Problem visualizing hydrogen bonds during a trajectory
Hello, I'm trying to visualize the hydrogen bonds of a small molecule in water over the trajectory of a molecular dynamics simulation, using the following commands: alias evalhb hide solvent; hb :LIG reveal true coordsets false makePseudobonds true ; view perframe evalhb; coordset #1 1,20 holdsteady :LIG; wait 20; ~perframe However, this does not work as expected. Could you please help me with this issue? Thank you, Ute
Hi Ute, This seems to be a problem in the interaction between the "perframe" and "coordset" commands. When the hydrogen bonds are evaluated, the coordinate set hasn't been advanced yet, so when the coordinate set later gets advanced the hydrogen bonds are gone. I will open a ticket in our bug-tracking database for this with you cc'ed. You can get close to what you were trying to get with the following two commands (though not 100% the same): hide solvent; hb :LIG reveal true coordsets true makePseudobonds true perframe view; coordset #1 1,20 holdsteady :LIG; wait 20; ~perframe --Eric Eric Pettersen UCSF Computer Graphics Lab
On Apr 30, 2024, at 5:51 AM, Ute Roehrig via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello,
I'm trying to visualize the hydrogen bonds of a small molecule in water over the trajectory of a molecular dynamics simulation, using the following commands:
alias evalhb hide solvent; hb :LIG reveal true coordsets false makePseudobonds true ; view perframe evalhb; coordset #1 1,20 holdsteady :LIG; wait 20; ~perframe
However, this does not work as expected. Could you please help me with this issue?
Thank you, Ute
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So following up on this with information from the ticket that was opened <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/15074>, Tom Goddard noted that with the original commands: perframe evalhb; coordset #1 1,20 holdsteady :LIG; wait 20; ~perframe the hydrogen bonds would be evaluated and then the coordinate set would be advanced, which result in no hydrogen bonds being displayed. So doing it in the opposite order produces the desired result: coordset #1 1,20 holdsteady :LIG; perframe evalhb; wait 20; ~perframe —Eric
On Apr 30, 2024, at 10:41 AM, Eric Pettersen via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Ute, This seems to be a problem in the interaction between the "perframe" and "coordset" commands. When the hydrogen bonds are evaluated, the coordinate set hasn't been advanced yet, so when the coordinate set later gets advanced the hydrogen bonds are gone. I will open a ticket in our bug-tracking database for this with you cc'ed. You can get close to what you were trying to get with the following two commands (though not 100% the same):
hide solvent; hb :LIG reveal true coordsets true makePseudobonds true perframe view; coordset #1 1,20 holdsteady :LIG; wait 20; ~perframe
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Apr 30, 2024, at 5:51 AM, Ute Roehrig via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Hello,
I'm trying to visualize the hydrogen bonds of a small molecule in water over the trajectory of a molecular dynamics simulation, using the following commands:
alias evalhb hide solvent; hb :LIG reveal true coordsets false makePseudobonds true ; view perframe evalhb; coordset #1 1,20 holdsteady :LIG; wait 20; ~perframe
However, this does not work as expected. Could you please help me with this issue?
Thank you, Ute
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participants (2)
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Eric Pettersen -
Ute Roehrig