VMD-L Mailing List

From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Fri May 27 2016 - 14:03:47 CDT

Hi Josh,

Thanks for the clarifications. Really appreciate this.

Chitrak.

On Thu, May 26, 2016 at 4:35 PM, Josh Vermaas <vermaas2_at_illinois.edu> wrote:

> No, you only need the $sel frame $i and the $sel update (and you only need
> the second one if the selected atoms might change between frames). I think
> the molinfo top set frame command just moves around which is the displayed
> frame. You are working with an atomselection, which can (and does) grab a
> timestep independently from the displayed timestep.
> -Josh
>
>
> On 05/26/2016 02:31 PM, Chitrak Gupta wrote:
>
> Hi Josh,
>
> I have a follow-up question. If I am doing "$sel frame $i" and "$sel
> update", do I still need to do "molinfo top set frame $i"? What I am seeing
> is that the results differ based on whether or not I put this molinfo
> command. My understanding was that the "$sel frame $i" and "$sel update"
> takes care of everything, is that not the case?
>
> On Thu, May 26, 2016 at 2:14 PM, Josh Vermaas <vermaas2_at_illinois.edu>
> wrote:
>
>> Well, I'm not actually sure what the default behavior is for which frame
>> gets picked if its not specified in the selection command. Is it the
>> current frame? Is it the last frame? Is it the first frame? If it picks the
>> current frame, the two loops should give identical results. Since they
>> don't, it must be one of the other two options, and that lesson must be the
>> reason why I've only ever seen it done the $sel frame then $sel update way.
>>
>> -Josh
>>
>>
>> On 05/26/2016 12:11 PM, Chitrak Gupta wrote:
>>
>> Hi Josh,
>>
>> Thanks a lot for the explanation. Could you clarify a bit on what you
>> meant by "doesn't depend on any default behavior for which frame gets
>> selected"?
>>
>> On Thu, May 26, 2016 at 7:46 AM, Josh Vermaas < <vermaas2_at_illinois.edu>
>> vermaas2_at_illinois.edu> wrote:
>>
>>> Hi Chitrak,
>>>
>>> The first one would be the one I recommend, as its the loop form I tend
>>> to use. It doesn't need the $sel delete statement to avoid leaking memory,
>>> and doesn't depend on any default behavior for which frame gets selected.
>>> The second loop could have something like:
>>>
>>> set sel [atomselect top "?? condition ??" frame $i]
>>>
>>> as well, which would technically make for shorter code, but in this case
>>> it might be a useful way of double checking that the second loop variant
>>> gives incorrect results.
>>>
>>> -Josh
>>>
>>>
>>> On 05/25/2016 09:05 PM, Chitrak Gupta wrote:
>>>
>>> Oops, don't know how that happened. Thanks for pointing this out.
>>>
>>> So here is my question. What is the difference between the following two
>>> ways?
>>>
>>> ...
>>> set sel [atomselect top "?? condition ??"]
>>> for {set i 0} {$i < $nf} {incr i 1} {
>>> $sel frame $i
>>> $sel update
>>> ...
>>> }
>>>
>>> As opposed to
>>>
>>> ...
>>> for {set i 0} {$i < $nf} {incr i 1} {
>>> molinfo top set frame $i
>>> set sel [atomselect top "?? condition ??"]
>>> ...
>>> }
>>>
>>>
>>> I am trying to look for choline Nitrogens within a specific distance of
>>> aromatic side chains, and I am getting different results based on these two
>>> methods.
>>>
>>>
>>> Regards,
>>> Chitrak
>>>
>>> On Wed, May 25, 2016 at 10:52 PM, John Stone < <johns_at_ks.uiuc.edu>
>>> johns_at_ks.uiuc.edu> wrote:
>>>
>>>> I'm afraid your email appears to have been truncated, and thus
>>>> nobody will be able to answer your question.
>>>>
>>>> Cheers,
>>>> John Stone
>>>> vmd_at_ks.uiuc.edu
>>>>
>>>> On Wed, May 25, 2016 at 02:07:49PM -0400, Chitrak Gupta wrote:
>>>> > Hello,
>>>> >
>>>> > I have this general question. When scripting in VMD, what is the
>>>> difference
>>>> > between the following two ways?
>>>>
>>>> --
>>>> NIH Center for Macromolecular Modeling and Bioinformatics
>>>> Beckman Institute for Advanced Science and Technology
>>>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>>>> http://www.ks.uiuc.edu/~johns/
>>>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ks.uiuc.edu_-7Ejohns_&d=CwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=zFfoK61upjM5BwyoRAsX8dLq7rwWm8aw7r7dqtjgcCE&m=lFWIxr7A6D2G9K7iKkjOW0Og6DvNtk1VrQUEexIBve8&s=zQmuF6cr_nJ4WNP7OSRtWpQ-6XTHlDinPHN6iCm590Y&e=>
>>>> Phone: 217-244-3349
>>>> http://www.ks.uiuc.edu/Research/vmd/
>>>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ks.uiuc.edu_Research_vmd_&d=CwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=zFfoK61upjM5BwyoRAsX8dLq7rwWm8aw7r7dqtjgcCE&m=lFWIxr7A6D2G9K7iKkjOW0Og6DvNtk1VrQUEexIBve8&s=ZM-r0a7aSdcfVGOTtAdCGZ8QI9-AJMnw_m-NFg53FMI&e=>
>>>>
>>>
>>>
>>>
>>
>>
>
>