[PyMOL] Modeling Protein-DNA complex

2016-08-16 Thread soumi
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-

Re: [PyMOL] Modeling protein-dna complex

2016-08-14 Thread Sampson, Jared M.
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 D

Re: [PyMOL] Modeling protein-dna complex

2016-08-13 Thread David Hall
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

[PyMOL] Modeling protein-dna complex

2016-08-13 Thread soumi
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

RE: [PyMOL] modeling

2005-05-04 Thread Warren DeLano
ilto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > jennifer.pfings...@uchsc.edu > Sent: Wednesday, May 04, 2005 8:28 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] modeling > > > Hi everyone, > > I have a question that probably has a simple solution. When >

[PyMOL] modeling

2005-05-04 Thread Jennifer.Pfingsten
Hi everyone, I have a question that probably has a simple solution. When two pdb files being displayed in pymol, is there away to rotate one molecule without the other one moving as well? Thankyou, Jen Pfingsten (UCHSC)

RE: [PyMOL] modeling in pymol

2004-09-24 Thread Warren DeLano
y, September 22, 2004 10:47 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] modeling in pymol > > Hi, > > I was wondering if PyMOL has some simple modeling > functionalities, such as rotate through a particular bond > (change the dihedral angle), delete/form bo

[PyMOL] modeling in pymol

2004-09-22 Thread S. Frank Yan
Hi, I was wondering if PyMOL has some simple modeling functionalities, such as rotate through a particular bond (change the dihedral angle), delete/form bonds, superimpose, etc., via mouse. These functions will be particularly useful for molecular modeling besides the wonderful graphics. Also,