VMD-L Mailing List

From: JeJoon Yeon (sonicturbulent_at_gmail.com)
Date: Wed May 13 2015 - 21:30:47 CDT

//Maxim

Thanks. I will use this for movie making, and obviously I need to read more
about proc command. But I also need to print out 'masked xyz result' for
the analysis.

// Josh

Thank you.

But can I draw RDF or do other analysis for original Si and 'user 1 Si' and
'user 5 Si'? I'm doing this masking not only for movie, but also for the
analysis among same type of atoms. (That is the main reason behind my
'masking alchemy', and that is why I prefer xyz file format) I have now
idea which file format can be chosen as output file for tags like 'user 1'.
and I don't know how to draw RDF or do other analysis those format (since
most of my post processing codes are based on xyz file format). Could you
help me to stick with the xyz format for this masking?

Thanks

2015-05-13 21:51 GMT-04:00 Josh Vermaas <vermaas2_at_illinois.edu>:

> Ahh. Don't do it with alchemy. Tag the user field instead, as that is
> stored per frame. Then you can easily pick out different atoms based on
> their "user" value.
>
> set a [atomselect top "index < 1338 and name Si and y>9 and within 5 of
> atom O]
> set t [atomselect top all]
>
> for { set i 0 } { $i < [molinfo top get numframes] } { incr i } {
> $t frame $i
> $t set user 0
> $a frame $i ; #changes the frame the selection will be based on
> $a update ; #Rechecks that its selecting the right stuff
> $a set user 1
> }
>
> I think then you can output your trajectory into a fileformat that stores
> the user field. Which is currently none of them, but for movie making this
> will totally work.
>
> -Josh
>
>
> On 05/13/2015 08:35 PM, JeJoon Yeon wrote:
>
> Thanks Josh,
>
> I checked with the smaller size file, and it seems the each frames
> converted in right manner. Thanks. But I need a single xyz file of all
> converted frames, not the 100,000 number of converted single frame xyz
> files. It will cost heavy hard disk drive and long time to merge them to
> single xyz file. Are there anyway to print out the result as single xyz
> file?
>
> It is just for post processing and visualization. I want to "mask" some
> specific atoms with different colors and size (=different atoms) based on
> my criteria of interest, which make them easily recognized from animation
> or picture. In addition, I need to analyze those 'different type of Si
> atoms', such as RDF and angular distribution or others. So, this 'masking
> using alchemy' is a really good skill to analyze the result xyz. (Sometimes
> I even masked O atoms using 10 different atoms, based on their 10 different
> criteria = positions and vicinity to other specific atoms)
>
> I can do this work with fortran or python. However, sometimes I feel
> really convenient to use some options of VMD-tcl's 'atomselect' command, to
> target and differentiate the atoms of interest. Because it is easy to
> understand and straightforward to classify and convert the target atom with
> "atomselect". I don't need to write subroutines or more code lines. That is
> why I try to do this in VMD-tcl. If you could recommend me the other good
> and easy 'masking alchemy' tool for visualization, RDF and other analysis,
> I will happily accept your suggestion.
>
> Thank you
>
>
> 2015-05-13 20:00 GMT-04:00 Josh Vermaas <vermaas2_at_illinois.edu>:
>
>> My understanding of how VMD works says that it cannot be done in a
>> single xyz file. Name, type, etc, are not allowed to vary per frame (which
>> works for 99.99% of all use cases). You want to let the identity of the
>> atoms vary, which is weird, and needs a weird workaround by outputing each
>> frame into a separate file.
>>
>> set a [atomselect top "index < 1338 and name Si and y>9 and within 5 of
>> atom O]
>> set t [atomselect top all]
>>
>> for { set i 0 } { $i < [molinfo top get numframes] } { incr i } {
>> $a frame $i ; #changes the frame the selection will be based on
>> $a update ; #Rechecks that its selecting the right stuff
>> $a set name C
>> $a set type C
>> $a set element C
>> $t frame $i
>> $t writexyz frame$i.xyz ; #You will get a ton of individual frames where
>> the Si atoms will be renamed.
>> #Reset everything to Si for the next frame
>> $a set name Si
>> $a set type Si
>> $a set element Si
>> }
>>
>> This will work, but I really wanna know why on earth this is a reasonable
>> thing to do. Silicon doesn't magically become carbon, which is why VMD
>> assumes that atom identities are static.
>>
>> -Josh Vermaas
>>
>>
>> On 05/13/2015 06:48 PM, JeJoon Yeon wrote:
>>
>> Yes, I want to do that "alchemy" using VMD. Swapping Si atoms to C atom,
>> under specific conditions I want. I can do that job without any problem for
>> a single frame. But what I really want to do is, do that "alchemy" for all
>> frames of xyz file. (There are 100000 frame inside my file) Unfortunately,
>> using my attempts, atoms didn't swapped, or incorrectly swapped.
>>
>> I think your mention "$a points always last frame in atomselection" is
>> the key. Because, all my attempts finished with the weird results: all
>> frame's target Si atoms were not properly swapped to C. Instead, the
>> swapped Si atoms during all frames, are the target Si atoms of the last
>> frame. As a result, my codes only properly swapped the last frame's target
>> Si atoms. To me, it looks like "VMD swapped last frame's target Si atoms to
>> C atom, then track those atom all the way to first frame"
>>
>> I put
>>
>> set a [atomselect top "index < 1338 and name Si and y>9 and within 5 of
>> atom O]
>> set all [atomselect top all]
>>
>> these two lines out of the for-loop, but the results are the same. Only
>> the last frame's target Si atoms were swapped properly. Others are just
>> traceback of the last frame. For example, in the first frame of result
>> file, 'some Si atoms' finished "alchemy", but they are not the target Si,
>> instead they are trace back of last frame's target Si atom. I think this is
>> because $a selected as the last frame, so VMD swapped all frame, but it is
>> only based on the position of last frame's information. How can I escape
>> from this situation?
>>
>>
>>
>> 2015-05-13 17:29 GMT-04:00 Josh Vermaas <vermaas2_at_illinois.edu>:
>>
>>> That isn't a complete for loop (should have a closing brace.). Beyond
>>> that, atomselections should happen outside the loop if at all possible.
>>> Atomselections within a loop need to be deleted to free up VMD internal
>>> memory, as they aren't *just* tcl objects, but also create datastructures
>>> within VMD that are not automatically deleted when the tcl atomselection
>>> object goes out of scope. What exactly are you trying to do? The way I've
>>> interpreted the code, you have a bunch of Silicon atoms, but if they are
>>> close enough to an oxygen, you want them to be a carbon instead (alchemy!
>>> VMD doesn't like alchemy), and only for that frame. Is that correct? Now
>>> you've muddled it a bit, since your $all variable is never called outside
>>> of changing its frame, which does nothing, and $a points to an
>>> atomselection that is always at the last frame, so I can't read your
>>> intent. Could you perhaps elaborate on what problem you are trying to
>>> solve?
>>>
>>>
>>> On 05/13/2015 04:22 PM, JeJoon Yeon wrote:
>>>
>>> There was mistake in previous email. My for-loop looks like
>>>
>>> for { set i 0 } { $i <= $nf } { incr i } {
>>> set a [atomselect top "index < 1338 and name Si and y>9 and within 5
>>> of atom O]
>>> set all [atomselect top all]
>>> $all frame $i
>>> $a set name C
>>> $a set type C
>>> $a set element C
>>>
>>> But I still think my way of writing is wrong...
>>>
>>> 2015-05-13 14:44 GMT-04:00 Josh Vermaas <vermaas2_at_illinois.edu>:
>>>
>>>> Also, you need to make sure your for loop is doing this sanely. Here is
>>>> how I'd approach it:
>>>>
>>>> set a [atomselect top "index < 1338 and name Si and y>9 and within 5 of
>>>> atom O]
>>>> set t [atomselect top all]
>>>>
>>>> for { set i 0 } { $i < [molinfo top get numframes] } { incr i } {
>>>>
>>>> $a frame $i ; #changes the frame the selection will be based on
>>>> $a update ; #Rechecks that its selecting the right stuff
>>>> $a set name C
>>>> $a set type C
>>>> $a set element C
>>>>
>>>> }
>>>>
>>>> However name, type, and element are not per-frame fields, so you do
>>>> know that you'll be changing it for all of them, right?
>>>> -Josh
>>>>
>>>>
>>>> On 05/13/2015 01:07 PM, Maxim Belkin wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> Have you tried the following?
>>>>>
>>>>> animate write xyz output.xyz beg 0 end -1 waitfor all
>>>>>
>>>>> Maxim
>>>>>
>>>>>
>>>>> On May 13, 2015, at 12:53 PM, JeJoon Yeon <sonicturbulent_at_gmail.com>
>>>>>> wrote:
>>>>>>
>>>>>> Hello all
>>>>>>
>>>>>> I can swap specific atoms for a single frame xyz only. Like
>>>>>>
>>>>>> mol new test.xyz type xyz waitfor all
>>>>>> set a [atomselect top "index < 1338 and name Si and y>9 and within 5
>>>>>> of atom O]
>>>>>> $a set name C
>>>>>> $a set type C
>>>>>> $a set element C
>>>>>> set t [atomselect top all]
>>>>>> $t writexyz swapped.xyz
>>>>>>
>>>>>>
>>>>>> But how can I do this with multiple frame? I tried to use for loop but
>>>>>> 1) Sometimes it causes error
>>>>>> 2) Sometimes it swaps the specific atoms for all frames, but the
>>>>>> criteria is based on only last frame's xyz position.
>>>>>>
>>>>>> So I don't know what to do anymore. Can anyone help or modify that
>>>>>> single frame code to work for multiple frames? Is this coming from read /
>>>>>> write problem?
>>>>>>
>>>>>> Thanks
>>>>>>
>>>>>> Best,
>>>>>>
>>>>>
>>>>>
>>>>
>>>
>>>
>>
>>
>
>