Re: [PyMOL] Fetching PDBs; how to load .cifs provided instead of .pdbs
Which version of PyMOL do you have? Mine is 1.7.4 and it is working just fine. So in case you have and older version( 1.3 I guess) it might not work properly. Lukas From: Brenton Horne [mailto:brentonho...@ymail.com] Sent: Friday, March 20, 2015 12:02 AM To: Lukáš Pravda Subject: Re: [PyMOL] Fetching PDBs; how to load .cifs provided instead of .pdbs Thanks for ya help but I'm afraid this isn't working. See it saves the fetched file as .sf format which it then fails to recognize. PyMOLfetch 4V7Y, type = cif please wait ... PyMOLas cartoon CmdLoad: .\4v7y.sf loaded as 4V7Y. On 19/03/2015 9:31 PM, Lukáš Pravda wrote: Hi Brenton, fetch 4v7y, type=cif is the command you are looking for All the best Lukas Pravda --- CEITEC - Central European Institute of Technology Masaryk University Brno, Czech Republic --- From: Brenton Horne [mailto:brentonho...@ymail.com] Sent: Thursday, March 19, 2015 4:55 AM To: pymol-users@lists.sourceforge.net mailto:pymol-users@lists.sourceforge.net Subject: [PyMOL] Fetching PDBs; how to load .cifs provided instead of .pdbs Hi, I have noticed that for some PDBs wwPDB doesn't contain PDB files (e.g., 4V7Y http://www.rcsb.org/pdb/explore/explore.do?structureId=4V7Y ), but rather they have mmCIF files instead and I was wondering if it was possible to get the fetch command to fetch these mmCIFs instead of PDBs. Now to be clear, I do understand how to load mmCIFs that I have downloaded manually from wwPDB by going to File-Open... but I'd like to know how to get PyMOL to fetch these files from wwPDB and load them. Thanks for your time, Brenton -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/___ 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] Fetching PDBs; how to load .cifs provided instead of .pdbs
Hi, For the version in Ubuntu 14.04 (1.7.0.0) it also defaults to downloading the structure factors in cif format, instead of the model coordinates, so I'm not sure this is the right way to do it, or perhaps something changed between 1.7.0.0 and 1.7.4 Best regards, Folmer 2015-03-20 10:26 GMT+01:00 Lukáš Pravda xpra...@ncbr.muni.cz: Which version of PyMOL do you have? Mine is 1.7.4 and it is working just fine. So in case you have and older version( 1.3 I guess) it might not work properly. Lukas *From:* Brenton Horne [mailto:brentonho...@ymail.com] *Sent:* Friday, March 20, 2015 12:02 AM *To:* Lukáš Pravda *Subject:* Re: [PyMOL] Fetching PDBs; how to load .cifs provided instead of .pdbs Thanks for ya help but I'm afraid this isn't working. See it saves the fetched file as .sf format which it then fails to recognize. PyMOLfetch 4V7Y, type = cif please wait ... PyMOLas cartoon CmdLoad: .\4v7y.sf loaded as 4V7Y. On 19/03/2015 9:31 PM, Lukáš Pravda wrote: Hi Brenton, fetch 4v7y, type=cif is the command you are looking for All the best Lukas Pravda --- CEITEC - Central European Institute of Technology Masaryk University Brno, Czech Republic --- *From:* Brenton Horne [mailto:brentonho...@ymail.com brentonho...@ymail.com] *Sent:* Thursday, March 19, 2015 4:55 AM *To:* pymol-users@lists.sourceforge.net *Subject:* [PyMOL] Fetching PDBs; how to load .cifs provided instead of .pdbs Hi, I have noticed that for some PDBs wwPDB doesn't contain PDB files (e.g., 4V7Y http://www.rcsb.org/pdb/explore/explore.do?structureId=4V7Y), but rather they have mmCIF files instead and I was wondering if it was possible to get the fetch command to fetch these mmCIFs instead of PDBs. Now to be clear, I do understand how to load mmCIFs that I have downloaded manually from wwPDB by going to File-Open... but I'd like to know how to get PyMOL to fetch these files from wwPDB and load them. Thanks for your time, Brenton -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ ___ 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 -- Folmer Fredslund -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/___ 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] Fetching PDBs; how to load .cifs provided instead of .pdbs
Hi Brenton, fetch 4v7y, type=cif is the command you are looking for All the best Lukas Pravda --- CEITEC - Central European Institute of Technology Masaryk University Brno, Czech Republic --- From: Brenton Horne [mailto:brentonho...@ymail.com] Sent: Thursday, March 19, 2015 4:55 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Fetching PDBs; how to load .cifs provided instead of .pdbs Hi, I have noticed that for some PDBs wwPDB doesn't contain PDB files (e.g., 4V7Y http://www.rcsb.org/pdb/explore/explore.do?structureId=4V7Y ), but rather they have mmCIF files instead and I was wondering if it was possible to get the fetch command to fetch these mmCIFs instead of PDBs. Now to be clear, I do understand how to load mmCIFs that I have downloaded manually from wwPDB by going to File-Open... but I'd like to know how to get PyMOL to fetch these files from wwPDB and load them. Thanks for your time, Brenton -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/___ 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
