Dear all, I tried to find a way to input initial TLS parameters for the groups into phenix. I know many times this is not advisable, but I wanted to test what comes out from TLSmd server. I could not find any reference on how to do this. Note that I know how to define the groups (a previous question in this bb), the point now is to input initial parameters (origin, T, L, S). Thanks, Jorge
Hi Jorge,
I tried to find a way to input initial TLS parameters for the groups into phenix.
There is absolutely no need to give phenix.refine a start input values for TLS groups: phenix.refine determines them automatically. All you need to provide are the selections for TLS groups.
I know many times this is not advisable, but I wanted to test what comes out from TLSmd server.
This is not advisable, indeed (and not possible to do as well). phenix.refine must do a better job in finding TLS parameters than TLSmd server simply because phenix.refine uses the experimental data + very sophisticated and robust refinement protocol, while the TLSmd server relies on the B-factors in input PDB file (as far as I know, correct me if it's not true). Pavel.
Hi Pavel, I thought one of the main advantages for using the TLSmd server was that it provided the crystallographer with suggestions for the TLS staring groups (as well as the TLS values for these groups) avoiding the need to make somewhat arbitrary choices about the TLS group boundaries. If phenix then refines the TLS values for the groups picked with help pf the TLSmd server analysis which is this less good that starting TLS refinement in phenix without input from the MD server? -----Original Message----- From: Pavel Afonine [mailto:[email protected]] Sent: Sun 2/24/2008 12:44 PM To: PHENIX user mailing list Subject: Re: [phenixbb] input initial TLS parameters Hi Jorge,
I tried to find a way to input initial TLS parameters for the groups into phenix.
There is absolutely no need to give phenix.refine a start input values for TLS groups: phenix.refine determines them automatically. All you need to provide are the selections for TLS groups.
I know many times this is not advisable, but I wanted to test what comes out from TLSmd server.
This is not advisable, indeed (and not possible to do as well). phenix.refine must do a better job in finding TLS parameters than TLSmd server simply because phenix.refine uses the experimental data + very sophisticated and robust refinement protocol, while the TLSmd server relies on the B-factors in input PDB file (as far as I know, correct me if it's not true). Pavel. _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Hi Mark,
I thought one of the main advantages for using the TLSmd server was that it provided the crystallographer with suggestions for the TLS staring groups (as well as the TLS values for these groups) avoiding the need to make somewhat arbitrary choices about the TLS group boundaries.
To do TLS refinement you need to define the selections for TLS groups. This can be done either manually by just looking at your model or by using TLSmd server. These selections for TLS groups is all phenix.refine needs to do TLS refinement. phenix.refine does not need the starting values for TLS, it finds them automatically from doing some preliminary group B-factors refinement and optimal splitting of total B into individual and group B (http://www.ccp4.ac.uk/newsletters/newsletter45/articles/Tmax-CCP4_Afonine-Ur...). Again, as far as I know, the TLSmd server automatically finds the selections for TLS groups using the B-factors from input PDB file. And I think this is a weak point about TLSmd since that B-factors can be biased by previously used restraints or somehow distorted, while phenix.refine uses the experimental data to find these starting values. Pavel.
Hi Mark, if I understand Pavel correctly I think he is saying that TLSmd can provide both group definitions and initial values for the TLS parameters. In phenix.refine the only information that is required is the group definitions - the values for the TLS parameters will be refined using a procedure that discards any of the input values anyway. This is one of the things that has been done to make the procedure more stable. The TLS parameter values from TLSmd are, in many cases, probably good estimates for the true parameters, but they would need to be refined anyway. Cheers, Paul Mayer, Mark (NIH/NICHD) [E] wrote:
Hi Pavel,
I thought one of the main advantages for using the TLSmd server was that it provided the crystallographer with suggestions for the TLS staring groups (as well as the TLS values for these groups) avoiding the need to make somewhat arbitrary choices about the TLS group boundaries.
If phenix then refines the TLS values for the groups picked with help pf the TLSmd server analysis which is this less good that starting TLS refinement in phenix without input from the MD server?
-----Original Message----- From: Pavel Afonine [mailto:[email protected]] Sent: Sun 2/24/2008 12:44 PM To: PHENIX user mailing list Subject: Re: [phenixbb] input initial TLS parameters
Hi Jorge,
I tried to find a way to input initial TLS parameters for the groups into phenix.
There is absolutely no need to give phenix.refine a start input values for TLS groups: phenix.refine determines them automatically. All you need to provide are the selections for TLS groups.
I know many times this is not advisable, but I wanted to test what comes out from TLSmd server.
This is not advisable, indeed (and not possible to do as well). phenix.refine must do a better job in finding TLS parameters than TLSmd server simply because phenix.refine uses the experimental data + very sophisticated and robust refinement protocol, while the TLSmd server relies on the B-factors in input PDB file (as far as I know, correct me if it's not true).
Pavel.
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Hi Paul and Pavel, This was my understanding, so TLSmd is still very useful for assigning the initial groups, which seems better than picking by eye. Its interesting to know than phenix then generates its own set of starting parameters Refmac uses the TLSmd parameter values as the input for further refinement, and in my experience is sometimes unstable. -----Original Message----- From: Paul Adams [mailto:[email protected]] Sent: Sun 2/24/2008 3:31 PM To: PHENIX user mailing list Subject: Re: [phenixbb] input initial TLS parameters Hi Mark, if I understand Pavel correctly I think he is saying that TLSmd can provide both group definitions and initial values for the TLS parameters. In phenix.refine the only information that is required is the group definitions - the values for the TLS parameters will be refined using a procedure that discards any of the input values anyway. This is one of the things that has been done to make the procedure more stable. The TLS parameter values from TLSmd are, in many cases, probably good estimates for the true parameters, but they would need to be refined anyway. Cheers, Paul Mayer, Mark (NIH/NICHD) [E] wrote:
Hi Pavel,
I thought one of the main advantages for using the TLSmd server was that it provided the crystallographer with suggestions for the TLS staring groups (as well as the TLS values for these groups) avoiding the need to make somewhat arbitrary choices about the TLS group boundaries.
If phenix then refines the TLS values for the groups picked with help pf the TLSmd server analysis which is this less good that starting TLS refinement in phenix without input from the MD server?
-----Original Message----- From: Pavel Afonine [mailto:[email protected]] Sent: Sun 2/24/2008 12:44 PM To: PHENIX user mailing list Subject: Re: [phenixbb] input initial TLS parameters
Hi Jorge,
I tried to find a way to input initial TLS parameters for the groups into phenix.
There is absolutely no need to give phenix.refine a start input values for TLS groups: phenix.refine determines them automatically. All you need to provide are the selections for TLS groups.
I know many times this is not advisable, but I wanted to test what comes out from TLSmd server.
This is not advisable, indeed (and not possible to do as well). phenix.refine must do a better job in finding TLS parameters than TLSmd server simply because phenix.refine uses the experimental data + very sophisticated and robust refinement protocol, while the TLSmd server relies on the B-factors in input PDB file (as far as I know, correct me if it's not true).
Pavel.
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
------------------------------------------------------------------------
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-- Paul Adams Deputy Division Director, Physical Biosciences Division, LBL Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 510-486-4225, Fax: 510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road, BLDG 64R0121 Berkeley, CA 94720, USA. -- _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
The only information that is vital for phenix.refine are the selections for TLS groups, for example: TLS grop #1: "chain A and resseq 1-200" TLS grop #2: "chain B and resseq 34-500" etc... This information is obtained from TLSmd server. Sometimes though it is very easy just to have a look at your model to say what your TLS groups are. The actual values of TLS matrices that TLSmd is producing as well are useless for phenix.refine simply because it has its own extremely sophisticated algorithm for finding these values. And this algorithm is much more powerful since it uses the experimental data. As an illustration, I re-refined 350 TLS containing structures from PDB using phenix.refine and I never observed any kind of refinement instability. Pavel.
This was my understanding, so TLSmd is still very useful for assigning the initial groups, which seems better than picking by eye. Its interesting to know than phenix then generates its own set of starting parameters Refmac uses the TLSmd parameter values as the input for further refinement, and in my experience is sometimes unstable.
-----Original Message----- From: Paul Adams [mailto:[email protected]] Sent: Sun 2/24/2008 3:31 PM To: PHENIX user mailing list Subject: Re: [phenixbb] input initial TLS parameters
Hi Mark,
if I understand Pavel correctly I think he is saying that TLSmd can provide both group definitions and initial values for the TLS parameters. In phenix.refine the only information that is required is the group definitions - the values for the TLS parameters will be refined using a procedure that discards any of the input values anyway. This is one of the things that has been done to make the procedure more stable. The TLS parameter values from TLSmd are, in many cases, probably good estimates for the true parameters, but they would need to be refined anyway.
Cheers, Paul
Mayer, Mark (NIH/NICHD) [E] wrote:
Hi Pavel,
I thought one of the main advantages for using the TLSmd server was that it provided the crystallographer with suggestions for the TLS staring groups (as well as the TLS values for these groups) avoiding the need to make somewhat arbitrary choices about the TLS group boundaries.
If phenix then refines the TLS values for the groups picked with help pf the TLSmd server analysis which is this less good that starting TLS refinement in phenix without input from the MD server?
-----Original Message----- From: Pavel Afonine [mailto:[email protected]] Sent: Sun 2/24/2008 12:44 PM To: PHENIX user mailing list Subject: Re: [phenixbb] input initial TLS parameters
Hi Jorge,
I tried to find a way to input initial TLS parameters for the groups into phenix.
There is absolutely no need to give phenix.refine a start input values for TLS groups: phenix.refine determines them automatically. All you need to provide are the selections for TLS groups.
I know many times this is not advisable, but I wanted to test what comes out from TLSmd server.
This is not advisable, indeed (and not possible to do as well). phenix.refine must do a better job in finding TLS parameters than TLSmd server simply because phenix.refine uses the experimental data + very sophisticated and robust refinement protocol, while the TLSmd server relies on the B-factors in input PDB file (as far as I know, correct me if it's not true).
Pavel.
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------------------------------------------------------------------------
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-- Paul Adams Deputy Division Director, Physical Biosciences Division, LBL Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology
Building 64, Room 248 Tel: 510-486-4225, Fax: 510-486-5909 http://cci.lbl.gov/paul
Lawrence Berkeley Laboratory 1 Cyclotron Road, BLDG 64R0121 Berkeley, CA 94720, USA.
------------------------------------------------------------------------
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The recently-rolled out version of the TLSMD server not only produces a .tlsin file for refmac, but also a .phenix file. This file contains only TLS groups info, and nothing else. Here is an example. refinement.refine { adp { tls="(chain A and resid 21:28)" tls="(chain A and resid 29:45)" tls="(chain A and resid 46:65)" tls="(chain A and resid 66:105)" tls="(chain A and resid 106:128)" } } So, users of phenix.refine can use this file, and rely on phenix for TLS values... Engin Pavel Afonine wrote:
The only information that is vital for phenix.refine are the selections for TLS groups, for example:
TLS grop #1: "chain A and resseq 1-200" TLS grop #2: "chain B and resseq 34-500" etc... This information is obtained from TLSmd server. Sometimes though it is very easy just to have a look at your model to say what your TLS groups are.
The actual values of TLS matrices that TLSmd is producing as well are useless for phenix.refine simply because it has its own extremely sophisticated algorithm for finding these values. And this algorithm is much more powerful since it uses the experimental data. As an illustration, I re-refined 350 TLS containing structures from PDB using phenix.refine and I never observed any kind of refinement instability.
Pavel.
This was my understanding, so TLSmd is still very useful for assigning the initial groups, which seems better than picking by eye. Its interesting to know than phenix then generates its own set of starting parameters Refmac uses the TLSmd parameter values as the input for further refinement, and in my experience is sometimes unstable.
-----Original Message----- From: Paul Adams [mailto:[email protected]] Sent: Sun 2/24/2008 3:31 PM To: PHENIX user mailing list Subject: Re: [phenixbb] input initial TLS parameters
Hi Mark,
if I understand Pavel correctly I think he is saying that TLSmd can provide both group definitions and initial values for the TLS parameters. In phenix.refine the only information that is required is the group definitions - the values for the TLS parameters will be refined using a procedure that discards any of the input values anyway. This is one of the things that has been done to make the procedure more stable. The TLS parameter values from TLSmd are, in many cases, probably good estimates for the true parameters, but they would need to be refined anyway.
Cheers, Paul
Mayer, Mark (NIH/NICHD) [E] wrote:
Hi Pavel,
I thought one of the main advantages for using the TLSmd server was that it provided the crystallographer with suggestions for the TLS staring groups (as well as the TLS values for these groups) avoiding the need to make somewhat arbitrary choices about the TLS group boundaries.
If phenix then refines the TLS values for the groups picked with help pf the TLSmd server analysis which is this less good that starting TLS refinement in phenix without input from the MD server?
-----Original Message----- From: Pavel Afonine [mailto:[email protected]] Sent: Sun 2/24/2008 12:44 PM To: PHENIX user mailing list Subject: Re: [phenixbb] input initial TLS parameters
Hi Jorge,
I tried to find a way to input initial TLS parameters for the groups into phenix.
There is absolutely no need to give phenix.refine a start input values for TLS groups: phenix.refine determines them automatically. All you need to provide are the selections for TLS groups.
I know many times this is not advisable, but I wanted to test what comes out from TLSmd server.
This is not advisable, indeed (and not possible to do as well). phenix.refine must do a better job in finding TLS parameters than TLSmd server simply because phenix.refine uses the experimental data + very sophisticated and robust refinement protocol, while the TLSmd server relies on the B-factors in input PDB file (as far as I know, correct me if it's not true).
Pavel.
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
------------------------------------------------------------------------
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
-- Paul Adams Deputy Division Director, Physical Biosciences Division, LBL Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology
Building 64, Room 248 Tel: 510-486-4225, Fax: 510-486-5909 http://cci.lbl.gov/paul
Lawrence Berkeley Laboratory 1 Cyclotron Road, BLDG 64R0121 Berkeley, CA 94720, USA.
------------------------------------------------------------------------
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participants (5)
-
Engin Ozkan -
iulek -
Mayer, Mark (NIH/NICHD) [E] -
Paul Adams -
Pavel Afonine