VMD-L Mailing List

From: Lisa Perez (mouse_at_mail.chem.tamu.edu)
Date: Wed Dec 22 2010 - 11:43:28 CST

Thank you. I did find the order option for measure fit (documented) in the vmd manual. :) I should have put "automated" instead of "easy way" to get the vmd measure fit to use the order I give it... I did write a little script to find the order parameter which may be of use to someone (need to use a newer version of vmd which has tcl that supports the -indices flag):

# need to find the transormation matrix to get the ordering correct (vmd reorders by increasing index)
# this routine is for 4 atoms (specified by serial number) used in the rmsd but can be modified for more.
       set ref {163 164 141 142}
       set other { 13 29 6 16 }
       set indexref [lsort -integer -increasing -indices $ref]
       set indexother [lsort -integer -increasing -indices $other]
       set reorder [list]
       for {set i 0} { $i < 4 } { incr i 1 } {
         for {set j 0} { $j < 4 } { incr j 1 } {
          if { [ lindex $indexref $i ] == [ lindex $indexother $j ] } { lappend reorder $j }
          }
         }

I do have another question... I noticed that in the documentation, the order option is not listed for measure rmsd I have tried both and get slightly different values but the results is still far too large (should be around 0.5 and I am getting 3.6) I am calling the measure rmsd after I use my transformation matrix to overlay the 2 molecules. The overlay looks good but the rmsd value does not...

Can I get the rmsd value directly from the measure fit command? I manually reordered the atoms of interest and the rmsd command gives the correct value... Is there another workaround or have I don't something wrong in the measure rmsd command?
 
set trans_matrix [measure fit $other_frame $ref_frame order "$reorder"]
set move_sel [atomselect 0 "all"]
$move_sel move $trans_matrix
set rmsdval [measure rmsd $other_frame $ref_frame order "$reorder"]

As I mentioned, the above gives a good visual overlay but a bad rmsd value...

Thank you,

Lisa M. Pérez, Ph.D.

Texas A&M University
Laboratory for Molecular Simulation, Manager
Graduate Faculty
http://lms.chem.tamu.edu/

Department of Chemistry
580 Ross Street
College Station, TX 77842

Chemistry Bldg. RM. 2109
Ofc: (979) 845-9384
Fax: (979) 845-2971

On Dec 21, 2010, at 9:40 PM, JC Gumbart wrote:

> Indeed, there is a way to do this with a (still undocumented?) order parameter. See Leo's post here: http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/10172.html
>
>
> On Dec 21, 2010, at 2:38 PM, Lisa Perez wrote:
>
>>
>> I just discovered that it is an ordering problem... Has anyone discovered an "easy way" to get vmd measure fit to use the order you give it instead of numerical order?
>>
>> Sincerely,
>>
>> Lisa M. Pérez, Ph.D.
>>
>> Texas A&M University
>> Laboratory for Molecular Simulation, Manager
>> Graduate Faculty
>> http://lms.chem.tamu.edu/
>>
>> Department of Chemistry
>> 580 Ross Street
>> College Station, TX 77842
>>
>> Chemistry Bldg. RM. 2109
>> Ofc: (979) 845-9384
>> Fax: (979) 845-2971
>>
>>
>>
>> On Dec 21, 2010, at 1:30 PM, Lisa Perez wrote:
>>
>>>
>>> I am trying to rmsd a small molecule against a small protein using a subset of 4 atoms and am getting odd results. If I remove all of the 4 atoms of interest from the pdb files and proceed with the rmsd fit, I get expected results but, if the other atoms are present, I get poor results. Here is the small script that I am using to rmsd my 2 molecules (molid 0 is my small molecule and molid 1 is my small protein):
>>>
>>> set ref_frame [ atomselect 1 "serial 163 164 141 142" ]
>>> set other_frame [ atomselect 0 "serial 13 29 6 16" ]
>>> set trans_matrix [measure fit $other_frame $ref_frame]
>>> set move_sel [atomselect 0 "all"]
>>> $move_sel move $trans_matrix
>>> set rmsdval [measure rmsd $other_frame $ref_frame]
>>> puts $rmsdval
>>>
>>> I have also tried using index instead of serial number. 1 atom overlays perfectly... more than 1 does not.
>>>
>>> Any comments and/or help would be greatly appreciated.
>>>
>>> Sincerely,
>>>
>>> Lisa M. Pérez, Ph.D.
>>>
>>> Texas A&M University
>>> Laboratory for Molecular Simulation, Manager
>>> Graduate Faculty
>>> http://lms.chem.tamu.edu/
>>>
>>> Department of Chemistry
>>> 580 Ross Street
>>> College Station, TX 77842
>>>
>>> Chemistry Bldg. RM. 2109
>>> Ofc: (979) 845-9384
>>> Fax: (979) 845-2971
>>>
>>>
>>>
>>
>