[PyMOL] Modeling Protein-DNA complex
Hi, I docked dna with homeodomain protein formed from modeller and get docked protein-dna complex.I want to incorporate water molecules within homeodomain protein-dna complex which we observe in RCSB PDB file.Can it be possible using Pymol?Thanks,Soumi-- ___ 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] Modeling protein-dna complex
Hi soumi - A command-line version of what David said is the following: save new_complex.pdb, protein_selection or dna_selection where `protein_selection` and `dna_selection` include all the atoms you want to have in the final PDB. They could be object names if you have each protein and the DNA in separate objects. Hope that helps. Cheers, Jared > On Aug 13, 2016, at 12:15 PM, David Hall wrote: > > Select the protein you want and the dna, then save the selection as a PDB. > > There are many ways to make a selection; visually, the easiest might be: > > You said you’ve removed the DNA from the protein-dna complex, so now you > should have: > > (1) an object that has just your protein that you want in the complex > (2) an object that has just your DNA that you want in the complex > > In the bottom right, where it typically says “Selecting Residues”, click > where it says Residues until that it says “Objects” > > Click on your protein > > Click on your dna > > Click on File->Save Molecule and save “sele” as a PDB file. > >> On Aug 13, 2016, at 8:22 AM, soumi wrote: >> >> Hi, >>I carry on my research work on protein-dna complex system.I have one dna >> pdb and one protein-dna complex pdb.I want to make new protein-dna complex >> pdb taking dna from single pdb and protein from protein-dna complex.Protein >> possess similar DNA-binding specificities.I superimpose two pdb file and >> remove dna from protein-dna complex pdb .But I can not save new protein-dna >> complex.Please let me know by pymol how I would be able to model of the >> referred paper was done. >> Thanks >> soumi >> -- >> What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic >> patterns at an interface-level. Reveals which users, apps, and protocols are >> consuming the most bandwidth. Provides multi-vendor support for NetFlow, >> J-Flow, sFlow and other flows. Make informed decisions using capacity >> planning reports. >> http://sdm.link/zohodev2dev___ >> 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 > > > -- > What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic > patterns at an interface-level. Reveals which users, apps, and protocols are > consuming the most bandwidth. Provides multi-vendor support for NetFlow, > J-Flow, sFlow and other flows. Make informed decisions using capacity > planning reports. http://sdm.link/zohodev2dev > ___ > 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 -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports. http://sdm.link/zohodev2dev ___ 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] Modeling protein-dna complex
Select the protein you want and the dna, then save the selection as a PDB. There are many ways to make a selection; visually, the easiest might be: You said you’ve removed the DNA from the protein-dna complex, so now you should have: (1) an object that has just your protein that you want in the complex (2) an object that has just your DNA that you want in the complex In the bottom right, where it typically says “Selecting Residues”, click where it says Residues until that it says “Objects” Click on your protein Click on your dna Click on File->Save Molecule and save “sele” as a PDB file. > On Aug 13, 2016, at 8:22 AM, soumi wrote: > > Hi, > I carry on my research work on protein-dna complex system.I have one dna > pdb and one protein-dna complex pdb.I want to make new protein-dna complex > pdb taking dna from single pdb and protein from protein-dna complex.Protein > possess similar DNA-binding specificities.I superimpose two pdb file and > remove dna from protein-dna complex pdb .But I can not save new protein-dna > complex.Please let me know by pymol how I would be able to model of the > referred paper was done. > Thanks > soumi > -- > What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic > patterns at an interface-level. Reveals which users, apps, and protocols are > consuming the most bandwidth. Provides multi-vendor support for NetFlow, > J-Flow, sFlow and other flows. Make informed decisions using capacity > planning reports. > http://sdm.link/zohodev2dev___ > 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 -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports. http://sdm.link/zohodev2dev ___ 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] Modeling protein-dna complex
Hi, I carry on my research work on protein-dna complex system.I have one dna pdb and one protein-dna complex pdb.I want to make new protein-dna complex pdb taking dna from single pdb and protein from protein-dna complex.Protein possess similar DNA-binding specificities.I superimpose two pdb file and remove dna from protein-dna complex pdb .But I can not save new protein-dna complex.Please let me know by pymol how I would be able to model of the referred paper was done.Thankssoumi-- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports. http://sdm.link/zohodev2dev___ 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
