Hi, I'll take the liberty of replying instead of Elad (my student) who probably won't be back on the net till next week.
The feature/problem he reported seems most likely as a difference between the linux and Windows version, unless there is also a difference between v 6.1.1 and 6.1.2 on that issue. Here is what we've done: 1) Elad sent a pdb file with Biso to the TLSMD server. This file included water molecules but we assumed those would be ignored (as has usually been the case, as far as I recall). With the tlsin from TSLMD and the pdb he sent, he ran TLS refinement in refmac, after which pdb with B-aniso for the protein and waters, but not for coafactors, was produced. He chopped the water with B-aniso and put water with Biso (from the previous cycle) , ran refmac with mixed iso/anison option and got back Baniso for the waters (unlike what's described in the refmac doc for this option. This was all done with the Windows version (ccp4 v6.1.2). 2) I repeated the same exercise (apart from re-sending coords. to TLSMD, that is I used the same tlsin file that was used under Windows) under linux (ccp4 v. 6.1.1) and got the pdb file with Biso, as it should be (and as I reccall refmac to function in all my previous runs). The refmac version in both cases is 5.5.102. So ??? Cheers, Boaz ----- Original Message ----- From: Martyn Winn <martyn.w...@stfc.ac.uk> Date: Thursday, August 27, 2009 19:04 Subject: Re: [ccp4bb] anisotropic temp for H2O To: CCP4BB@JISCMAIL.AC.UK > In the latest versions of refmac, it has a default selection of TLS > groups so that you don't need to create a TLSIN file. I believe this > default selection includes waters in the first hydration shell. You > should be able to override this with an explicit selection in TLSIN. > > Cheers > Martyn > > On Thu, 2009-08-27 at 09:37 -0700, Ethan Merritt wrote: > > On Thursday 27 August 2009, Elad Binshtien wrote: > > > Dear all, > > > I run refmac5 on TLS & restrained refinement mode. my pdb > input file contain anisotropic temp for the amino acid and > isotropic temp for the cofactors and water. The refinement > parameters is set on mixed isotropic/ anisotropic temp and in > TLS parameters the check box add TLS contribution is marked. > > > > But in your definition of TLS groups (the *.tls input file) > > do you list the water residues as belonging to one of the TLS > groups?> If so, don't do that. > > > > Ethan > > > > > > > In the pdb output the cofactor stay with isotropic temp BUT > the water get anisotropic temp. > > > How can i leave the water with the isotropic tepm > > > (i work on win version) > > > > > > thanks Elad > > > > > > > > > > > > Elad Binshtein > > > Ph.D student > > > Department of Life Science > > > Ben Gurion University of the Negev > > > Ph: 972-8-6461325 > > > > -- > *********************************************************************** > * * > * Dr. Martyn Winn * > * * > * STFC Daresbury Laboratory, Daresbury, Warrington, > WA4 4AD, U.K. * > * Tel: +44 1925 603455 E-mail: > martyn.w...@stfc.ac.uk * > * Fax: +44 1925 603825 Skype name: > martyn.winn * > * URL: http://www.ccp4.ac.uk/martyn/ * > *********************************************************************** > Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan
