VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Thu May 26 2016 - 15:35:18 CDT

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
> <mailto: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 <mailto: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 <mailto: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 <mailto: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 <tel: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=>
>>>
>>>
>>
>>
>
>