Dear Oliver, there is a simple work-around: first merge, then renumber. I learned this the hard way, too, and learned it quickly ;-)
Cheers, Tim On 03/18/2014 12:30 AM, Oliver Clarke wrote: > Hi all, > > Coot seems to be renumbering residues when I merge chains, even when the > numbering of the chains does not overlap. This seems like a bug? > > It only seems to happen when I am merging helices placed with coot (which > incidentally seem to lack chain IDs by default now). It is a little dismaying > to find after having carefully renumbered many individual helices that all > the numbers have changed after merging the helices together in a single > molecule. > > I am running Coot 0.8-pre r4966 on Ubuntu 13.10. > > Oliver. > On Mar 14, 2014, at 8:00 PM, COOT automatic digest system > <[email protected]> wrote: > >> There are 7 messages totaling 427 lines in this issue. >> >> Topics of the day: >> >> 1. Per chain ramachandran? (2) >> 2. Delete chain >> 3. unable to launch coot (4) >> >> ---------------------------------------------------------------------- >> >> Date: Thu, 13 Mar 2014 22:59:49 -0400 >> From: Oliver Clarke <[email protected]> >> Subject: Per chain ramachandran? >> >> 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. >> >> ------------------------------ >> >> Date: Fri, 14 Mar 2014 04:00:50 +0000 >> From: Oliver Clarke <[email protected]> >> Subject: Re: Delete chain >> >> I realised the script I posted previously to delete a chain doesn't take >> account of insertion codes etc. >> >> The attached script hopefully fixes that and adds a couple of other widgets >> that I find useful into a "Custom" menu (when placed in the >> ~/.coot-preferences directory). >> >> Oliver. >> >> ------------------------------ >> >> Date: Fri, 14 Mar 2014 09:21:31 +0000 >> From: Andreas Förster <[email protected]> >> Subject: Re: 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 >> >> ------------------------------ >> >> Date: Fri, 14 Mar 2014 17:23:42 +0000 >> From: Ignacio Mir Sanchis <[email protected]> >> Subject: 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 "$@" >> >> Can anyone tell me what I'm doing wrong? >> Thank you so much in advance. >> >> Nacho >> >> ------------------------------ >> >> Date: Fri, 14 Mar 2014 13:47:17 -0400 >> From: Scott Horowitz <[email protected]> >> Subject: Re: unable to launch coot >> >> On that note, I actually recently assigned 60 students to do an assignment >> for class using Coot to solve the structure of a protein using maps >> downloaded from EDS. And almost every student who had mavericks on their >> mac had major issues getting it to work. Older versions of OS X were fine. >> >> Scott >> >> PS The students loved the assignment- I highly recommend trying it >> >> >> On Fri, Mar 14, 2014 at 1:23 PM, Ignacio Mir Sanchis < >> [email protected]> wrote: >> >>> Dear cooters, >>> I installed fink and packages (in OS X 10.9.2) following directions from >>> Scott lab web page ( >>> http://scottlab.ucsc.edu/~wgscott/xtal/wiki/index.php/Quick_Start#Unix_Shell_Environment_Set_Up >>> ) >>> When I try to launch coot this message appears: >>> >>> dyld: Symbol not found: __ZNK5RDKit4Dict5toanyISsEEN5boost3anyET_ >>> Referenced from: /sw/lib/libcoot-lidia-core.0.dylib >>> Expected in: /sw/lib/rdkit/libRDGeneral.1.dylib >>> in /sw/lib/libcoot-lidia-core.0.dylib >>> /sw/bin/coot: line 9: 9411 Trace/BPT trap: 5 /sw/bin/coot-real "$@" >>> >>> 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 >> >> ------------------------------ >> >> Date: Fri, 14 Mar 2014 11:11:28 -0700 >> From: "William G. Scott" <[email protected]> >> Subject: Re: 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 <[email protected]> >> 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 "$@" >>> >>> Can anyone tell me what I'm doing wrong? >>> Thank you so much in advance. >>> >>> Nacho >> >> William G. Scott >> Professor >> Department of Chemistry and Biochemistry >> and The Center for the Molecular Biology of RNA >> University of California at Santa Cruz >> Santa Cruz, California 95064 >> USA >> http://scottlab.ucsc.edu/scottlab/ >> >> ------------------------------ >> >> Date: Fri, 14 Mar 2014 11:40:42 -0700 >> From: "William G. Scott" <[email protected]> >> Subject: Re: unable to launch coot >> >> I am updating the “stable” coot in fink to rev. 4965 which should work fine >> with the latest rkdit. >> >> >> On Mar 14, 2014, at 11:11 AM, William G. Scott <[email protected]> wrote: >> >>> Dear Nacho: >>> >>> The “coot-pre” package should work. In updating that, I think I probably >>> broke the “stable” coot package. >>> >>> Also, the stand-alone ones all work (just tested). >>> >>> http://scottlab.ucsc.edu/~wgscott/xtal/wiki/index.php/Stand-Alone_Coot >>> >>> Sorry, >>> >>> Bill >>> >>> >>> >>> On Mar 14, 2014, at 10:23 AM, Ignacio Mir Sanchis >>> <[email protected]> wrote: >>> >>>> Dear cooters, >>>> I installed fink and packages (in OS X 10.9.2) following directions from >>>> Scott lab web page >>>> (http://scottlab.ucsc.edu/~wgscott/xtal/wiki/index.php/Quick_Start#Unix_Shell_Environment_Set_Up) >>>> When I try to launch coot this message appears: >>>> >>>> dyld: Symbol not found: __ZNK5RDKit4Dict5toanyISsEEN5boost3anyET_ >>>> Referenced from: /sw/lib/libcoot-lidia-core.0.dylib >>>> Expected in: /sw/lib/rdkit/libRDGeneral.1.dylib >>>> in /sw/lib/libcoot-lidia-core.0.dylib >>>> /sw/bin/coot: line 9: 9411 Trace/BPT trap: 5 /sw/bin/coot-real "$@" >>>> >>>> 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/ >>> >>> >>> >> >> ------------------------------ >> >> End of COOT Digest - 13 Mar 2014 to 14 Mar 2014 (#2014-40) >> ********************************************************** > -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
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