Re: [COOT] unable to launch coot
I am updating the “stable” coot in fink to rev. 4965 which should work fine with the latest rkdit. On Mar 14, 2014, at 11:11 AM, William G. Scott wrote: > Dear Nacho: > > The “coot-pre” package should work. In updating that, I think I probably > broke the “stable” coot package. > > Also, the stand-alone ones all work (just tested). > > http://scottlab.ucsc.edu/~wgscott/xtal/wiki/index.php/Stand-Alone_Coot > > Sorry, > > Bill > > > > On Mar 14, 2014, at 10:23 AM, Ignacio Mir Sanchis > wrote: > >> Dear cooters, >> I installed fink and packages (in OS X 10.9.2) following directions from >> Scott lab web page >> (http://scottlab.ucsc.edu/~wgscott/xtal/wiki/index.php/Quick_Start#Unix_Shell_Environment_Set_Up) >> When I try to launch coot this message appears: >> >> dyld: Symbol not found: __ZNK5RDKit4Dict5toanyISsEEN5boost3anyET_ >> Referenced from: /sw/lib/libcoot-lidia-core.0.dylib >> Expected in: /sw/lib/rdkit/libRDGeneral.1.dylib >> in /sw/lib/libcoot-lidia-core.0.dylib >> /sw/bin/coot: line 9: 9411 Trace/BPT trap: 5 /sw/bin/coot-real "$@" >> >> Can anyone tell me what I'm doing wrong? >> Thank you so much in advance. >> >> Nacho > > William G. Scott > Professor > Department of Chemistry and Biochemistry > and The Center for the Molecular Biology of RNA > University of California at Santa Cruz > Santa Cruz, California 95064 > USA > http://scottlab.ucsc.edu/scottlab/ > > >
Re: [COOT] unable to launch coot
Dear Nacho: The “coot-pre” package should work. In updating that, I think I probably broke the “stable” coot package. Also, the stand-alone ones all work (just tested). http://scottlab.ucsc.edu/~wgscott/xtal/wiki/index.php/Stand-Alone_Coot Sorry, Bill On Mar 14, 2014, at 10:23 AM, Ignacio Mir Sanchis wrote: > Dear cooters, > I installed fink and packages (in OS X 10.9.2) following directions from > Scott lab web page > (http://scottlab.ucsc.edu/~wgscott/xtal/wiki/index.php/Quick_Start#Unix_Shell_Environment_Set_Up) > When I try to launch coot this message appears: > > dyld: Symbol not found: __ZNK5RDKit4Dict5toanyISsEEN5boost3anyET_ > Referenced from: /sw/lib/libcoot-lidia-core.0.dylib > Expected in: /sw/lib/rdkit/libRDGeneral.1.dylib > in /sw/lib/libcoot-lidia-core.0.dylib > /sw/bin/coot: line 9: 9411 Trace/BPT trap: 5 /sw/bin/coot-real "$@" > > Can anyone tell me what I'm doing wrong? > Thank you so much in advance. > > Nacho William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA University of California at Santa Cruz Santa Cruz, California 95064 USA http://scottlab.ucsc.edu/scottlab/
Re: [COOT] unable to launch coot
On that note, I actually recently assigned 60 students to do an assignment for class using Coot to solve the structure of a protein using maps downloaded from EDS. And almost every student who had mavericks on their mac had major issues getting it to work. Older versions of OS X were fine. Scott PS The students loved the assignment- I highly recommend trying it On Fri, Mar 14, 2014 at 1:23 PM, Ignacio Mir Sanchis < imirsanc...@uchicago.edu> wrote: > Dear cooters, > I installed fink and packages (in OS X 10.9.2) following directions from > Scott lab web page ( > http://scottlab.ucsc.edu/~wgscott/xtal/wiki/index.php/Quick_Start#Unix_Shell_Environment_Set_Up > ) > When I try to launch coot this message appears: > > dyld: Symbol not found: __ZNK5RDKit4Dict5toanyISsEEN5boost3anyET_ > Referenced from: /sw/lib/libcoot-lidia-core.0.dylib > Expected in: /sw/lib/rdkit/libRDGeneral.1.dylib > in /sw/lib/libcoot-lidia-core.0.dylib > /sw/bin/coot: line 9: 9411 Trace/BPT trap: 5 /sw/bin/coot-real "$@" > > Can anyone tell me what I'm doing wrong? > Thank you so much in advance. > > Nacho -- Scott Horowitz, Ph.D. Research Associate Howard Hughes Medical Institute University of Michigan Department of Molecular, Cellular, and Developmental Biology Bardwell lab 830 N. University Ave, Room 4007 Ann Arbor, MI 48109 phone: 734-647-6683 fax: 734-615-4226
[COOT] unable to launch coot
Dear cooters, I installed fink and packages (in OS X 10.9.2) following directions from Scott lab web page (http://scottlab.ucsc.edu/~wgscott/xtal/wiki/index.php/Quick_Start#Unix_Shell_Environment_Set_Up) When I try to launch coot this message appears: dyld: Symbol not found: __ZNK5RDKit4Dict5toanyISsEEN5boost3anyET_ Referenced from: /sw/lib/libcoot-lidia-core.0.dylib Expected in: /sw/lib/rdkit/libRDGeneral.1.dylib in /sw/lib/libcoot-lidia-core.0.dylib /sw/bin/coot: line 9: 9411 Trace/BPT trap: 5 /sw/bin/coot-real "$@" Can anyone tell me what I'm doing wrong? Thank you so much in advance. Nacho
Re: [COOT] Per chain ramachandran?
I second that. Andreas On 14/03/2014 2:59, Oliver Clarke wrote: Hi all, is there anyway to access/modify the Ramachandran plot display via a python or scheme function? I would like to display a Ramachandran plot calculated just for the currently selected protein chain. do_ramachandran() only seems to take a molecule number, not chain ID. In cases where there many chains in the asymmetric unit, I think this would be useful while building. Cheers, Oliver. -- Andreas Förster Crystallization and X-ray Facility Manager Centre for Structural Biology Imperial College London
