From: Adrian Koh (kohsj_at_ihpc.a-star.edu.sg)
Date: Tue Jul 04 2006 - 23:07:57 CDT

Hi John,

Thanks for your reply. Please pardon me if this is a silly question...
But I kept seeing replies suggesting a series of commands to achieve an
action. How do I get it done in VMD (Windows version)? Do I type in
the commands in a text file, save it as script.vmd, and then do "File
--> Load State" in the VMD Main window?

Could similar actions be achieved by just using the available forms in
the VMD Main window?

Finally, if the name I intended to use for renaming do not exist in the
trajectory file in the first place, could a new name be created and then
renamed in a portion of the molecule? For instance, if my original
trajectory files only consists of names "Pt" and "Frz", would it be
possible for me to rename part of the molecule to "Ni"? (this could be
already in your reply but apparently, I did not quite understand the
script :)).

Thanks!

Best Regards,
Adrian.

John Stone wrote:
> Adrian,
> Yes, if you rename any atom, it is immediately renamed for all frames,
> since the atom names are only stored once-per-molecule, not once-per-frame
> currently. e.g.:
> set sel [atomselect top all]
> set oldnames [lsort -unique [$sel get name]]
>
> set casel [atomselect top "name CA"]
> $casel set name foo
> set newnames [lsort -unique [$sel get name]]
> puts "oldnames: $oldnames"
> puts "newnames: $newnames"
>
> John
>
> On Tue, Jul 04, 2006 at 02:44:28PM +0800, Adrian Koh wrote:
>
>> Hi,
>>
>> I have with me, an .xyz trajectory file containing two atom names "Pt"
>> and "Frz", containing 250 frames. Would it be possible to rename a
>> selected region of the molecule (for instance, sqrt(sqr(x)+sqr(y))>10)
>> to another name say "Cu", at frame 1, which would then apply to all
>> other frames?
>>
>> Thanks :).
>>
>>
>> Best Regards,
>> Adrian.
>>
>>
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