VMD-L Mailing List

From: Ioana Cozmuta (icozmuta_at_mail.arc.nasa.gov)
Date: Wed Mar 15 2006 - 23:33:46 CST

Hi John,

Thanks for the suggestion with the macro, it works fine both in
text/graphical mode.

Ioana

John Stone wrote:
> Ioana,
> Just to be clear, does your selection text max out in a VMD GUI window
> input field somewhere, or is this happening from a Tcl or Python script?
> I'd try something like this if you're having troubles otherwise:
>
> atomselect macro hugesel { \
> ((nucleic or resname RA5 or resname RA3) or (protein and same residue as \
> within 2 of (protein and resid 11 23 35 47 59 71 83)) or ((resname SPM and \
> same residue as within 2 of (nucleic or resname RA5 or resname RA3)) and \
> (resname SPM and same residue as within 3 of (protein and same residue as \
> within 2 of (protein and resid 11 23 35 47 59 71 83))))) \
> }
>
> Once youv'e got a macro defined, you can use that in the GUI windows
> and in your scripts like this:
> set sel [atomselect top "hugesel"]
>
> Try that and let me know if you still have any trouble.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
>
> On Tue, Mar 14, 2006 at 04:17:46PM -0800, Ioana Cozmuta wrote:
>
>> Hi John,
>>
>> This is what I want to select from my entire structure:
>> the DNA strand
>> the protein aminoacids 2A away from certain numbered residues
>> the common water molecules within 2 of protein and DNA
>>
>> I came up with the following that I just cant use in a script. I want
>> the selection below to be written out from several frames of a
>> trajectory. That's why I want to define the selection only once and then
>> use the $sel writexyz test.xyz command to write it out.
>>
>> ((nucleic or resname RA5 or resname RA3) or (protein and same residue as
>> within 2 of (protein and resid 11 23 35 47 59 71 83)) or ((resname SPM and
>> same residue as within 2 of (nucleic or resname RA5 or resname RA3)) and
>> (resname SPM and same residue as within 3 of (protein and same residue as
>> within 2 of (protein and resid 11 23 35 47 59 71 83)))))
>>
>> Any help would be greatly appreciated.
>> Thanks,
>> Ioana
>>
>> John Stone wrote:
>>
>>> Ioana,
>>> Have you tried using atom selection macros to help make your selection
>>> text a little more compact?
>>>
>>> John Stone
>>> vmd_at_ks.uiuc.edu
>>>
>>> On Tue, Mar 14, 2006 at 04:00:27PM -0800, Ioana Cozmuta wrote:
>>>
>>>
>>>> Hi,
>>>>
>>>> I have a very long selection that I want to define however it seems that
>>>> I reach the max number of characters allocated by default for a
>>>> selection. I could split the selection in smaller parts but I don't know
>>>> how to write all of them after that in the same output file. Is there a
>>>> way to 'append' information into an output file?
>>>>
>>>>
>>>> Thanks,
>>>> ioana
>>>>
>>>> --
>>>> Ioana Cozmuta, Ph.D
>>>> Eloret Corporation
>>>> NASA Ames Research Center
>>>> Mail Stop 230-3
>>>> Moffett Field, CA 94035
>>>> phone (650) 604-0993
>>>> e-mail: icozmuta_at_mail.arc.nasa.gov
>>>> http://people.nas.nasa.gov/~ioana/
>>>>
>>>>
>>>
>>>
>> --
>> Ioana Cozmuta, Ph.D
>> Eloret Corporation
>> NASA Ames Research Center
>> Mail Stop 230-3
>> Moffett Field, CA 94035
>> phone (650) 604-0993
>> e-mail: icozmuta_at_mail.arc.nasa.gov
>> http://people.nas.nasa.gov/~ioana/
>>
>
> 

-- 
Ioana Cozmuta, Ph.D
Eloret Corporation
NASA Ames Research Center
Mail Stop 230-3
Moffett Field, CA  94035
phone (650) 604-0993
e-mail: icozmuta_at_mail.arc.nasa.gov
http://people.nas.nasa.gov/~ioana/