Re: [PyMOL] secondary structure disappears
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 -- ___ 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
Re: [PyMOL] secondary structure disappears
I'm posting the following solution on behalf of Thomas Holder (whose sourceforge.nethttp://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/ On Jul 23, 2015, at 2:42 PM, Robert Campbell robert.campb...@queensu.camailto: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.commailto: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.camailto:robert.campb...@queensu.ca http://pldserver1.biochem.queensu.ca/~rlc -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.netmailto: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 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. = -- ___ 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
[PyMOL] secondary structure disappears
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! 3ow9.pdb Description: Protein Databank data H. Adam Steinberg7904 Bowman RdLodi, WI 53555608/592-2366 -- ___ 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
Re: [PyMOL] secondary structure disappears
The secondary structure is only there for the first set of strands, and then that is used for the other strands when you split_states, but how do I change that entry so it applies to the other strands? Here is that entry from the file that I attached: SHEET1 A 2 LEU A 2 PHE A 5 0 SHEET2 A 2 LEU B 2 PHE B 5 -1 O VAL B 3 N PHE A 4 On Jul 23, 2015, at 10:48 AM, Smith Liu smith_liu...@163.com wrote: I think the secondary structure record (SS) has been lost during your splitting. So just add and edit the SS record in the PDB file to the lost ones. Smith At 2015-07-23 22:23:24, H. Adam Steinberg 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 -- ___ 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
