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I have a simple system where my dyes are placed on the 5' ends of my dsDNA construct. When I try and select the 5' oxygen for dye attachment I am returned the error:
"Position "D". Attachment atom could not be selected. Specified selection defines 0 atoms instead of one: 'chain D and resid 1 and resname DA and name O5' "
followed by
47:syntax error

Copying the above selection algebra and inputting it into pymol returns the correct atom, I tried messing with which symbol I use to represent prime ' or ′, neither seem to work.

I'm guessing this has something to do with the ' symbol being read incorrectly as any other ' marked atoms return the same error while all other atoms work as expected. I can bypass the issue by renaming the atom name to omit the ' symbol.

Add an option to select specific sticky atoms rather than assuming the whole surface to be sticky.

I am trying to use Olga to troubleshoot a smFRET experiment... in the future, I will first use Olga then do the labeling.

Will you please clarify the following:

1. Is the .pdb output file from NMSim the topology input file for Olga?
2. How can I generate the .dcd trajectory file?

I apologize if these questions are naive... I have read your 2020 publication but I am still unclear on the process.

Thanks in advance for any help you can give!

Doing long/computations when determining informative FRET pairs in Olga is currently “risky”, as there is no

1. option to open saved FRET efficiency tables for a search of informative pairs

2. “safety net” that prevents accidental closing of OIga

Adding these two options could significantly improve the workflow / user experience.

Bug in calculation/definition of distance distribution

I loaded a settings file generated with Olga-20190326.
The distance distribution is defined as follows in the .json file:

"Distance distribution": {
    "CT-SNAP": {
        "bin_size": 1,
        "histograms_path": "E:/Users/Hemmen/Olga_win64/histogram_CT-SNAP_inactive.dat",
        "max_distance": 200,
        "min_distance": 0,
        "position1_name": "SNAP-CT",
        "position2_name": "eGFP-IL3-S"

When opening this file in Olga_win64_master-61e08437, the following error occurs:

9:syntax error
Position "unknown". Attachment atom could not be selected. Specified selection defines 0 atoms instead of one: 'resid 0 and name '
error, attachment atom is not found in the stripped molecule
D:/FPSVortrag/Demo/Olga/membrane_5jqh_inactive.pdb#0 simulation unknown failed: empty AV
ERROR! Task is invalid (exception): D:/FPSVortrag/Demo/Olga/membrane_5jqh_inactive.pdb#0 eGFP-CT-SNAP

->Note: Both AV files of SNAP-CT and eGFP-IL3-S and the mean distance & FRET efficiency are calculated without problems.

I then re-prepared the settings file with the new version of Olga:
(1) Immediate calculation is correct
(2) Upon re-opening the structure and loading of just saved settings file, the distribution is recalculated BUT for both labeling positions are IDENTICAL
(3) Inspection of the exported settings file:

"Distance distribution": {
    "eGFP-CT-SNAP copy": {
        "bin_size": 1,
        "histograms_path": "C:/Seidel_Software_2017/Olga_win64/histogram_eGFP-CT-SNAP.dat",
        "max_distance": 200,
        "min_distance": 0,
        "position_name": "eGFP-IL3-S"

(4) giving two positions (either as position1_name or as position_name1) always produces the above stated error.

Let user edit evaluators in-place instead of copy->change->save

Flatten the frames in trajectories

Does Olga support labeling schemes between molecules?

I see two possible approaches to this:

1. load two trajectories into Olga (not sure if it's possible)
2. perform the simulation myself on a larger system (NMSim has a size limit) then load it into Olga

I am attempting to model smFRET experiments with two singly-labeled molecules i.e., sigma70 of E. coli RNA polymerase (donor) and DNA template/non-template (acceptor). Since NMSim doesn't like multiple subunits, I am not sure how I can generate the trajectory file. I realize that this is a loaded question, as MD is an entire field, but maybe you can point me in the right direction?

PositionEvaluator should have a force_linker option. If enabled, program would automatically increase allowed_sphere_radius and ignore the minimum_volume.

Step1: import of all 2620 structures from the selected folder
Step 2: creation of one dye labeling position evaluator
Step 3: addition of multiple labeling positions using the wizard (all possible labeling positions = 184x)
Step 4: creation of one distance evaluator
Step5: addition of multiple distances using the wizard
--> immediately after starting the wizard the program stopped working because it tried to debug itself

(after the repitition of step 1 to step 5 for a second time, there was no problem at all)

version:
Olga v. 2019-12-12-master-9178f0d ubuntu 18.04 x64

description:

1. edit the residue name
   2.enter correct name e.g. "L2_a"
2. This is corrected to "L2_A"
3. the latter description is not recognised

workaround:
edit in file editor

Hi,
Just wonder if you would be able to provide Olga installation for Mac?
Thank you
Mathi