Thanks so much Elaine! Regarding #2 it's OK! Regarding #1 - I have tried to set new chains via Tools menu but unfortunatelly in the model where chains has not been asigned the whole sequence is defined as Principal chain without partitition on sub-segments. BTW in case If another model of the same protein is loaded in the same session as the second ensemble where the chains are assigned correctly is it possible to copy chains ID from it to the first model (Ensemble) using Match-align plugin for intance? And finally the question #3 For my particular case - each ensembles represent several snapshots of the docking poses between 2 proteins - one produced by protein-protein docking and the another one - as the result of clustetring of several independet long MD trajectories (taking one representative snapshot from each of the trajectory - corresponded to the established macromolecular complex). Having those two ensembles I need to compareit in terms of the distribution of the docking poses within each to find some shared trends in each of them e.g RMSD of the distances between common residues-pairs found in contact map analysis or something else. What are most trivial suggestions might be in that particular case? Thanks for help ! Gleb 2016-06-10 2:08 GMT+02:00 Elaine Meng <meng@cgl.ucsf.edu>:

Hi Gleb, Unfortunately, the short answer is “not really” to both parts.

For #1 you’d need to do it semi-manually with Tools… Structure Editing…. Change Chain IDs (or command “changechains”). <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/changechains.html>

For #2 if you just had individual models (not ensembles), you could spread them out with Tools… Utilities… Tile Structures (or command “tile”). Unfortunately if you try this on the ensembles, the invidual members of the ensembles will be spread out. As far as I know, there is no way just to tile the 2 groupings. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ensembletile/ensembletile.html>

A similar approach is if you had opened the two ensembles as models #1,2 you could translate them apart, e.g. command:

move x 50 model #2

… and then set independent rotation, e.g. command:

set independent

The basic problem remains that each individual member (not ensembles collectively) will then rotate about its own individual center, and the ensemble members will diverge from one another as you rotate with the mouse, rather than keeping together as a tight unit.

Sorry for the limitations, 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 Jun 9, 2016, at 7:06 AM, James Starlight <jmsstarlight@gmail.com> wrote:

Dear Chimera Users!

I have loaded 2 NMR ensembles each of which is consisted of several models as 2 different object and now would like to do:

1 - becasue actually two esembles made from the conformers of the same protein (one from experiment (NMR) and another one from MD simulation) with totally equal sequence - I would like to copy from the first ensemble the chain information to the second one where such information is absent but the order of residues and atoms are the same.

2- Is it possible to set visualization mode as split view to see on the screen both ensembles in the adjacent positions with the posibility to easily browes separate models within each of them (like pymol style)?

Thanks for help !

Gleb

Thanks so much Elaine! To simplify the problem - I have 2 cases both of which are the same process: binding established between A and B caputred by means of i) docking ii) MD simulation. Let's assumes that contact map is the most important criterioum for my case - because one of the *docking* ensemble was driven by means of experiemtal restraits so the contacts between pairs of the residues of A and B can be considered here as the reference which I want to reproduce in the second MD ensemble in unbiassed fassion. Is it possible to calculate contact maps for both ensembles separately using MD movie and than calculate some statistical variance or RMSD of established contact pairs between A and B within each of the ensembles and after all to compare both outputs to understand what are the cotacts from the MD ensembles has most statistical significance? Gleb 2016-06-13 18:42 GMT+02:00 Elaine Meng <meng@cgl.ucsf.edu>:

Hi Gleb, For #1, there isn’t anything to automatically copy chain IDs like you describe. However, if you text-edit the PDB files to put a TER between the chains, then the Change Chain IDs tool will allow you to change the ID of each part separately.

For #3, I can’t think of anything very automatic to do the comparison. You could maybe do something with Chimera command scripts and “distance” and “angle” command measurements between the two proteins (possibly also with “define” to calculate centroids, planes, and axes which could then be used in the “distance” and “angle” measurements). Another idea is to open each ensemble as a trajectory and then use the MD Movie tool’s plotting of distances, angles, etc. (MD Movie menu: Analysis… Plot…). There is a “Dump Values” button on the plot window to write the measurements to file.

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/distance.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/angle.html>

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#plotting>

I hope this helps, Elaine

...

On Jun 13, 2016, at 3:03 AM, James Starlight <jmsstarlight@gmail.com> wrote:

Thanks so much Elaine!

Regarding #2 it's OK! Regarding #1 - I have tried to set new chains via Tools menu but unfortunatelly in the model where chains has not been asigned the whole sequence is defined as Principal chain without partitition on sub-segments. BTW in case If another model of the same protein is loaded in the same session as the second ensemble where the chains are assigned correctly is it possible to copy chains ID from it to the first model (Ensemble) using Match-align plugin for intance?

And finally the question #3 For my particular case - each ensembles represent several snapshots of the docking poses between 2 proteins - one produced by protein-protein docking and the another one - as the result of clustetring of several independet long MD trajectories (taking one representative snapshot from each of the trajectory - corresponded to the established macromolecular complex). Having those two ensembles I need to compareit in terms of the distribution of the docking poses within each to find some shared trends in each of them e.g RMSD of the distances between common residues-pairs found in contact map analysis or something else. What are most trivial suggestions might be in that particular case?

Thanks for help !

Gleb

2016-06-10 2:08 GMT+02:00 Elaine Meng <meng@cgl.ucsf.edu>:

...

Hi Gleb, Unfortunately, the short answer is “not really” to both parts.

For #1 you’d need to do it semi-manually with Tools… Structure Editing…. Change Chain IDs (or command “changechains”). <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/changechains.html>

For #2 if you just had individual models (not ensembles), you could spread them out with Tools… Utilities… Tile Structures (or command “tile”). Unfortunately if you try this on the ensembles, the invidual members of the ensembles will be spread out. As far as I know, there is no way just to tile the 2 groupings. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ensembletile/ensembletile.html>

A similar approach is if you had opened the two ensembles as models #1,2 you could translate them apart, e.g. command:

move x 50 model #2

… and then set independent rotation, e.g. command:

set independent

The basic problem remains that each individual member (not ensembles collectively) will then rotate about its own individual center, and the ensemble members will diverge from one another as you rotate with the mouse, rather than keeping together as a tight unit.

Sorry for the limitations, 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 Jun 9, 2016, at 7:06 AM, James Starlight <jmsstarlight@gmail.com> wrote:

Dear Chimera Users!

I have loaded 2 NMR ensembles each of which is consisted of several models as 2 different object and now would like to do:

1 - becasue actually two esembles made from the conformers of the same protein (one from experiment (NMR) and another one from MD simulation) with totally equal sequence - I would like to copy from the first ensemble the chain information to the second one where such information is absent but the order of residues and atoms are the same.

2- Is it possible to set visualization mode as split view to see on the screen both ensembles in the adjacent positions with the posibility to easily browes separate models within each of them (like pymol style)?

Thanks for help !

Gleb

Thanks for the suggestions again, Elaine! For my particular case calculation of the contact pairs from the MDmovies produced reasonable results. Going to the analysis of the output logs 1) what determine the statistical value - at the end of each string e.g ALA 252.B vdw GLY 75.C 1.4 ALA 71.C vdw ILE 117.B 1 ASP 178.B vdw GLY 54.C 1.2 GLN 120.B vdw HIS 53.C 1.2 ARG 198.B vdw GLU 64.C 0.6 ALA 252.B vdw ASN 68.C 1.4 does the value of 1.4 corresponds to most likely contact (observed on bigger number of snapshots) than 0.6 for intance? 2) Obtaining two such logs where the string order (contact pairs ranged to its statistical weights) are mixed within it- what are the trivial suggestion for the comparison such two logs to establish shared contact pairs with equal statistical weights? Thanks! Gleb 2016-06-14 18:14 GMT+02:00 Elaine Meng <meng@cgl.ucsf.edu>:

Hi Gleb, As you probably saw already, you can calculate a contact map for each ensemble. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#rins>

However, there is nothing to do such a statistical analysis automatically. For each contact map, you would just get a set of edges and their values. Maybe if you had a large number of snapshots (frames) for each of the two ensembles, you could take several different samples from each one (thus multiple contact maps from each ensemble) and then somehow use all those edge values to calculate some statistics. However, I am not a statistical expert and cannot advise on what methodology would be valid or most appropriate for your data.

Best, Elaine

...

On Jun 14, 2016, at 6:41 AM, James Starlight <jmsstarlight@gmail.com> wrote:

Thanks so much Elaine!

To simplify the problem - I have 2 cases both of which are the same process: binding established between A and B caputred by means of i) docking ii) MD simulation.

Let's assumes that contact map is the most important criterioum for my case - because one of the *docking* ensemble was driven by means of experiemtal restraits so the contacts between pairs of the residues of A and B can be considered here as the reference which I want to reproduce in the second MD ensemble in unbiassed fassion.

Is it possible to calculate contact maps for both ensembles separately using MD movie and than calculate some statistical variance or RMSD of established contact pairs between A and B within each of the ensembles and after all to compare both outputs to understand what are the cotacts from the MD ensembles has most statistical significance?

Gleb