clearly shouldn’t write e-mails before having my morning coffee. Those % symbols should have been pounds, I was aiming to make comments
As an example: fetch 1acb, prot, async=0 stored.y=[] iterate_state 1, prot, stored.y.append(y) alter prot, b=stored.y.pop(0) spectrum b On Nov 18, 2015, at 9:12 AM, Smith Liu <smith_liu...@163.com> wrote: Dear David, I am unfamiliar with the pymol scripts so I do not understands where your scripts end at each line. Can we write this way, stored.y=[] iterate_state 1, prot, stored.y.append(y) alter prot, b=stored.y.pop(0) which means those from % in your scripts will be not used in each line for pymol reading? Can you introduce a website to introduce the pymol scripts? For stored.y=， following y= is it the file name of file stores y for each coordinates? Can you introduce to me a server or software which can extract y coordinates from the PDB and save it as another file? Can you introduce to me a server of software which can delete the original b-factors in the original PDB and have the ys pasted on the b-factors positions in the PDB file? Smith At 2015-11-18 21:13:05, "David Hall" <li...@cowsandmilk.net> wrote: I forgot: spectrum b at the end. On Wed, Nov 18, 2015 at 8:11 AM, David Hall <li...@cowsandmilk.net> wrote: > Assuming you are ok with overwriting the B-factors > > > stored.y=[] > iterate_state 1, prot, stored.y.append(y) % prot here should be replaced > with your pymol object name > alter prot, b=stored.y.pop(0) % again, replace prot with your pymol object > name > > > > > On Wed, Nov 18, 2015 at 7:49 AM, Smith Liu <smith_liu...@163.com> wrote: > >> Dear All, >> >> Is any way we can colour the molecule by pymol based on the y values in >> the z y z coordinates, so that we can view easily the residues (or atoms) >> with equivalent position in the primary sequence but has a y-axis shift in >> the 3-D structure? >> >> Smith >> >> >> >> >> >> ------------------------------------------------------------------------------ >> >> _______________________________________________ >> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> > >
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