How do different sections of TLS groups affect refinment
Greetings everyone, I am still fairly new to crystallography, so forgive me for my naivety. My question involves how the TLSMD server segments my protein and the effects it has on refinement. For instance when i use "Multi-Chain Alignment Analysis", which lines the sequence for all of my chains (a total of 12) and shows how TLS groups are divided among them, it shows varying selections of TLS groups among the different chains. It should be noted that the sequence is the same for all the chains in my protein. Also if a TLS group splits a alpha helix into multiple parts, would this be valid? I have come to understand that helices move more like rigid bodies than segmented groups... Thanks! -Aaron
Cutting out two pipes without insulation while the wall is open should be VERY easy and inexpensive. Maybe this is not even worth hassling over, but rather should just do it for owners who want it. G George N. Phillips, Jr., Ph.D. Professor of Biochemistry and of Computer Sciences University of Wisconsin-Madison 433 Babcock Dr. Madison, Wi 53706 Phone/FAX (608) 263-6142 On Jan 20, 2010, at 3:38 PM, Bart, Aaron G wrote:
Greetings everyone, I am still fairly new to crystallography, so forgive me for my naivety.
My question involves how the TLSMD server segments my protein and the effects it has on refinement. For instance when i use "Multi-Chain Alignment Analysis", which lines the sequence for all of my chains (a total of 12) and shows how TLS groups are divided among them, it shows varying selections of TLS groups among the different chains. It should be noted that the sequence is the same for all the chains in my protein.
Also if a TLS group splits a alpha helix into multiple parts, would this be valid? I have come to understand that helices move more like rigid bodies than segmented groups...
Thanks!
-Aaron _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Plumbing meets crystallography?
2010/1/20 George Phillips
Cutting out two pipes without insulation while the wall is open should be VERY easy and inexpensive. Maybe this is not even worth hassling over, but rather should just do it for owners who want it.
G
George N. Phillips, Jr., Ph.D. Professor of Biochemistry and of Computer Sciences University of Wisconsin-Madison 433 Babcock Dr. Madison, Wi 53706 Phone/FAX (608) 263-6142
On Jan 20, 2010, at 3:38 PM, Bart, Aaron G wrote:
Greetings everyone, I am still fairly new to crystallography, so forgive me for my naivety.
My question involves how the TLSMD server segments my protein and the effects it has on refinement. For instance when i use "Multi-Chain Alignment Analysis", which lines the sequence for all of my chains (a total of 12) and shows how TLS groups are divided among them, it shows varying selections of TLS groups among the different chains. It should be noted that the sequence is the same for all the chains in my protein.
Also if a TLS group splits a alpha helix into multiple parts, would this be valid? I have come to understand that helices move more like rigid bodies than segmented groups...
Thanks!
-Aaron _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
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Hi Aaron, TLSMD server suggests you possible optimal selections for TLS groups. If I remember correctly, it gives you a list of 20 options or so. It's up to you which one to choose. Usually you look at the graphic "residual vs number_of_tls_groups" and see at which point the curve stops dropping sharply. Also, you need to use common sense too, say, I wouldn't choose a set of TLS groups that brakes a helix into multiple parts. I'm actually puzzled about how that happened. I think it is a good question for Ethan Merritt, the author of TLSMD tool. Also, you may want to try a few possible TLS separations and see which one gives your better refinement results. Pavel. On 1/20/10 1:38 PM, Bart, Aaron G wrote:
Greetings everyone, I am still fairly new to crystallography, so forgive me for my naivety.
My question involves how the TLSMD server segments my protein and the effects it has on refinement. For instance when i use "Multi-Chain Alignment Analysis", which lines the sequence for all of my chains (a total of 12) and shows how TLS groups are divided among them, it shows varying selections of TLS groups among the different chains. It should be noted that the sequence is the same for all the chains in my protein.
Also if a TLS group splits a alpha helix into multiple parts, would this be valid? I have come to understand that helices move more like rigid bodies than segmented groups...
Thanks!
-Aaron _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
The tlsmd documentation is very helpful in explaining the rationale.
There are many examples of helices flexing or breaking in comparing
strucures of the same protein bound to different ligands, so don't
worry about that.
You might find it worthwhile to try a few different tls groups in
parallel. In my experience, lower resolution structures are more
sensitive to the number of groups.
Kendall Nettles
On Jan 20, 2010, at 4:40 PM, "Bart, Aaron G"
Greetings everyone, I am still fairly new to crystallography, so forgive me for my naivety.
My question involves how the TLSMD server segments my protein and the effects it has on refinement. For instance when i use "Multi-Chain Alignment Analysis", which lines the sequence for all of my chains (a total of 12) and shows how TLS groups are divided among them, it shows varying selections of TLS groups among the different chains. It should be noted that the sequence is the same for all the chains in my protein.
Also if a TLS group splits a alpha helix into multiple parts, would this be valid? I have come to understand that helices move more like rigid bodies than segmented groups...
Thanks!
-Aaron _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
There are many examples of helices flexing or breaking in comparing strucures of the same protein bound to different ligands, so don't worry about that.
If I understood your point correctly... I think there are two different things: 1) different helix shapes across multiple crystal structures (and multiple datasets associated with them), and 2) a helix in a particular crystal structure (with one single dataset associated with it) that flexes-bends-brakes back-and-forth enough to accept that it can be broken down into multiple (tls-refinable) rigid bodies. In refinement we deal with "2)" and therefore I was skeptical about such possibility. Pavel.
I was suggesting that tls motions may be representative of larger
motions that occur in solution, which we may get snapshots of by
comparing different structures.
Kendall
On Jan 20, 2010, at 7:03 PM, "Pavel Afonine"
There are many examples of helices flexing or breaking in comparing strucures of the same protein bound to different ligands, so don't worry about that.
If I understood your point correctly... I think there are two different things:
1) different helix shapes across multiple crystal structures (and multiple datasets associated with them), and 2) a helix in a particular crystal structure (with one single dataset associated with it) that flexes-bends-brakes back-and-forth enough to accept that it can be broken down into multiple (tls-refinable) rigid bodies.
In refinement we deal with "2)" and therefore I was skeptical about such possibility.
Pavel.
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participants (5)
-
Bart, Aaron G -
George Phillips -
Kendall Nettles -
Pavel Afonine -
Peter Zwart