Hi Alex, the sequence view is ordered by identifiers, not by connectivity. There seems to be no mechanism to automatically deal with duplicated residue numbers when fusing objects. I think the only safe way is to make sure that chain and/or residue numbers do not overlap in both objects. Examples:
1) duplicated identifiers fab ACD, m1 fab EFG, m2 fuse last (m1 and name C), first (m2 and name N) -> yields AECFDG (mixed) 2) increase residue numbers in one selection fab ACD, m1 fab EFG, m2 alter m2, resi=resv+3 fuse last (m1 and name C), first (m2 and name N) -> yields ACDEFG (correct) 3) set different chain ids fab ACD, m1 fab EFG, m2 alter m1, chain="A" alter m2, chain="B" fuse last (m1 and name C), first (m2 and name N) -> yields ACDEFG (correct) There is also a "renumber" script on the PyMOLWiki which can set residue numbers based on connectivity: http://pymolwiki.org/index.php/Renumber Hope that helps. Cheers, Thomas Alex Truong wrote, On 06/07/12 22:57: > Hi All, > > I am trying to append four residues (MQFF) to the N-terminus (G) of a > protein fragment, and whenever I generate the 4-residue peptide and fuse > the appropriate atoms together, it always reads MQFGF instead of MQFFG, > like the fragment has somehow invaded the N-terminus instead of latching > to the end. When I change views and select individual residues there's a > conspicuous gap. I fixed this issue by appending FF, then Q (because F > then F resulted in some wonky behavior too, and QFF resulted in QFGF), > but I cannot seem to add M (by itself) without getting QMFFG. Obviously, > I want MQFFG. What's wrong here, and how can I append correctly? I'm > using the same command every time (fuse (pk2),(pk1) ; 2 then 1 is just a > quirk of my selections and definitely not the issue). > > Elsewhere in my project, I'm trying to fuse two large fragments > together, but no matter how I specify my selections, they are not lining > up correctly in the sequence display. I want to link ...MRDE to KRTH... > To form ...MRDEKRTH... but when I fuse it always puts the wrong ends > with each other (i.e. the end of fragment 2 with the beginning of > fragment 1 as opposed to the end of fragment 1 with the beginning of > fragment 2 as desired). However, it fuses properly visually. Also, the > sequence displays it as two objects stitched together, and not as one > continuous object like when I added the 4 residues to my first fragment. > There's a standard numbering scheme for the first fragment, then a > double slash, then it restarts with the scheme associated with the > second fragment. Is there anyway to make it so the fused fragments read > as one object with a seamless residue sequence? > > Thank you, > > Alex -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ 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
