Re: trajectories

From: Jerome Henin (
Date: Mon Jul 14 2008 - 14:45:23 CDT

Did you try just using "resname HEME"?

A general hint: when you tell the list "I already know a solution but
I don't want to do it that way", you should explain why, otherwise
people who would be able to help may consider it a waste of their

Second remark: this question is not related to namd but vmd... Wrong
mailing list?


On Mon, Jul 14, 2008 at 2:38 PM, <> wrote:
> Dear users,
> I'm currently in the process of writing a short script that pipes
> trajectory data into a data file (if there is such a program that exists I
> would greatly appreciate a pointing of the direction to the source). I
> seem to have run into a problem that has been brought up due to this
> writing. I've been trying to measure the trajectory of the heme in a
> globular protein and here is where the problem begins. When I bring up my
> atom selection in the form of:
> set sel [atomselect top "protein and resname HEME"]
> I realize that the HEME is not a member of the protein chain, as
> recognized by the creation of the psf. It is a chain upon itself entitled
> chain O. Now, I also recognize that if I change protein to chain O I have
> no problem measuring the trajectory, I would like not to do that. The
> question is, how can I make the HEME as a member of the protein chain?
> I've tried every which way but to no avail.
> Kind regards,
> John

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