I am working with a protein PDB 4KHZ. It is a recent PDB deposition of the maltose transporter system. It is a multisubunit protein complex. There are five separate chains that come together. I know how to select and visualize each of them or in pairs or whatever. Two of the subunits have a maltose substrate bound within their interior. I know how to visualize the maltose molecules using the Select menu. When I go to the Select menu, open Residues - click on GLC (Glucose) all of the maltose molecules become visible in both proteins. Is it possible somehow to visualize only one of the maltose molecules in one of the proteins in this case the maltose in chain E. - and not have the maltose in G or F visualized. Thank you Arthur G. Szabo Professor Emeritus Chemistry and Biochemistry. Wilfrid Laurier University.
Hi Arthur, In the command line (show from Favorites menu) you can easily specify the chain ID along with residue name or number. For example, command: select :GLC.E — or — select :glc.e ...selects the GLC residues in chain E only. You don’t have to capitalize the residue name or chain ID. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> Two alternative methods: (1) if you want to use menu only to select these residues, it is more steps. Menu: Select… Residue… GLC Select… Selection Mode… intersect Select… Chain E Select… Selection Mode… replace (the last one just puts the selection mode back to normal so you wouldn’t get confused later). (2) of course, if it is already displayed you can select it with Ctrl-click on one of its atoms or bonds, then pressing keyboard up arrow to select that whole GLC residue, then if you want the whole oligosaccharide (more than one GLC bonded together), press keyboard up arrow again 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 Dec 9, 2015, at 7:23 AM, A G Szabo <agszabo@bell.net> wrote:
I am working with a protein PDB 4KHZ. It is a recent PDB deposition of the maltose transporter system.
It is a multisubunit protein complex. There are five separate chains that come together. I know how to select and visualize each of them or in pairs or whatever.
Two of the subunits have a maltose substrate bound within their interior. I know how to visualize the maltose molecules using the Select menu. When I go to the Select menu, open Residues – click on GLC (Glucose) all of the maltose molecules become visible in both proteins.
Is it possible somehow to visualize only one of the maltose molecules in one of the proteins in this case the maltose in chain E. – and not have the maltose in G or F visualized.
Thank you
Arthur G. Szabo
Professor Emeritus Chemistry and Biochemistry.
Wilfrid Laurier University.
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participants (2)
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A G Szabo -
Elaine Meng