Big thank you to all of you! I really need to find some time to better learn code. :/
> On Jul 23, 2015, at 4:36 PM, Sampson, Jared <jared.samp...@nyumc.org> wrote: > > I'm posting the following solution on behalf of Thomas Holder (whose > sourceforge.net <http://sourceforge.net/> email address is currently down due > to SF server issues), to ensure it is added to this thread in the archive: > >> This is due to chain identifier conflict. He's merging 6 models with >> identical identifiers. A simple fix would be: >> >> fetch 3ow9, type=pdb1, async=0 >> split_states 3ow9 >> alter 3ow9_000*, segi=model[-1] >> create combined, 3ow9_000* > > Changing the chain IDs as Rob suggested would also work. > > Cheers, > > Jared > > -- > Jared Sampson > Xiangpeng Kong Lab > NYU Langone Medical Center > http://kong.med.nyu.edu/ <http://kong.med.nyu.edu/> > > > > > > > On Jul 23, 2015, at 2:42 PM, Robert Campbell <robert.campb...@queensu.ca > <mailto:robert.campb...@queensu.ca>> wrote: > >> Hi Adam, >> >> I think you also want to make sure that each strand as a distinct chain >> ID if you want the cartoon representation to work correctly. >> >> Unfortunately that means you have to use "alter" but to change the >> chain IDs on the objects created by the split_states command before >> merging them all into one object. >> >> It worked for me when I tried that with 3ow9. >> >> Cheers, >> Rob >> >> On Thu, 2015-07-23 09:23 EDT, "H. Adam Steinberg" >> <h.adam.steinb...@gmail.com <mailto:h.adam.steinb...@gmail.com>> wrote: >> >>> Hi All, >>> >>> If you fetch 3ow9 in PyMOL, >>> split_states to get all six of the strands, >>> select all, then copy to object, >>> You only get the two strands, not all six, I need all six to be >>> duplicated into one object so I can make a long amyloid fibril. >>> >>> If I open the pdb file for 3ow9 in text edit and remove all the text >>> for the individual models (and the waters), then open that file in >>> PyMOL I get all six strands, but all the cartoon secondary structure >>> is missing except for the two original strands. I tired running the >>> alter command in PyMOL, it changes the secondary structure in the >>> other objects I have open but not in this pdb. >>> >>> I see the Sheet entry in the pdb file but I don’t know how to >>> duplicate and change the sheet entry so it applies to the other four >>> strands in the file. >>> >>> Could someone point me to a place on the web that explains how to >>> change the sheet entry (I’d like to learn how to do it)? or tell me >>> how to fix this pdb file? >>> >>> Thanks! >>> >>> >>> >>> H. Adam Steinberg >>> 7904 Bowman Rd >>> Lodi, WI 53555 >>> 608/592-2366 >>> >> >> >> >> >> -- >> Robert L. Campbell, Ph.D. >> Senior Research Associate/Adjunct Assistant Professor >> Dept. of Biomedical & Molecular Sciences, Botterell Hall Rm 644 >> Queen's University, >> Kingston, ON K7L 3N6 Canada >> Tel: 613-533-6821 >> <robert.campb...@queensu.ca <mailto:robert.campb...@queensu.ca>> >> http://pldserver1.biochem.queensu.ca/~rlc >> <http://pldserver1.biochem.queensu.ca/~rlc> >> >> ------------------------------------------------------------------------------ >> _______________________________________________ >> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net >> <mailto:PyMOL-users@lists.sourceforge.net>) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> <https://lists.sourceforge.net/lists/listinfo/pymol-users> >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> <http://www.mail-archive.com/pymol-users@lists.sourceforge.net> > > ------------------------------------------------------------ > This email message, including any attachments, is for the sole use of the > intended recipient(s) and may contain information that is proprietary, > confidential, and exempt from disclosure under applicable law. Any > unauthorized review, use, disclosure, or distribution is prohibited. If you > have received this email in error please notify the sender by return email > and delete the original message. Please note, the recipient should check this > email and any attachments for the presence of viruses. The organization > accepts no liability for any damage caused by any virus transmitted by this > email. > ================================= > H. Adam Steinberg 7904 Bowman Rd Lodi, WI 53555 608/592-2366
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