I am using NCS restraints with TLS. It seems that the NCS B-factor restraints are applied to the overall B-factor, rather than just the non-TLS part. Is this correct? In my structure, the disorder varies quite a bit among equivalent molecules, and I don't get good results unless the b_factor_weight is about 1e-3 or less. I am experimenting with NCS restraints in CNS, where each pair of coordinates allows an LSQ fit of B-factor scale and offset to be excluded from the B restraints. It would probably work even better with TLS, which CNS does not have. I don't know if anyone has tried this, but I think that overall molecular B-factor differences are fairly common. Joe Krahn
Hi Joe,
I am using NCS restraints with TLS. It seems that the NCS B-factor restraints are applied to the overall B-factor, rather than just the non-TLS part. Is this correct?
the total B-factor is: Btotal = Btls + Bcrystal + Batoms. The restraints, including NCS, are applied to Batoms only. The positive definiteness constraint is applied to Btotal only, and not to individual component of the above sum. Pavel.
Hi Joe, Try doing NCS refinement in CNS and then when you have done considerable refinement use the final pdb file (when you think your model is complete) for TLS refinement in REFMAC. This has worked for me.You just need to define a TLS unit and use that as an input. Shya
I am using NCS restraints with TLS. It seems that the NCS B-factor restraints are applied to the overall B-factor, rather than just the non-TLS part. Is this correct?
In my structure, the disorder varies quite a bit among equivalent molecules, and I don't get good results unless the b_factor_weight is about 1e-3 or less.
I am experimenting with NCS restraints in CNS, where each pair of coordinates allows an LSQ fit of B-factor scale and offset to be excluded from the B restraints. It would probably work even better with TLS, which CNS does not have. I don't know if anyone has tried this, but I think that overall molecular B-factor differences are fairly common.
Joe Krahn _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Shya, as PHENIX developer I would be delighted to know what exactly did not work in phenix.refine so you decided to create some extra work for you and follow the detour you mentioned below. Thanks! Pavel. On 9/25/09 1:03 PM, [email protected] wrote:
Hi Joe, Try doing NCS refinement in CNS and then when you have done considerable refinement use the final pdb file (when you think your model is complete) for TLS refinement in REFMAC. This has worked for me.You just need to define a TLS unit and use that as an input. Shya
I am using NCS restraints with TLS. It seems that the NCS B-factor restraints are applied to the overall B-factor, rather than just the non-TLS part. Is this correct?
In my structure, the disorder varies quite a bit among equivalent molecules, and I don't get good results unless the b_factor_weight is about 1e-3 or less.
I am experimenting with NCS restraints in CNS, where each pair of coordinates allows an LSQ fit of B-factor scale and offset to be excluded from the B restraints. It would probably work even better with TLS, which CNS does not have. I don't know if anyone has tried this, but I think that overall molecular B-factor differences are fairly common.
Joe Krahn _______________________________________________ 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
I think the conclusion may be that you should first try to get good convergence with NCS, and then include TLS. The choice of CNS+REFMAC versus PHENIX is probably not important. Joe Pavel Afonine wrote:
Shya,
as PHENIX developer I would be delighted to know what exactly did not work in phenix.refine so you decided to create some extra work for you and follow the detour you mentioned below.
Thanks! Pavel.
On 9/25/09 1:03 PM, [email protected] wrote:
Hi Joe, Try doing NCS refinement in CNS and then when you have done considerable refinement use the final pdb file (when you think your model is complete) for TLS refinement in REFMAC. This has worked for me.You just need to define a TLS unit and use that as an input. Shya
I am using NCS restraints with TLS. It seems that the NCS B-factor restraints are applied to the overall B-factor, rather than just the non-TLS part. Is this correct?
In my structure, the disorder varies quite a bit among equivalent molecules, and I don't get good results unless the b_factor_weight is about 1e-3 or less.
I am experimenting with NCS restraints in CNS, where each pair of coordinates allows an LSQ fit of B-factor scale and offset to be excluded from the B restraints. It would probably work even better with TLS, which CNS does not have. I don't know if anyone has tried this, but I think that overall molecular B-factor differences are fairly common.
Joe Krahn
Hi Joe, Thanks for answering Pavel's question.I think there is no problem in using phenix if you want (whatever works for you). Shya
I think the conclusion may be that you should first try to get good convergence with NCS, and then include TLS. The choice of CNS+REFMAC versus PHENIX is probably not important.
Joe
Pavel Afonine wrote:
Shya,
as PHENIX developer I would be delighted to know what exactly did not work in phenix.refine so you decided to create some extra work for you and follow the detour you mentioned below.
Thanks! Pavel.
On 9/25/09 1:03 PM, [email protected] wrote:
Hi Joe, Try doing NCS refinement in CNS and then when you have done considerable refinement use the final pdb file (when you think your model is complete) for TLS refinement in REFMAC. This has worked for me.You just need to define a TLS unit and use that as an input. Shya
I am using NCS restraints with TLS. It seems that the NCS B-factor restraints are applied to the overall B-factor, rather than just the non-TLS part. Is this correct?
In my structure, the disorder varies quite a bit among equivalent molecules, and I don't get good results unless the b_factor_weight is about 1e-3 or less.
I am experimenting with NCS restraints in CNS, where each pair of coordinates allows an LSQ fit of B-factor scale and offset to be excluded from the B restraints. It would probably work even better with TLS, which CNS does not have. I don't know if anyone has tried this, but I think that overall molecular B-factor differences are fairly common.
Joe Krahn
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Hi all I have come across a new error while running the phenix.automr as follows, it works fine untill last week? Not sure what causes this error. :Output&, TNT::Vector<double>, double, TNT::Vector<double>, TNT::Vector<double>&, double, double, double, bool&, bool&)+0x1bf0) [0x2aaab34594b0] /home/pgm/phenix-installer-1.4-147/phenix-1.4-147/build/intel-linux-2.6-x86_64/lib/phaser_ext.so(phaser::Minimizer::ShiftScore(double, phaser::RefineBase&, TNT::Vector<double>&, TNT::Vector<double>&, TNT::Vector<double>&, phaser::Output*, bool)+0x45) [0x2aaab3457845] /home/pgm/phenix-installer-1.4-147/phenix-1.4-147/build/intel-linux-2.6-x86_64/lib/phaser_ext.so(phaser::RefineANO::targetFn()+0x1a4) [0x2aaab34d9054] /lib64/libc.so.6 [0x3e6c830070] Floating-point error (Python and libc call stacks above) This crash may be due to a problem in any imported Python module, including modules which are not part of the cctbx project. To disable the traps leading to this message, define these environment variables (e.g. assign the value 1): BOOST_ADAPTBX_FPE_DEFAULT BOOST_ADAPTBX_SIGNALS_DEFAULT This will NOT solve the problem, just mask it, but may allow you to proceed in case it is not critical. any help? Thanks venkat
Dear Venkat, Could you try this with the latest nightly build? We've just fixed a bug in the anisotropy correction in Phaser (which is the part where the error was triggered). The bug crept in sometime in August and was just fixed on Friday. If this doesn't fix the problem, then perhaps you could send me the data (offline) and I could try to reproduce the problem. Best wishes, Randy Read On 28 Sep 2009, at 18:04, r n wrote:
Hi all
I have come across a new error while running the phenix.automr as follows, it works fine untill last week? Not sure what causes this error.
:Output&, TNT::Vector<double>, double, TNT::Vector<double>, TNT::Vector<double>&, double, double, double, bool&, bool&)+0x1bf0) [0x2aaab34594b0] /home/pgm/phenix-installer-1.4-147/phenix-1.4-147/build/intel- linux-2.6-x86_64/lib/ phaser_ext.so(phaser::Minimizer::ShiftScore(double, phaser::RefineBase&, TNT::Vector<double>&, TNT::Vector<double>&, TNT::Vector<double>&, phaser::Output*, bool)+0x45) [0x2aaab3457845] /home/pgm/phenix-installer-1.4-147/phenix-1.4-147/build/intel- linux-2.6-x86_64/lib/phaser_ext.so(phaser::RefineANO::targetFn() +0x1a4) [0x2aaab34d9054] /lib64/libc.so.6 [0x3e6c830070] Floating-point error (Python and libc call stacks above) This crash may be due to a problem in any imported Python module, including modules which are not part of the cctbx project. To disable the traps leading to this message, define these environment variables (e.g. assign the value 1): BOOST_ADAPTBX_FPE_DEFAULT BOOST_ADAPTBX_SIGNALS_DEFAULT This will NOT solve the problem, just mask it, but may allow you to proceed in case it is not critical.
any help?
Thanks
venkat
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------ Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: [email protected] Cambridge CB2 0XY, U.K. www- structmed.cimr.cam.ac.uk
The build with the required fix isn't currently accessible. We hope it will be tomorrow. Ralf
participants (6)
-
Joe Krahn -
Pavel Afonine -
r n -
Ralf W. Grosse-Kunstleve -
Randy Read -
sbiswas2＠ncsu.edu