Thanks Tim - yes, that is what I have been doing subsequently also On Mar 18, 2014, at 7:10 PM, Tim Gruene <[email protected]> wrote: Thanks Tim - yes, that is what I have been doing subsequently. This seems to be different to Coot’s behavior in the past though, or am I misremembering?
I seem to recall that in the past, when merging two chains of the same name, the chains would always be renamed to avoid renumbering issues - the current behavior is better in some situations, for sure, but not in all situations, I think. Also coot seems to be sometimes creating “dummy molecules” for want of a better word when I copy molecules - additional molecules that are present in the display manager but do not seem to exist otherwise. Oliver. > 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 >
