VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Mon Feb 01 2016 - 16:02:49 CST

>From the command line you can't run with this sort of syntaxing. Put the
command in a file. And run the file from the command line like I explained
before. Alternatively, load the molecule into VMD and run the command you
want in the TKconsole.
On Feb 2, 2016 9:25 AM, "Shashidhar Rao" <shashidharr_at_gmail.com> wrote:

> Thank you very much, Ashar.
>
> Before venturing on modifying the script to adjust the "atomselect"
> command in the first of the script, I tried to make that command work on
> the vmd command line by typing:
>
> atomselect 1 LEU74.CA [I am hoping to select the CA atom in Leu74 of
> molecule ID 1]
>
> I obtained the following error message:
>
> ERROR) Bad character:46:.
> ERROR) syntax error
> atomselect: can not parse selection text: LEU74.CA
>
> Not sure what is going wrong. Any guidance will be very much appreciated.
>
> Thanks,
> Shashi Rao
>
> On Mon, Feb 1, 2016 at 12:52 PM, Ashar Malik <asharjm_at_gmail.com> wrote:
>
>> You will save this in a text parsable file maybe one exclusively end in
>> .tcl and run it using the TKconsole included in VMD. Alternatively from the
>> command line using
>>
>> vmd -dispdev text -eofexit < script.tcl
>>
>> Cant read the script but i think i programmed $id to hold the molecule
>> ID. To change selection of atom selected in the reference molecule you need
>> to adjust the atomselect command in the first part of the script.
>> On Feb 2, 2016 5:57 AM, "Shashidhar Rao" <shashidharr_at_gmail.com> wrote:
>>
>>> Hello Ashar,
>>>
>>> Many thanks for sending the script. However, I am not entirely clear on
>>> how I will use this script (which I assume will be executed from the VMD
>>> command line). Will I replace the $id by the atom number or is there a way
>>> of denoting it as for example the C-alpha atom of residue 74 (resid 74 and
>>> atom ca)?
>>>
>>> Thank you again for your efforts in putting together the script.
>>>
>>> Shashi Rao
>>>
>>> On Sun, Jan 31, 2016 at 12:26 AM, Ashar Malik <asharjm_at_gmail.com> wrote:
>>>
>>>> I am not sure if there exists a direct selection command to go across
>>>> molecules. It may exist so it maybe helpful to wait, however I have put
>>>> together a small script which should pretty much do what you asked.
>>>>
>>>> Assuming you have two molecules loaded into VMD with ID 0 and 1.
>>>> Use the following code.
>>>>
>>>> set id_ 0 ;#select reference molecules ID
>>>> set s0 [atomselect $id_ "index 1" ] ;#select 1 atom from this molecule
>>>> which is your reference
>>>> set ref_ [lindex [$s0 get {x y z}] 0] ;#grab the x,y and z coordinates
>>>>
>>>> #the additional lindex command in the last line is a sanity check to
>>>> ensure 1 atom is selected.
>>>>
>>>> set id_ 1 ;#select next molecules ID
>>>> set s1 [atomselect $id_ all] ;#select everything in this new molecule
>>>> set tar_ [$s1 get {x y z}] ;#get atom coordinates of everything in as
>>>> list
>>>>
>>>> set n_o_A [llength $tar_] ;#get number of atoms for the for loop
>>>>
>>>> for {set i 0} {$i < $n_o_A} {incr i} { ;# loop over all atoms in
>>>> selection to compare with reference
>>>> set temp [lindex $tar_ $i] ;# store current atom in a temp variable
>>>> set dist_ [vecdist $ref_ $temp] ;# get distance between current
>>>> atom and reference
>>>> if {$dist_ < 5} {
>>>> lappend tar_atoms [expr $i+1] ;# if distance below cut off save index
>>>> of atom from current molecule.
>>>> # note that in the previous line $i is the index of the atom in the
>>>> list which is probably off by 1 -- i just added 1 to it to fix this
>>>> # and haven't tested it. Be careful when using it.
>>>> }
>>>> }
>>>>
>>>> When you run this code -- a list of index of atoms in molecule id 1
>>>> will be generated which are within a cutoff (5A) of the reference atom in
>>>> molecule id 0. This is basically a template. You could have the lower part
>>>> of this in a for loop and run the same changing the "id_" variable in each
>>>> iteration for the total number of molecules you have. For that you may also
>>>> have to log the molecule id along with target atoms or you might loose the
>>>> distinction in the target atoms identified as to which molecule do they
>>>> originate from.
>>>>
>>>> If you are unable to log the molID along with the target atoms
>>>> identified, post again and you will get a reply.
>>>>
>>>> This code is not optimized - meaning thre might (probably does) exist a
>>>> better way of accomplishing this.
>>>>
>>>> Good luck and hope this helps.
>>>>
>>>> Best,
>>>> /A
>>>>
>>>> On Sat, Jan 30, 2016 at 5:45 AM, Shashidhar Rao <shashidharr_at_gmail.com>
>>>> wrote:
>>>>
>>>>> Hello VMD Gurus,
>>>>>
>>>>> I am trying to find a way by which I can select residues/atoms within
>>>>> molecule ID 1 which are within 5 angstroms of a given residue in molecule
>>>>> ID 2. Thus, my selection is across multiple molecules. as an extension, I
>>>>> may have 10 molecule IDs and I would like to select all the residues within
>>>>> 5 angstroms of a given residue in molecule ID 2 in all the remaining
>>>>> molecule IDs.
>>>>>
>>>>> I need this recipe to identify a set of water molecules simulated
>>>>> separately in a PDB file using the PDB structure of a solute molecule which
>>>>> is placed in the context of the water molecules.
>>>>>
>>>>> thanks for your help
>>>>>
>>>>> --
>>>>> Shashidhar N. Rao
>>>>> 3 SERINA DRIVE
>>>>> PLAINSBORO
>>>>> NEW JERSEY 08536 USA
>>>>>
>>>>> shashidharr_at_gmail.com
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Best,
>>>> /A
>>>>
>>>
>>>
>>>
>>> --
>>> Shashidhar N. Rao
>>> 3 SERINA DRIVE
>>> PLAINSBORO
>>> NEW JERSEY 08536 USA
>>>
>>> shashidharr_at_gmail.com
>>>
>>
>
>
> --
> Shashidhar N. Rao
> 3 SERINA DRIVE
> PLAINSBORO
> NEW JERSEY 08536 USA
>
> shashidharr_at_gmail.com
>