This definitely seems like a bug… even when I change the chain IDs beforehand, coot is still changing all the chain IDs back to A and renumbering when I merge the molecules.
I can get around that by doing PDB manipulations elsewhere, but it used to work very well in coot. Oliver. On Mar 18, 2014, at 7:27 PM, Oliver Clarke <[email protected]> wrote: > 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 >> >
