[ccp4bb] Off topic: Selecting atoms within a given distance from a target atom
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
Re: [ccp4bb] Off topic: Selecting atoms within a given distance from a target atom
Hi, You can do this with MOLMOL. The official page from Wuthrich's group seems to be no longer supported. You can find it on the web from several other websites. For example: (http://pjf.net/science/molmol.html), ( http://blog.louic.nl/?p=397). 1) SelectAtom '#1:10@CA' (Structure 1, residue 10, atom CA') 2) SetRef (Sets atom as a reference) 3) SelectAtom 'd 5.0' (selects all atoms with distance more than 5.0 from that particular CA) 4) From the menus: remove all selected atoms. The remaining ones are all atoms with a distance under 5.0. 5) From the menus: write a pdb file of the remaining atoms. Hope this helps, Yannis Dr A.I. Karsisiotis Research Associate Room Y028 School of Biomedical Sciences University of Ulster Coleraine campus Cromore Road Coleraine Co. Londonderry BT52 1SA +44(0)28701 24336 ai.karsisio...@ulster.ac.uk On 17 November 2012 20:04, 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
Re: [ccp4bb] Off topic: Selecting atoms within a given distance from a target atom
Hi Rex, 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. This is simple to do in PyMOL. After loading your structure just use the mouse to select your target atom. After that, on the PyMOL command line type, select all within 5 of (sele) That will quickly identify those atoms within 5 Angstroms of your selection. For more help check out the PyMOLWiki (http://pymolwiki.org) especially selections (http://www.pymolwiki.org/index.php/Selection_Algebra). Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120
Re: [ccp4bb] Off topic: Selecting atoms within a given distance from a target atom
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.comwrote: 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
[ccp4bb] 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 ScottWilliam G. ScottProfessorDepartment of Chemistry and Biochemistryand The Center for the Molecular Biology of RNA228 Sinsheimer LaboratoriesUniversity of California at Santa CruzSanta Cruz, California 95064USA
