From: Shashidhar Rao (shashidharr_at_gmail.com)
Date: Mon Feb 01 2016 - 16:27:39 CST

Thank you very much, Ashar, for the clarification.

Shashi Rao

On Mon, Feb 1, 2016 at 5:02 PM, Ashar Malik <asharjm_at_gmail.com> wrote:

> 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
>>
>

-- 
Shashidhar N. Rao
3 SERINA DRIVE
PLAINSBORO
NEW JERSEY 08536 USA
shashidharr_at_gmail.com