I had exactly the same thing happen this year to a 2008 macbook pro. Computer still worked while attached to power but unsurprisingly the battery did not work after that.
On Nov 18, 2012, at 7:00 PM, CCP4BB automatic digest system <lists...@jiscmail.ac.uk> wrote: > There are 8 messages totaling 1223 lines in this issue. > > Topics of the day: > > 1. OT: Has anyone experienced problems with Apple laptop battery expansion? > (3) > 2. Off topic: Selecting atoms within a given distance from a target atom (5) > > ---------------------------------------------------------------------- > > Date: Sat, 17 Nov 2012 16:28:07 -0800 > From: "William G. Scott" <wgsc...@ucsc.edu> > Subject: OT: Has anyone experienced problems with Apple laptop battery > expansion? > > Hi folks: > > I'm trying to get a sense for how frequently this sort of thing occurs: > > > > That was a macbook air that served me well for four years, but then > self-destructed. (I took it to the Apple store. They generously offered to > repair it for $800 or to sell me a new one, and suggested this was normal if > you leave the power cord attached after the battery charges, even while > giving a lecture or seminar.) It strikes me as a bit dangerous. > > --Bill Scott > > > > > > William G. Scott > Professor > Department of Chemistry and Biochemistry > and The Center for the Molecular Biology of RNA > 228 Sinsheimer Laboratories > University of California at Santa Cruz > Santa Cruz, California 95064 > USA > > > > ------------------------------ > > Date: Sun, 18 Nov 2012 08:01:37 +0000 > From: Laura Spagnolo <laura.spagn...@ed.ac.uk> > Subject: Re: OT: Has anyone experienced problems with Apple laptop battery > expansion? > > Dear Bill, > > Yes, the same happened a year ago or so to me, with a 17 inch MacBookPro > bought in 2008. > The Apple store in Glasgow replaced it for free within roughly one week, and > the laptop works well. > > I agree that this is really dangerous, I wonder if it could also cause the > leak of material from inside (mine exposed some really ugly brown stuff). > Laura > > > On Nov 18, 2012, at 12:28 AM, William G. Scott wrote: > >> Hi folks: >> >> I'm trying to get a sense for how frequently this sort of thing occurs: >> >> <CIMG4451.jpeg> >> >> That was a macbook air that served me well for four years, but then >> self-destructed. (I took it to the Apple store. They generously offered to >> repair it for $800 or to sell me a new one, and suggested this was normal if >> you leave the power cord attached after the battery charges, even while >> giving a lecture or seminar.) It strikes me as a bit dangerous. >> >> --Bill Scott >> >> >> >> >> >> William G. Scott >> Professor >> Department of Chemistry and Biochemistry >> and The Center for the Molecular Biology of RNA >> 228 Sinsheimer Laboratories >> University of California at Santa Cruz >> Santa Cruz, California 95064 >> USA >> >> >> > > Dr Laura Spagnolo > Institute of Structural Molecular Biology > University of Edinburgh > Room 506, Darwin Building > King's Buildings Campus > Edinburgh EH9 3JR > United Kingdom > T: +44 (0)131 650 7066 > F: +44 (0)131 650 8650 > http://www.biology.ed.ac.uk/research/institutes/structure/homepage.php?id=lspagnolo > laura.spagn...@ed.ac.uk > > > > > > > > > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > ------------------------------ > > Date: Sun, 18 Nov 2012 16:52:08 +0100 > From: "Bernhard C. Lohkamp" <bernh...@chem.gla.ac.uk> > Subject: Re: Off topic: Selecting atoms within a given distance from a target > atom > > In Coot: > > Centre on the atom/place of interest. > > Extensions->Modelling->New Molecule by Sphere > > then select the molecule and sphere radius. > > B > >> I would like to specify a target atom in a pdb file and then isolate all >> atoms within a given distance of the target. The selected atoms are then to >> be placed in a new pdb file. >> Any suggestions please. >> >> Rex Palmer >> http://www.bbk.ac.uk/biology/our-staff/emeritus-staff >> http://rexpalmer2010.homestead.com >> >> >> ----- >> No virus found in this message. >> Checked by AVG - www.avg.com >> Version: 2013.0.2793 / Virus Database: 2629/5896 - Release Date: 11/15/12 >> > > ------------------------------ > > Date: Sun, 18 Nov 2012 12:14:43 -0500 > From: "Bosch, Juergen" <jubo...@jhsph.edu> > Subject: Re: Off topic: Selecting atoms within a given distance from a target > atom > > Hi Pavel, > > does this also work for symmetry related atoms ? > > Jürgen > > ...................... > Jürgen Bosch > Johns Hopkins Bloomberg School of Public Health > Department of Biochemistry & Molecular Biology > Johns Hopkins Malaria Research Institute > 615 North Wolfe Street, W8708 > Baltimore, MD 21205 > Phone: +1-410-614-4742 > Lab: +1-410-614-4894 > Fax: +1-410-955-3655 > http://lupo.jhsph.edu > > On Nov 17, 2012, at 14:26, "Pavel Afonine" > <pafon...@gmail.com<mailto:pafon...@gmail.com>> wrote: > > Hi Rex, > > as easy as: > > phenix.pdb_atom_selection model.pdb "within(3, chain L and resseq 9 and name > CA)" --write-pdb-file=cut.pdb > > which in the above example selects all atoms within 3 A from CA atom in chain > A of residue number 9, and writes them into cut.pdb file. > > Pavel > > On Sat, Nov 17, 2012 at 12:04 PM, Rex Palmer > <rex.pal...@btinternet.com<mailto:rex.pal...@btinternet.com>> wrote: > I would like to specify a target atom in a pdb file and then isolate all > atoms within a given distance of the target. The selected atoms are then to > be placed in a new pdb file. > Any suggestions please. > > Rex Palmer > http://www.bbk.ac.uk/biology/our-staff/emeritus-staff > http://rexpalmer2010.homestead.com > > ------------------------------ > > Date: Sun, 18 Nov 2012 10:27:06 -0700 > From: James Stroud <xtald...@gmail.com> > Subject: Re: Off topic: Selecting atoms within a given distance from a target > atom > > In O, the command is called symm_sphere. > http://xray.bmc.uu.se/alwyn/A-Z_of_O/everything_s.html#anchor536668 > > James > > > On Nov 18, 2012, at 10:14 AM, Bosch, Juergen wrote: > >> Hi Pavel, >> >> does this also work for symmetry related atoms ? >> >> Jürgen >> >> ...................... >> Jürgen Bosch >> Johns Hopkins Bloomberg School of Public Health >> Department of Biochemistry & Molecular Biology >> Johns Hopkins Malaria Research Institute >> 615 North Wolfe Street, W8708 >> Baltimore, MD 21205 >> Phone: +1-410-614-4742 >> Lab: +1-410-614-4894 >> Fax: +1-410-955-3655 >> http://lupo.jhsph.edu >> >> On Nov 17, 2012, at 14:26, "Pavel Afonine" <pafon...@gmail.com> wrote: >> >>> Hi Rex, >>> >>> as easy as: >>> >>> phenix.pdb_atom_selection model.pdb "within(3, chain L and resseq 9 and >>> name CA)" --write-pdb-file=cut.pdb >>> >>> which in the above example selects all atoms within 3 A from CA atom in >>> chain A of residue number 9, and writes them into cut.pdb file. >>> >>> Pavel >>> >>> On Sat, Nov 17, 2012 at 12:04 PM, Rex Palmer <rex.pal...@btinternet.com> >>> wrote: >>> I would like to specify a target atom in a pdb file and then isolate all >>> atoms within a given distance of the target. The selected atoms are then to >>> be placed in a new pdb file. >>> Any suggestions please. >>> >>> Rex Palmer >>> http://www.bbk.ac.uk/biology/our-staff/emeritus-staff >>> http://rexpalmer2010.homestead.com >>> > > ------------------------------ > > Date: Sun, 18 Nov 2012 12:30:45 -0500 > From: "Bosch, Juergen" <jubo...@jhsph.edu> > Subject: Re: OT: Has anyone experienced problems with Apple laptop battery > expansion? > > Bill I think that's crap. > I had issues on a 2005 MacBook Pro with inflating battery and it was replaced > (after about 6 months). There were troubles with those batteries and > impurities but mine still had apple care at that time and the batteries were > exchangeable. > I have not heard of the build in batteries to have problems but yours sure > did. Send Tim Cook an email with the picture. This should not have happened > and also keeping the power cord on leading to this problem should not have > happened. For what did they introduce the trickling charging ? If you can't > leave the coord plugged in how many nice wooden US households gave caught > fire due to Apple products ? > > Jürgen > ...................... > Jürgen Bosch > Johns Hopkins Bloomberg School of Public Health > Department of Biochemistry & Molecular Biology > Johns Hopkins Malaria Research Institute > 615 North Wolfe Street, W8708 > Baltimore, MD 21205 > Phone: +1-410-614-4742 > Lab: +1-410-614-4894 > Fax: +1-410-955-3655 > http://lupo.jhsph.edu > > On Nov 17, 2012, at 16:28, "William G. Scott" <wgsc...@ucsc.edu> wrote: > >> Hi folks: >> >> I'm trying to get a sense for how frequently this sort of thing occurs: >> >> <CIMG4451.jpeg> >> >> That was a macbook air that served me well for four years, but then >> self-destructed. (I took it to the Apple store. They generously offered to >> repair it for $800 or to sell me a new one, and suggested this was normal if >> you leave the power cord attached after the battery charges, even while >> giving a lecture or seminar.) It strikes me as a bit dangerous. >> >> --Bill Scott >> >> >> >> >> >> William G. Scott >> Professor >> Department of Chemistry and Biochemistry >> and The Center for the Molecular Biology of RNA >> 228 Sinsheimer Laboratories >> University of California at Santa Cruz >> Santa Cruz, California 95064 >> USA >> >> >> > > ------------------------------ > > Date: Sun, 18 Nov 2012 18:57:31 +0100 > From: "Bernhard C. Lohkamp" <bernh...@chem.gla.ac.uk> > Subject: Re: Off topic: Selecting atoms within a given distance from a target > atom > > Of course (sort of): > > Extensions->Maps->Export Local Map Fragment > > B > >> This is nice. Can it do the same for the map? >> Thanks >> Jim Brannigan >> >> On 18 November 2012 15:52, Bernhard C. Lohkamp >> <bernh...@chem.gla.ac.uk>wrote: >> >>> In Coot: >>> >>> Centre on the atom/place of interest. >>> >>> Extensions->Modelling->New Molecule by Sphere >>> >>> then select the molecule and sphere radius. >>> >>> B >>> >>> I would like to specify a target atom in a pdb file and then isolate all >>>> atoms within a given distance of the target. The selected atoms are then to >>>> be placed in a new pdb file. >>>> Any suggestions please. >>>> >>>> Rex Palmer >>>> http://www.bbk.ac.uk/biology/**our-staff/emeritus-staff<http://www.bbk.ac.uk/biology/our-staff/emeritus-staff> >>>> http://rexpalmer2010.**homestead.com <http://rexpalmer2010.homestead.com> >>>> >>>> >>>> ----- >>>> No virus found in this message. >>>> Checked by AVG - www.avg.com >>>> Version: 2013.0.2793 / Virus Database: 2629/5896 - Release Date: 11/15/12 >>>> >>>> >> >> >> >> ----- >> No virus found in this message. >> Checked by AVG - www.avg.com >> Version: 2013.0.2793 / Virus Database: 2629/5896 - Release Date: 11/15/12 >> > > ------------------------------ > > Date: Sun, 18 Nov 2012 14:44:46 -0500 > From: Ed Pozharski <epozh...@umaryland.edu> > Subject: Re: Off topic: Selecting atoms within a given distance from a target > atom > > On 11/17/2012 03:04 PM, Rex Palmer wrote: >> I would like to specify a target atom in a pdb file and then isolate >> all atoms within a given distance of the target. The selected atoms >> are then to be placed in a new pdb file. > > AWKward BASHing: > > #! /bin/bash > read x y z <<<$(awk '{if(substr($0,1,4)=="ATOM" && > int(substr($0,7,5))==75) print > substr($0,31,8),substr($0,39,8),substr($0,47,8);}' model.pdb) > awk -v x=$x -v y=$y -v z=$z '{if(substr($0,1,4)=="ATOM" && > sqrt((substr($0,31,8)-x)^2+(substr($0,39,8)-y)^2+(substr($0,47,8)-z)^2)<4.0) > print;}' model.pdb > out.pdb > > You did not specify your atom selection criteria, so I simply use the > atom serial number. To make it more flexible so that it takes model pdb > file name, atom serial number for selection, distance cutoff and output > file name, this should work > > #! /bin/bash > read x y z <<<$(awk -v num=$2 '{if(substr($0,1,4)=="ATOM" && > int(substr($0,7,5))==num) print > substr($0,31,8),substr($0,39,8),substr($0,47,8);}' $1) > awk -v cutoff=$3 -v x=$x -v y=$y -v z=$z '{if(substr($0,1,4)=="ATOM" && > sqrt((substr($0,31,8)-x)^2+(substr($0,39,8)-y)^2+(substr($0,47,8)-z)^2)<cutoff) > > print;}' $1 > $4 > > It takes about 27ms on a ~3000 atom model (core i7 2600K@3.4GHz, running > precise pangolin). It's not hard to modify the atom selection, if > necessary. I wonder if this is, surprisingly, much faster than all > other options that rely on external programs. For example, it takes > over 120ms just to open and close pymol in batch mode, over 2 seconds > for coot. phenix.pdb_atom_selection takes about 2.5s. > > Cheers, > > Ed. > > -- > Oh, suddenly throwing a giraffe into a volcano to make water is crazy? > Julian, King of Lemurs > > ------------------------------ > > End of CCP4BB Digest - 17 Nov 2012 to 18 Nov 2012 (#2012-327) > *************************************************************
