VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Thu Dec 03 2015 - 21:14:13 CST

Hi Bryan,
It isn’t really an MWE if we don’t have the structure that you’re looking at to try it out. But I’m pretty sure what you’re running into is that the elementary object being enumerated by measure contacts is the *atom pair*. You get two ordered lists, and the ith element of each list defines a single pair of atoms in contact with each other. Viewed this way, it would make no sense to list the 11498-11497 contact and the 11497-11498 contact — they refer to the same thing.
Best,
Peter

> On Dec 3, 2015, at 8:34 PM, Bryan Roessler <roessler_at_uab.edu> wrote:
>
> Since I am unsure of whether or not my question is clear, I am including a MWE:
>
> proc my_contacts {} {
> set A [atomselect top "resid 968 543"]
> set my_contacts [measure contacts 1.8 $A]
> echo $my_contacts
> }
>
> returns:
> {{11498 11505 11505 7810 11500 7813 11504 11503 11492} {11497 11504 11503 7811 11501 7814 7816 11504 11491}}
>
> Perhaps I am not understanding how measure contacts works, but I would expect that the two lists would be identical since selection2 is omitted.
>
> contacts cutoff selection1 [selection2]: Find all atoms in selection1 that are within cutoff of any atom in selection2 and not bonded to it. If selection2 is omitted, it is taken to be the same as selection1. selection2 and selection1 can either be from the same of from different molecules. Returns two lists of atom indices, the first containing the first index of each pair (taken from selection1) and the second containing the second index (taken from selection2). Note that the index is the global index of the atom with respect to its parent molecule, as opposed to the index within the given atom selection that contains it.
>
> When I add selection2 manually I get the exact same output:
>
> proc my_contacts {} {
> set A [atomselect top "resid 968 543"]
> set B [atomselect top "resid 968 543"]
> set my_contacts [measure contacts 1.8 $A $B]
> echo $my_contacts
> }
>
> returns:
> {{11498 11505 11505 7810 11500 7813 11504 11503 11492} {11497 11504 11503 7811 11501 7814 7816 11504 11491}}
>
>
> What am I running into here?
>
> Thanks,
>
> Bryan
>
> Bryan Roessler | Graduate Research Assistant
> UAB | The University of Alabama at Birmingham
> uab.edu/cmdb
> Knowledge that will change your world
>
> On Wed, Dec 2, 2015 at 4:51 PM, Bryan Roessler <roessler_at_uab.edu> wrote:
> Hello,
>
> I have a single atomselection with two residues that I am trying to run a measure contacts on, however measure contacts is not working as expected.
>
> set A [atomselect top "resid 543 968"]
> measure contacts 3.0 $A
> (note this is a simplified version of what I am trying to do, thus running an atomsel on resid 543 and an atomsel on 968 and using both in the contacts command would not work)
>
> Output:
> {7805 7805 7805 7806 7806 7805 7805 7806 7806 7805 7806 7807 7808 7807 7808 7808 7818 7818 7808 7807 7807 7807 7808 7808 7808 11504 11502 11502 11504 11504 11505 11504 11505 11502 11502 11502 11504 11504 11504 11505 11505 11505 11504 11502 11502 11504 11504 11505 11505 11504 7817 7817 7817 7817 11494 11494 11494 11494 11494 11494 11494 11494 11494 7810 7810 7810 7813 7810 7812 7813 7814 7814 7812 7813 7814 11503 11503 11503 7815 7815 7815 7815 7816 7816 7815 7816 11493 11493 11493 11495 11495 11495 11497 11497 11498 11493 11493 11493 11493 11495 11495 11495 11495 11495 11496 11496 11498 11498 11493 11496 11496 11497 11498 11498 11493 11496 11498 11499 11486 11486 11486 11487 11487 11487 11487 11488 11489 11486 11489 11490 11491 11488 11489 11491 11486 11488 11500 11501 11501 11492} {7808 7818 7819 7807 7808 7810 7813 7810 7813 7809 7809 7819 7818 7811 7809 7811 7809 7811 7815 7810 7812 7813 7812 7813 7817 11505 7817 11494 7817 11494 11494 11503 11503 11493 11496 11497 11493 11496 11499 11496 11497 11499 78
15 11500 11501 11500 11501 11500 11501 11492 11494 7812 7813 7816 11488 11489 11490 11492 11495 11496 11497 11499 11501 7812 7813 7814 7814 7811 7811 7809 7809 7811 11489 11489 11489 11500 11501 11499 7809 7811 7813 7814 7812 7814 11489 11489 11497 11498 11499 11496 11497 11498 11498 11499 11499 11487 11488 11489 11491 11486 11487 11488 11490 11491 11490 11491 11490 11491 11501 11500 11501 11500 11500 11501 11492 11492 11492 11492 11489 11490 11491 11488 11489 11490 11491 11491 11490 11506 11506 11506 11506 11492 11492 11492 11507 11507 11501 11492 11490 11506}
>
> Since no selection2 is specified, then the atomsel "resid 543 968" should be used for both the first and second selections. For instance, there should be duplicated atom pairs in both lists since we are measuring both the contacts between 543-968 AND 968-543 (as well as 543-543 and 968-968). However, measure contacts is only outputting 3 contacts between 543-968 and 6 contacts between 968-543, indicating that some of the contacts have been filtered out. Am I missing something? Is this intentional? is there a workaround?
>
> Thank you,
>
> Bryan
>
>
>
>
> Bryan Roessler | Graduate Research Assistant
> UAB | The University of Alabama at Birmingham
> uab.edu/cmdb
> Knowledge that will change your world
>
>