Dear all, I would like to fit two protein monomers that form a dimer into an em density map. I know from previous mutagenesis studies that the binding takes place with two tryptophan residues and the counterpart binding pocket. How can I set this interaction as fixed so that chimera fits the rest of the molecule according to the density map without continuously changing this part of the essential protein protein interaction? I would like to fit that interaction manually and then exclude it from the automatic procedure. Thank you very much in advance. Bests Christoph Wigge
Hi Christoph, If you have the monomers already in the desired positions relative to one another, you could combine them into a single model (for example using the "copy/combine" function in the Model Panel), and then fit the single model as a rigid body into the map. However, if you meant you only wanted to constrain the distance between the monomers but not fully fix (freeze) their relative positions, you may need to use some program other than Chimera. Chimera doesn't do flexible fitting with constraints. Besides simple rigid-body fitting, the options in Chimera are: sequential fitting of multiple structures (find good position for one rigid body, then find nonoverlapping good position for next rigid body, ...) and symmetric fitting of rigid-body copies of the same structure. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multifit/multifit....> I'm not qualified to make recommendations in this area, and can only mention a few programs that might be relevant: PyRy3D (Monte Carlo fitting with restraints) has a plugin to use Chimera as the graphical interface: <http://genesilico.pl/pyry3d/> <http://genesilico.pl/pyry3d/pyryextension/> IMP: <http://salilab.org/imp/> Molecular Dynamics Flexible Fitting (MDFF): <http://www.ks.uiuc.edu/Research/mdff/> Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Oct 22, 2013, at 4:37 AM, Christoph Wigge <wigge.christoph@gmail.com> wrote:
Dear all, I would like to fit two protein monomers that form a dimer into an em density map. I know from previous mutagenesis studies that the binding takes place with two tryptophan residues and the counterpart binding pocket. How can I set this interaction as fixed so that chimera fits the rest of the molecule according to the density map without continuously changing this part of the essential protein protein interaction? I would like to fit that interaction manually and then exclude it from the automatic procedure. Thank you very much in advance. Bests Christoph Wigge
Hi Elaine, Thanks for the quick reply. I will definitely try out your advice. I have another question because a colleague told me that it might also be possible to use the truncated part of the dimer that formed the binding site in the crystal and then to superimpose the very homologue full protein on that. Then to write out out the superimposed full molecule as one pdb file and do a rigid body fitting. What do you think of that solution? Bests Christoph Am 23.10.2013 um 00:46 schrieb Elaine Meng:
Hi Christoph, If you have the monomers already in the desired positions relative to one another, you could combine them into a single model (for example using the "copy/combine" function in the Model Panel), and then fit the single model as a rigid body into the map.
However, if you meant you only wanted to constrain the distance between the monomers but not fully fix (freeze) their relative positions, you may need to use some program other than Chimera. Chimera doesn't do flexible fitting with constraints. Besides simple rigid-body fitting, the options in Chimera are: sequential fitting of multiple structures (find good position for one rigid body, then find nonoverlapping good position for next rigid body, ...) and symmetric fitting of rigid-body copies of the same structure.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multifit/multifit....>
I'm not qualified to make recommendations in this area, and can only mention a few programs that might be relevant:
PyRy3D (Monte Carlo fitting with restraints) has a plugin to use Chimera as the graphical interface: <http://genesilico.pl/pyry3d/> <http://genesilico.pl/pyry3d/pyryextension/>
IMP: <http://salilab.org/imp/>
Molecular Dynamics Flexible Fitting (MDFF): <http://www.ks.uiuc.edu/Research/mdff/>
Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 22, 2013, at 4:37 AM, Christoph Wigge <wigge.christoph@gmail.com> wrote:
Dear all, I would like to fit two protein monomers that form a dimer into an em density map. I know from previous mutagenesis studies that the binding takes place with two tryptophan residues and the counterpart binding pocket. How can I set this interaction as fixed so that chimera fits the rest of the molecule according to the density map without continuously changing this part of the essential protein protein interaction? I would like to fit that interaction manually and then exclude it from the automatic procedure. Thank you very much in advance. Bests Christoph Wigge
Hi Christoph, It depends on whether you believe your protein forms the dimer in the same way as the homolog with known dimeric structure. It sounds like a reasonable hypothesis, at least, and I believe other people have done similar things. You could try it and see if the shape of your modeled dimer appears to be compatible with the shape of the density. If the fit is very poor, then you might consider alternative hypotheses. Best Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Oct 23, 2013, at 12:01 AM, Christoph Wigge wrote:
Hi Elaine, Thanks for the quick reply. I will definitely try out your advice. I have another question because a colleague told me that it might also be possible to use the truncated part of the dimer that formed the binding site in the crystal and then to superimpose the very homologue full protein on that. Then to write out out the superimposed full molecule as one pdb file and do a rigid body fitting. What do you think of that solution? Bests Christoph
Hi Christoph, If I understand your question you have two PDB files of monomers that form a dimer and you want to fit them into a density map as a rigid unit without disturbing how they bind to each other. This is easy to do in Chimera. If you are using the Fit in Map dialog just select both monomers (e.g. command "select #1,2") then use the Fit "selected atoms" setting in the dialog. This will move selected two monomers rigidly as one unit to the locally optimal position in the density map. You can do this with a command instead of the fitting dialog "fit #1,2 #3". Tom On Oct 22, 2013, at 4:37 AM, Christoph Wigge wrote:
Dear all,
I would like to fit two protein monomers that form a dimer into an em density map. I know from previous mutagenesis studies that the binding takes place with two tryptophan residues and the counterpart binding pocket. How can I set this interaction as fixed so that chimera fits the rest of the molecule according to the density map without continuously changing this part of the essential protein protein interaction? I would like to fit that interaction manually and then exclude it from the automatic procedure. Thank you very much in advance.
Bests
Christoph Wigge _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Dear all, I would like to load the upper limits for the distances (constraints) between pairs of atoms (upl file) into my final of structures family. I would like to ask if this is possible with Chimera program best regards Francesca Cantini ------------------ University of Florence, CERM
Hi Francesca, Chimera does not read CYANA upl files directly. You would have to change the atom descriptions to Chimera command-line specifiers and then either read them in as pseudobonds or as distance commands. I’m looking at the upl file description here: <http://www.cyana.org/wiki/index.php/Distance_restraint_file> …example starts with # Upper distance limit 91 THR HB 93 GLN H 5.50 81 ILE HB 82 PRO HA 5.19 (1) to read in as pseudobonds in Chimera, remove the comment at the top, and these atom lines could be something like :91@hb :93@h :81@hb :82@ha …or if you have more than one model and/or chain you can also specify those, for example with model #0 chain A: #0:91.a@hb #0:93.a@h #0:81.a@hb #0:82.a@ha You would read in this plain text file with the Pseudobond Reader tool (in menu under Tools…Depiction). <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/pbreader/pbreader....> As shown in the link above, you could also give a color and a label on each line, so you could label with the distance value of the constraint. (2) if you want to see a label of the current distance in the structure (which might be different than the constraint distance), instead change the file to a distance command file. This is also plain text with the same pairs of atoms, but you would also put “distance” before each pair and name the file ending with .com or .cmd and open it with the “open” command or menu: File… Open. The lines would be something like the following, with atom specifiers as needed to specify exactly two atoms: distance :91@hb :93@h distance #0:81.a@hb #0:82.a@ha <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/distance.html> (Finally, you might consider using ChimeraX instead of Chimera since it has more features for looking at pseudobonds, like histograms by length with the “crosslinks “ command. approaches 1) and 2) above are much the same except (a) chain specification is different, e.g. distance :91@hb :93@h distance #0/a:81@hb #0/a:82@ha (b) there is no option to label the pseudobond with the constraint distance, you can only show current distance using the distance command-file approach instead (c) the pseudobond file should be named ending in .pb and the command file should be named ending in .cxc) <http://www.rbvi.ucsf.edu/chimerax/index.html> <http://rbvi.ucsf.edu/chimerax/docs/user/pseudobonds.html> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/crosslinks.html> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/distance.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 22, 2019, at 4:44 AM, Francesca Cantini <cantini@cerm.unifi.it> wrote:
Dear all, I would like to load the upper limits for the distances (constraints) between pairs of atoms (upl file) into my final of structures family. I would like to ask if this is possible with Chimera program best regards Francesca Cantini
participants (4)
-
Christoph Wigge -
Elaine Meng -
Francesca Cantini -
Tom Goddard