VMD-L Mailing List

From: Bryan Roessler (roessler_at_uab.edu)
Date: Wed Dec 02 2015 - 16:51:04 CST

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 7815
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 <http://uab.edu/cmdb>*
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