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) > **********************************************************
