VMD-L Mailing List

From: Josh Ward (wardjm_at_purdue.edu)
Date: Tue Mar 29 2005 - 09:36:39 CST

I initially had that idea as well, but when I replaced "alpha" with
"name CA" the problem persists. I'm still confused.

Main console display active (Tcl8.4.1 / Tk8.4.1)
(martin) 37 % set a0 [atomselect 0 "name CA"]
atomselect0
>Main< (martin) 38 % set a1 [atomselect 1 "name CA"]
atomselect1
>Main< (martin) 39 % set a2 [atomselect 2 "name CA"]
atomselect2
>Main< (martin) 40 % set a3 [atomselect 3 "name CA"]
atomselect3
>Main< (martin) 41 % set a4 [atomselect 4 "name CA"]
atomselect4
>Main< (martin) 42 % llength [$a0 get index]
106
>Main< (martin) 43 % llength [$a1 get index]
106
>Main< (martin) 44 % llength [$a2 get index]
46
>Main< (martin) 45 % llength [$a3 get index]
106
>Main< (martin) 46 % llength [$a4 get index]
46
>Main< (martin) 47 %

John Stone wrote:

>Josh,
> The atom selection keyword "alpha" depends on the secondary structure.
>VMD gets the secondary structure for a molecule by running the STRIDE
>program, which calculates it heuristically, based on the 3-D structure.
>It is quite possible that the reason you're having trouble is because
>STRIDE is assigning a differing number of atoms as alpha helices in the
>various structures you've got. You can see that's what's going on by
>comparing the atom counts as you did below. Given this result, I'd
>suggest changing your alignment script to use a selection such as
>"name CA" or something of that sort. Otherwise, another way to solve
>the problem is to extract the list of atom indices from the "alpha"
>selection for your zeroth molecule, make a new atom selection macro
>from that list of indices, and then use the macro to select the same
>set of atoms for all molecules, and that will solve your problem.
>The issue here is just that when you used the "alpha" selection, you're
>relying on STRIDE to make exactly the same secondary structure prediction
>for all of your molecules, which as you can see it won't necessarily do.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
>
>On Thu, Mar 24, 2005 at 04:49:44PM -0500, Josh Ward wrote:
>
>
>>I think I have found a MOLID-dependent bug in atomselection using TCL.
>>I'm running VMD 1.8.3 on Debian Sarge Linux with TCL 8.4.1 / TK8.4.1
>>
>>I have three structures of the same protein in charmm crd format that I
>>am trying to align. Each loaded seperately - result = molids 0, 1, and
>>2 are used. When I tried to align, molid 0 and molid 1 align without
>>problem, but tcl complains that the number of selected atoms differes
>>between 0 and 2.
>>
>>After double checking the integrety of the crd file, I loaded a single
>>file multiple times and tried to realign, getting the same error
>>result. Loading the same file 5 times and trying to align, I got the
>>following output in the TK console:
>>
>>Main console display active (Tcl8.4.1 / Tk8.4.1)
>>37 % set a0 [atomselect 0 "alpha"]
>>atomselect0
>>
>>
>>>Main< 38 % set a1 [atomselect 1 "alpha"]
>>>
>>>
>>atomselect1
>>
>>
>>>Main< 39 % set a2 [atomselect 2 "alpha"]
>>>
>>>
>>atomselect2
>>
>>
>>>Main< 40 % set a3 [atomselect 3 "alpha"]
>>>
>>>
>>atomselect3
>>
>>
>>>Main< 41 % set a4 [atomselect 4 "alpha"]
>>>
>>>
>>atomselect4
>>
>>
>>>Main< 42 % llength [$a0 get index]
>>>
>>>
>>106
>>
>>
>>>Main< 43 % llength [$a1 get index]
>>>
>>>
>>106
>>
>>
>>>Main< 44 % llength [$a2 get index]
>>>
>>>
>>43
>>
>>
>>>Main< 45 % llength [$a3 get index]
>>>
>>>
>>106
>>
>>
>>>Main< 46 % llength [$a4 get index]
>>>
>>>
>>43
>>
>>
>>>Main< 47 %
>>>
>>>
>>This alignment procedure worked until we upgraded to 1.8.3 I'm not sure
>>if the bug might be in TCL. It won't align when I downgrade to 1.8.2
>>either.
>>
>>Thanks in advance,
>>Josh
>>
>>--
>>Josh Ward
>>Graduate Research Assistant
>>Purdue University
>>Department of Medicinal Chemistry and Molecular Pharmacology
>>Lily Hall of Life Sciences
>>Phone: (765) 494-2191
>>
>>
>
>
> 

-- 
Josh Ward
Graduate Research Assistant
Purdue University
Department of Medicinal Chemistry and Molecular Pharmacology
Lily Hall of Life Sciences
Phone: (765) 494-2191