From: Warren L. D. <wa...@de...> - 2003-08-06 16:39:02
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David, You found a bug -- it turns out PyMOL was getting confused by the presence of a "P" atom in P-tyr. It thought the residue contained both protein and DNA, and so the cartoon had an extra gap. The following workaround should get you a complete cartoon with 1fmk. Future versions of PyMOL should not suffer from this problem. alter all.type=3D'ATOM' alter name P,name=3D'P1' sort Thanks for your help in quashing that bug! Cheers, Warren -- mailto:wa...@de... Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154=20 Fax (650)-593-4020 > -----Original Message----- > From: David A. Horita [mailto:dh...@wf...] > Sent: Wednesday, August 06, 2003 5:27 AM > To: Warren L. DeLano > Subject: RE: [PyMOL] cartoons through nonstandard residues >=20 > Warren, > Thanks for the reply, but I still don't get the cartoon running through > the phosphotyrosine. I've tried it on Src (1fmk.pdb), and still get a > break between residues Gln526, Ptr 527 and Gln 528. > Regards, > David Horita >=20 > > -----Original Message----- > > From: Warren L. DeLano [mailto:wa...@de...] > > Sent: Tuesday, August 05, 2003 7:17 PM > > To: David A. Horita; pym...@li... > > Subject: RE: [PyMOL] cartoons through nonstandard residues > > > > > > David, > > > > The problem: PyMOL sorts PDB hetatms apart from molecules. The > > solution: > > > > alter all, type=3D'ATOM' > > sort > > rebuild > > > > I'm thinking about disabling this behavior before the next release... > > > > Cheers, > > Warren > > > > -- > > mailto:wa...@de... > > Warren L. DeLano, Ph.D. > > Principal Scientist > > DeLano Scientific LLC > > Voice (650)-346-1154 > > Fax=A0=A0 (650)-593-4020 > > -----Original Message----- > > From: pym...@li... > > [mailto:pym...@li...] On Behalf Of > > David A. Horita > > Sent: Tuesday, August 05, 2003 1:53 PM > > To: pym...@li... > > Subject: [PyMOL] cartoons through nonstandard residues > > > > Hi, > > When I try to draw a cartoon through the backbone of a > > nonstandard residue (in this case, phosphotyrosine), the > > cartoon strand=A0stops prior to the PTR and starts after.=A0 How > > do I get a continuous strand through the phosphotyrosine > > backbone (or other residues, in the general case)? > > Ribbons seem to go through the PTR without problem, and > > selenomets don't seem to cause trouble, either. Thanks, David Horita > > ----------------------------- > > David A. Horita, Ph.D. > > Department of Biochemistry > > Wake Forest University School of Medicine > > Winston-Salem, NC 27157-1016 > > Tel: 336 713-4194 > > Fax: 336 716-7671 > > email:=A0 dh...@wf... > > web:=A0 http://www.wfubmc.edu/biochem/faculty/Horita/ > > > > > > |