Dear All, I am trying to refine using TLS parameter as in the attached file generated in ccp4. my protein contains a core part from where are inserted several domains. I am defining each of the insertions as a group and this is fine. The problem comes when I try to define the core protein (discontinuous residue ranges). As example, I want to define residues 1:230, 416:568, 629:794 in chain A of the protein; and in the same group I would like also to include 3 bases of RNA, bases 84-87 of chain B. I have seen several questions related to TLS definitions in the archive mailing list, including an answer from Anastasis Perrakis with files attached which I can not extract, but so far I have not find the solution. Could anybody help on that? thanks in advance, Andrés Palencia -- Andres Palencia, PhD Protein RNA Group EMBL Grenoble Outstation 6 rue Jules Horowitz BP181, 38042 Grenoble Cedex 9, France email: [email protected] phone: + 33 (0)476 20 7860(office)/ + 33 (0)476 20 7014(lab) fax: + 33 (0)476 20 7199 http://www.embl-grenoble.fr/
Hi Andres,
I am trying to refine using TLS parameter as in the attached file generated in ccp4.
which program you use to refine your model? If it is phenix.refine then the attached file is not suitable to define TLS groups for phenix.refine. For example, translation of these lines: TLS RANGE 'A 1.' 'A 230.' ALL RANGE 'A 416.' 'A 568.' ALL RANGE 'A 629.' 'A 794.' ALL RANGE 'A 899.' 'A 899.' ALL RANGE 'A 900.' 'A 900.' ALL RANGE 'B 84.' 'B 87.' ALL ORIGIN -26.886 1.710 -76.557 T 0.1151 0.0090 0.0533 0.0096 0.0154 0.0014 L 2.1545 1.4001 0.7879 1.1375 -0.4178 -0.5303 S -0.0027 -0.0004 -0.0810 0.0603 -0.0219 0.1132 -0.0538 0.0233 TLS RANGE 'B 1.' 'B 83.' ALL ORIGIN -58.568 8.877 -85.204 T 0.0929 0.0996 0.2885 -0.0113 -0.0037 0.0229 L 2.4389 2.2023 1.2365 0.2174 0.7759 -0.0156 S 0.2584 -0.1495 -0.0520 0.1045 0.5167 0.0232 0.0277 -0.3204 (...) into phenix.refine format would look like this (I guess): refinement { refine { adp { tls = (chain A and (resseq 1:230 or resseq 416:568)) or (chain B and resseq 84:87) tls = chain B and resseq 1:83 #... and so on for all other groups } } } Note, you don't need to provide initial values for TLS matrices and origin - they are determined as part of refinement. Also, you can use (or equivalent in the GUI) phenix.find_tls_groups model.pdb that will find TLS groups for you and output in ready-to-use in phenix.refine format. Pavel.
participants (2)
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Andres Palencia -
Pavel Afonine