May 2018 - Chimera-users - RBVI Mailing Lists

trying to use per-frame pdb 'CONECT' information in movie maker
by Black, Kersey 04 May '18

04 May '18

Hi, Just recently back to using Chimera after a long time, so a bit rusty on this. I am reading in a trajectory of a small hydrocarbon for a single pdb file, and with each fram I include the geometry and the connectivity I want with ‘CONECT’ lines. But, when I use the Movie Maker tool to read it in, it seems to using one or more frames (perhaps the last one? to detect connectivity to auto detect connectivity and then applying it to all geometries, and this is putting bonds in places where I do not want them. Does movie maker honor CONECT information for each step? Is there a way to have it do so? Or is connectivity set once for the entire trajectory? Thanks much for any help on this, Kersey

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Coloring ensemble atoms by distance from mean structure
by Tom Goddard 03 May '18

03 May '18

Hi David, I’ve attached a Python script mean_distance.py that can compute the distance of each atom in an ensemble from the mean structure. Then you can color using that distance. Here’s an example set of Chimera commands. open 1mtx show open mean_distance.py rangecolor distance_from_mean 0 blue 3 white 6 red The script uses all open molecules as the ensemble. The coloring can also be done with menu Tools / Depiction / Render by Attribute. Tom > On May 3, 2018, at 10:10 AM, Morgan, David Gene wrote: > > Tom, > > Hope you are doing well. Jim Powers and I here at IU keep thinking we need to invite you and/or the team back for another chimera workshop, but we haven't done the ground work to see how possible that would really be. But I keep hoping! > > In the meantime, I have a question about whether chimera can do something, and if not, I have a feature request... I was watching a grad student give a talk showing lots of superposed atomic structures. The structures included some molecular dynamics simulations and some crystal structures of the same protein in subtly different conformations (packing into a viral capsid, where the different subunits in the asymmetric unit have slightly different conformations). It occurred to me that _after_ showing the mess of spaghetti he had, the points he needed to make would be better served with a different visual: If he were to average the ensemble of MD atomic positions to a single chain (and color-code by the ensemble RMS difference from the average) and do the same for all his ensemble of X-ray structures, it would be much easier to talk about and show the consistencies and inconsistencies in the atomic co-ordinates from all the data. This same sort of averaging an ensemble of atomic co-ordinates is sometimes done with NMR structure ensembles (but I don't know about the color coding with the RMS). > > I have looked at lots of packages that manipulate atomic co-ordinates, but haven't found anything that seems to actually do what I want to do. For example, gromacs is supposed to do the averaging but it really wants to work with MD data and at a minimum, I'm not smart enough to make it work with a series of standard PDB files. My NMR colleague suggested molmol for the averaging, and I need to explore that more. But there doesn't seem to be a recent linux version nor does it seem to be "scriptable" (i.e., if I wanted to do this for a dozen different ensembles, I would have to painfully mouse click my way through the process). On top of all that, I ran into numerous on-line discussions about how averaging was "the wrong thing to do." All those people had valid reasons for saying so, but right now, I'm really talking about a more simple visual that conveys some of the information contained in any sort of ensemble of atomic co-ordinates. > > So my first question is: does chimera have a utility that would do this sort of thing? I looked at various commands but did not see anything that looked like it would do this. If not, can I put a feature request into the queue? > > Looking forward to hearing from you and chatting some more. > > -- > politics is more difficult than physics. > A. Einstein > > David Gene Morgan > Electron Microscopy Center > 047D Simon Hall > IU Bloomington > 812 856 1457 (office) > 812 856 3221 (3200) > http://iubemcenter.indiana.edu >

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Question regarding rotating dihedrals
by Rodrigo Galindo-Murillo 02 May '18

02 May '18

Hello! I need to do a dihedral scan around the phi/psi angles of alanine dipeptide and to create the input files to later do single point calculations I am using the cmd script: open ../scan.pdb rotation 0 @/serialNumber=7 @/serialNumber=9 rotation 0 180 write format pdb #0 test.pdb I need to use atom serial numbers since the idea is later do the scan with non-canonical peptides that will not work with the native phi/psi descriptions. The script is not modifying any angle but I can see that is generating test.pdb correctly. Could you please orient me if this is the correct set of instructions? Thank you! Rodrigo.

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Changing depth cue to side to side from front to back
by Trevor Harris 02 May '18

02 May '18

Hello, I would like to know if it is possible to change the depth cue to side to side rather than front to back. I don’t want to change the position of the molecule. Is it possible? Thanks, Trevor

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