[PyMOL] Iterate scenes smoothly
Dear users, I'm trying to make a movie during which a surface changes its color. I followed the tutorials from the wiki and successfully created two scenes with the desired colors. However, I can't make them iterate smoothly. Instead, The first half of the frames display the first scene and the second half the second scene. I'm using the following commands: mset 1x 60 scene 001, store scene 002, store frame 1 mview store, scene=001 frame 60 mview store, scene=002 mview interpolate Also, the scenes doesn't change smoothly when I press PgUp/Down. Am I doing something wrong? Best regards, Leandro -- Find and fix application performance issues faster with Applications Manager Applications Manager provides deep performance insights into multiple tiers of your business applications. It resolves application problems quickly and reduces your MTTR. Get your free trial! https://ad.doubleclick.net/ddm/clk/302982198;130105516;z___ 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] How can I iterate scenes smoothly?
Dear users, I'm trying to make a movie during which a surface changes its color. I followed the tutorials from the wiki and successfully created two scenes with the desired colors. However, I can't make them iterate smoothly. Instead, The first half of the frames display the first scene and the second half the second scene. I'm using the following commands: mset 1x 60 scene 001, store scene 002, store frame 1 mview store, scene=001 frame 60 mview store, scene=002 mview interpolate Also, the scenes doesn't change smoothly when I press PgUp/Down, as the wiki say they should. Am I doing something wrong? Best regards, Leandro -- Mobile security can be enabling, not merely restricting. Employees who bring their own devices (BYOD) to work are irked by the imposition of MDM restrictions. Mobile Device Manager Plus allows you to control only the apps on BYO-devices by containerizing them, leaving personal data untouched! https://ad.doubleclick.net/ddm/clk/304595813;131938128;j___ 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] (no subject)
Hi, You probably have a pdb file which has multiple possible conformations for some residues. You can check this by visual inspection of such residues. They have two side chains coming from the same CA. In the text file you can see the conformations marked as A and B in the residue name field, e.g. APHE BPHE. If that is the case, you have to choose one of them either manually or with some other molecular modeling software, e.g. gromacs. I hope it helps! Regards, Leandro On Mon, Apr 3, 2017 at 5:47 PM, Vivien Schoonenberg < vivienschoonenb...@gmail.com> wrote: > Hi there, > > > > I’m saving the sequences from each chain of the PDB via pymol with > > >>save something.fasta, chain A > > > > This is the same sequence that is shown in pymol and seems to correspond > to the structure I am looking at. > > However, when I loaded new B-factors in my structure, I noticed something > funny happened. The list which I made corresponding to the sequence I saved > earlier was too short. > > I found out by iterating that some residues repeated themselves(>>iterate > (chain A and n. CA), print resn). They carry the same residue number, and > are not shown in the sequence. However, when I load my B-factors my list > shifts because of these repeats, making it too short for the complete chain > and loading the wrong value onto residues. > > > > Does anyone know why this happens and how I can fix this? > > > > Thank you, > > Vivien > > > -- > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > ___ > 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 > -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ 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] Install pymol as module in python in linux
Hi, I also had some problem with this. The "trick", I believe, is to compile/install pymol with: python2.7 setup.py build install --home=path_to_pymol/ --install-lib=path_to_pymol/modules/ --install-scripts=path_to_pymol/ The part you are interested in is the modules. I needed to install something called msgpack-c before compiling pymol. In addition, you need to add path_to_pymol/modules/ to your python paths. You can add these to the .bashrc file: export PYMOL_PATH=path_to_pymol/ export PYTHONPATH=$PYTHONPATH:$PYMOL_PATH/modules: Have fun! Leandro On Tue, Jul 25, 2017 at 8:27 PM, Vivien Schoonenberg < vivienschoonenb...@gmail.com> wrote: > Hi all, > > > > I have been trying for a while, but cannot seem to figure out how to > install pymol on my unix server so that I can run pymol from within a > python script. (So that I can use it with the command ‘ import pymol’. I > did manage to do this on my windows with a wheel, but don’t know how to > solve it on my unix system) > > > > Any tips would be very welcome! > > > > Thanks, > > Vivien > > > -- > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > ___ > 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 > -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ 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
