I have no idea how atomselect got autocorrected to atombox… atomselect (
https://www.ks.uiuc.edu/Research/vmd/vmd-1.7.1/ug/node108.html).
If a reviewer just wants to know at what time things happening in a rendered movie, you could potentially just do this “in post”. Any capable video editing software should be able to just insert labels showing time at different playback-times. As you know the length of the simulation in “real time” and the length of the rendered movie, you could just correlate playback-time to simulation-time and insert appropriate labels, rendering a new movie with these labels included. I would go so far as to claim that some software could likely just edit in a counter somehow, indicating playback time or current frame.
This is roughly the same thing that you are trying to accomplish with VMD, though would probably go a lot faster. Then you would buy yourself some time developing a plugin of which I'd become an early adopter
// Gustaf
> On 26 Feb 2020, at 10:44, Fabian Glaser <fabian.glaser.gmail.com> wrote:
>
> Dear Gustaf,
>
> Thanks a lot, I do present the entire interval movie, but a reviewer asked for the time tick to be added… anyway I would be happy to try your suggestion but I don’t find the Atombox comand not in tcl and not in vmd command list, could you please direct me where to find it?
>
> Thanks!
>
> Best,
>
> Fabian
>
> Fabian Glaser PhD
>
> Bioinformatics Knowledge Unit - BKU
> The Lorry I. Lokey Center for Life Sciences and Engineering
> Technion - Israel Institute of Technology, Haifa, Israel
> Web https://lokey.technion.ac.il/bioinformatic-knowledge-unit/
> Tel +972 (0) 4 8293701
>
>> On 26 Feb 2020, at 10:59, Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
>>
>> Never tried to do this. As I know the time-step I usually present a specific time (at X) or the entire intervall.
>>
>> It might done though I don’t think it would intuitive. I don’t know if you can insert a “custom text label” or something similar at a givet coordinate/place in the simulation box. Atombox has a “frame” feature which returns the animation frame associated with the selection. If you know the “current frame” and the total number of frames, even better also the timestep you could maybe be able to use the “update” feature on a label printing the output of a calculation using the (current frame number)*timestep or (current frame numer)/(total number of frames)*100% to get some indication of time progression.
>>
>> As this feature is not yet available (to the best of my knowledge) and it could be a nice addition for users and developed as a plugin?
>>
>> Best regards
>> // Gustaf
>>
>>
>>> On 26 Feb 2020, at 08:50, Fabian Glaser <fabian.glaser.gmail.com> wrote:
>>>
>>> Come on guys, I tried VMD list, AMBER list, google, etc. Links dont’ work or scripts are not linked.
>>>
>>> Anybody has a script to draw a time bar progression on vmd?
>>>
>>> Highly appreciated,
>>>
>>> Best,
>>>
>>> Fabian
>>>
>>> Fabian Glaser PhD
>>>
>>> Bioinformatics Knowledge Unit - BKU
>>> The Lorry I. Lokey Center for Life Sciences and Engineering
>>> Technion - Israel Institute of Technology, Haifa, Israel
>>> Web https://lokey.technion.ac.il/bioinformatic-knowledge-unit/
>>> Tel +972 (0) 4 8293701
>>>
>>>> On 23 Feb 2020, at 20:19, James Kress <jimkress_58.kressworks.org> wrote:
>>>>
>>>> You might have better luck with your question if you posted it to the VMD discussion group:
>>>>
>>>> vmd-l.ks.uiuc.edu <mailto:vmd-l.ks.uiuc.edu>
>>>>
>>>> James Kress Ph.D., President
>>>> The KressWorks® Institute
>>>> An IRS Approved 501 (c)(3) Charitable, Nonprofit Corporation
>>>> “ENGINEERING THE CURE” ©
>>>> (248) 573-5499
>>>>
>>>> Learn More and Donate At:
>>>> Website: http://www.kressworks.org <http://www.kressworks.org/>
>>>> Facebook: https://www.facebook.com/KressWorks.Institute/ <https://www.facebook.com/KressWorks.Institute/>
>>>>
>>>> Confidentiality Notice | This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or proprietary information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, immediately contact the sender by reply e-mail and destroy all copies of the original message.
>>>>
>>>> -----Original Message-----
>>>> From: Fabian Glaser <fabian.glaser.gmail.com <mailto:fabian.glaser.gmail.com>>
>>>> Sent: Sunday, February 23, 2020 10:12 AM
>>>> To: AMBER Mailing List <amber.ambermd.org <mailto:amber.ambermd.org>>
>>>> Subject: [AMBER] vmd progress time
>>>>
>>>> Hi,
>>>>
>>>> I would like to ask a maybe trivial question to this list, to which I cannot find an easy solution… I would like to add the time for each frame in a vmd trajectory movie, I found some information but not a clear description of how to do that, can somebody please send me a pointer to a good tutorial?
>>>>
>>>> Thanks and sorry to bother with this,
>>>>
>>>> Best,
>>>>
>>>> Fabian
>>>>
>>>> Fabian Glaser PhD
>>>>
>>>> Bioinformatics Knowledge Unit - BKU
>>>> The Lorry I. Lokey Center for Life Sciences and Engineering Technion - Israel Institute of Technology, Haifa, Israel Web https://lokey.technion.ac.il/bioinformatic-knowledge-unit/ <https://lokey.technion.ac.il/bioinformatic-knowledge-unit/> <https://lokey.technion.ac.il/bioinformatic-knowledge-unit/ <https://lokey.technion.ac.il/bioinformatic-knowledge-unit/>>
>>>> Tel +972 (0) 4 8293701
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org <mailto:AMBER.ambermd.org>
>>>> http://lists.ambermd.org/mailman/listinfo/amber <http://lists.ambermd.org/mailman/listinfo/amber>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Feb 26 2020 - 03:00:02 PST
