors (contents determined when the selector is defined, and does not change when additional structures are opened). So you could define an 'ldsa' selector that refers to the sequence LDSA in the structures open at the time it's defined with: sel seq LDSA ; name frozen ldsa sel Then 'ldsa' can be used like any other selector,, .e.g. "color ldsa red". You could use the 'alias' command to make it easier to create these selectors, which means you could put the aliases in your startup commands, and use the alias when you need it. --Eric Eric Pettersen UCSF Computer Graphics Lab
participants (3)
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Eric Pettersen -
James Procter (Staff) -
Kumpula, Esa-Pekka