Re: [ccp4bb] TLS refinement in Refmac gets stuck

2009-02-24 Thread Graeme Winter
Hi Folks, If anyone wants to do this on an Intel mac you will need a fortran compiler, which is not installed by XCode. There is a compatible gfortran here: http://r.research.att.com/tools/ which in my experience works fine, though is completely incapable of producing static binaries. There are

Re: [ccp4bb] TLS refinement in Refmac gets stuck

2009-02-24 Thread Garib Murshudov
Child killing and/or wrong bus seems to be related with static compilation on Mac intel OS 10.5. Existence of this bug is the reason why the version with bug fixes was not announced. If you build from source code then this bug can be overcomed Download source files and copy them to ccp4 source

Re: [ccp4bb] TLS refinement in Refmac gets stuck

2009-02-24 Thread Eleanor Dodson
Yes - I found that irritating bug; it is a disaster for less experienced users.. It doesnt seem to happen with the linux installation.. Eleanor Anita Lewit-Bentley wrote: Hi Ian, A bug was reported with that version of Refmac, though I've no idea if that would cause your problem: you shou

Re: [ccp4bb] TLS refinement in Refmac gets stuck

2009-02-24 Thread Anita Lewit-Bentley
Hi Ian, A bug was reported with that version of Refmac, though I've no idea if that would cause your problem: you should upgrade to the latest version from the York website. Done - and here is what happens: 1) the latest CCP4 package (6.1.1) runs the same version of Refmac (5.5.0066) and

Re: [ccp4bb] TLS refinement in Refmac gets stuck

2009-02-23 Thread Ian Tickle
Hi Anita A bug was reported with that version of Refmac, though I've no idea if that would cause your problem: you should upgrade to the latest version from the York website. Cheers -- Ian > -Original Message- > From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk] On

[ccp4bb] TLS refinement in Refmac gets stuck

2009-02-23 Thread Anita Lewit-Bentley
Dear ccp4 folks, I am refining a structure in several crystal forms, with several molecules in the asymmetric unit. The structure is rather flexible, so I am using TLS refinement, having first submitted the coordinates to the TLSMD server (http://skuld.bmsc.washington.edu/~tlsmd/). The TL

Re: [ccp4bb] TLS refinement in REFMAC

2007-12-25 Thread Garib Murshudov
Dear Yogesh Could you please try the version from York www.ysbl.york.ac.uk/refmac/latest_refmac.html You need to take appropriate refmac 5.4 (it is current stable version) and dictionary. I remember that in older version there was a problem in one of RNA bases and it has now been corrected

[ccp4bb] TLS refinement in REFMAC

2007-12-24 Thread Yogesh Gupta PhD
Dear CCP4 users, I refined my final model (protein-RNA complex) using TLS refinement in Refmac but when i am validating the coordinates I am having an issue with Bond Distances and Bond Angles of some of the bases of RNA, these values for some of the bases are higher ( >6 times) then the standard