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That would ease the compilation for a user. But the external libraries Coot uses still need to be fetched, compiled, installed ... and getting ready compiled binaries is just so much easier (especially if they are regularly updated whenever a patch becomes available or a new feature is implemented). Distributing static binaries is the way to go I think. Ok, OsX doesn't do this properly (as did SGI/Irix), but on Linux we're distributing a single binary for all our software for the last 8 years - and this single binary (compiled over the years on various Linux distributions we considered 'stable') has *never* to my knowledge failed to run on any Linux system. Cheers Clemens On Fri, Oct 27, 2006 at 06:12:26PM +0200, Mark Brooks wrote: > Or use Automake: > http://www.gnu.org/software/automake/ > > What are the reasons Coot doesn't use this type of build system? > Portability? > > Coot's myriad dependencies mean that compiling isn't an option for most > users. Automake (or a similar build system) could be very useful in this > regard. > > Mark > > On 27/10/06, Clemens Vonrhein <[EMAIL PROTECTED]> wrote: > > > >*** For details on how to be removed from this list visit the *** > >*** CCP4 home page http://www.ccp4.ac.uk *** > > > > > >The absolute easiest option would be if Paul could compile Coot as a > >static binary ... well, easiest for us users because it puts the > >burdon onto poor Paul ;-) > > > >It might be possible to get rid of most shared libraries, but I'm not > >sure it would work for 100%. But glibc should be doable: > > > > % g++ -static -static-libgcc > > > >does it for us. > > > >Cheers > > > >Clemens > > > >On Fri, Oct 27, 2006 at 05:14:47PM +0200, Tim Gruene wrote: > >> *** For details on how to be removed from this list visit the *** > >> *** CCP4 home page http://www.ccp4.ac.uk *** > >> > >> > >> glibc is a very basic library. I dare say, the easiest option would be > >to > >> update your system. The second easiest would be to compile coot > >yourself. > >> well, it is second because I do not see another option ;-) > >> > >> Tim > >> > >> -- > >> Tim Gruene > >> Institut fuer anorganische Chemie > >> Tammannstr. 4 > >> D-37077 Goettingen > >> > >> GPG Key ID = A46BEE1A > >> > >> > >> On Fri, 27 Oct 2006, D. Eric Dollins wrote: > >> > >> >*** For details on how to be removed from this list visit the *** > >> >*** CCP4 home page http://www.ccp4.ac.uk *** > >> > > >> > > >> >Paul, > >> >You're right about the version of coot I was using when getting the > >> >NCS problems. I was using 0.1.1. Now I'm onto the next problem. I > >> >went to download version 0.1.3. After installation, I get library > >> >errors. The errors look something like this: > >> > > >> >/usr/local/coot/Linux-bubbles-pre-release/bin/coot-real: > >> >/lib/i686/libpthread.so.0: version `GLIBC_2.3.2' not found (required > >> >by > >/usr/local/coot/Linux-bubbles-pre-release/bin/coot-real).........there > >> >were some more errors looking for /usr/lib/libGL.so.1. > >> > > >> >I am running an admittingly old version of Linux redhat 8.0. How can > >> >I get around this dependency issue? I looks through RPMfind.net and > >> >couldn't find any GLIBC_2.3.2 for redhat 8.0. Any idead how to get > >> >around those errors? > >> > > >> >Cheers, > >> >Eric > >> > > >> > > >> > > >> > > >> >On 10/27/06, Paul Emsley <[EMAIL PROTECTED]> wrote: > >> >>On Wed, 2006-10-25 at 16:45 -0400, D. Eric Dollins wrote: > >> >>> *** For details on how to be removed from this list visit the *** > >> >>> *** CCP4 home page http://www.ccp4.ac.uk *** > >> >>> > >> >>> > >> >>> Hello all, > >> >>> I wondered if anyone can help with a NCS problem in coot. I have a > >> >>> 3.2A structure with 5 homodimers (10 chains) in the ASU. Given the > >> >>> resolution, there are 10 chains for NCS. Obviously, I am > >disinterested > >> >>> in refining all of them. I've tried using NCS in coot, however, when > >I > >> >>> try to apply the edits from my master chain (which I changed from > >> >>> chain "A" to the chain with the best density- happens to be "G"), > >coot > >> >>> only applies changes to some of the chains. Not only that, but the > >> >>> chains which the changes are applied to also seems to be random. > >> >> > >> >>There indeed was an error in applying NCS edits to other chains. I > >> >>thought that I'd fixed that for 0.1.2. Which version are you running? > >> >> > >> >>> I've > >> >>> gone through this several times now and the changes have been > >applied > >> >>> to different chains each time. When I load in the model, coot does > >> >>> find NCS for all chains A-J. > >> >> > >> >>> I wonder if this might be a buffer issue given the ridiculous size > >of > >> >>> my ASU (>0.5 Megadalton)? > >> >> > >> >>That's not it, I'd guess. > >> >> > >> >>> I noticed also that coot can use a set of strict NCS matrices. Is > >> >>> this similar to CNS where you reduce your number of molecules, in my > >> >>> case, from 10 to 1. If so, how do you re-apply the matrices to > >> >>> re-constiture the full ASU for a run in refmac? > >> >> > >> >>There is no straightforward way in coot to do this. You can mess with > >> >>copy-molecule and applying an R/T op to each copy, then merge > >molecules > >> >>(I've not tried to do that). Using pdbset to generate the other > >> >>molecules? You'd need to then "concat and edit" the resulting pdb > >files > >> >>- bleugh. > >> >> > >> >>Paul. > >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > >> > > >> > > >> >-- > >> >D. Eric Dollins > >> >C266 LSRC, Box 3813 > >> >Duke University Medical Center > >> >Durham, NC 27710 > >> >(919)681-1668 > >> > > >> > > > >-- > > > >*************************************************************** > >* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com > >* > >* Global Phasing Ltd. > >* Sheraton House, Castle Park > >* Cambridge CB3 0AX, UK > >*-------------------------------------------------------------- > >* BUSTER Development Group (http://www.globalphasing.com) > >*************************************************************** > > > > > > -- > Mark BROOKS > Telephone: 0169157968 > Fax: 0169853715 > INSTITUT de BIOCHIMIE et de BIOPHYSIQUE MOLECULAIRE et CELLULAIRE > UMR8619 - Bât 430 - Université de Paris-Sud > 91405 ORSAY CEDEX -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) ***************************************************************
