Difference between atoms' coordinates on screen and in a PDB file
Hello, I load 3 protein models into Chimera and enter several "move" commands. The structures change their positions. Then, I save them as a PDB file, and immediately open the PDB file. The structures are not overlapping (screenshot: http://i.imgur.com/gtGBN.png ). Why does it work like this and what can I do to obtain accurate coordinates on my screen without re-opening the model (after I finish my sequence of translations)? Mateusz
Hi Mateusz, To retain the spatial relationships between the structures when you have moved them independently, you need to save the PDBs "relative to" the same model. For example, save models 0,1,2 all relative to 0. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 13, 2012, at 6:26 PM, Mateusz Dobrychłop wrote:
Hello, I load 3 protein models into Chimera and enter several "move" commands. The structures change their positions. Then, I save them as a PDB file, and immediately open the PDB file. The structures are not overlapping (screenshot: http://i.imgur.com/gtGBN.png ). Why does it work like this and what can I do to obtain accurate coordinates on my screen without re-opening the model (after I finish my sequence of translations)? Mateusz
Hi Elaine, Thank you for your reply! I'm trying to recreate the components' moves from another software (in order to record it and export it to a movie file). The software generates a text "history" file with a list of all the moves the components make and a PDB file which is a result of those transformations. After applying all the transformations listed in the history file using Chimera, the stuff that's displayed on screen does not match the "result" model from this other software. Hovewer, if I save the result of my Chimera transformations into a PDB file, it perfectly matches the result file from the other software. What I'm trying to say is that the PDB file that I create is actually okay, but I'm trying to generate an animation so I much more care about the things that are displayed in Chimera window. Is there maybe a way to move (not save) the structures relatively to one of them? Mateusz 2012/9/14 Elaine Meng <meng@cgl.ucsf.edu>
Hi Mateusz, To retain the spatial relationships between the structures when you have moved them independently, you need to save the PDBs "relative to" the same model. For example, save models 0,1,2 all relative to 0. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 13, 2012, at 6:26 PM, Mateusz Dobrychłop wrote:
Hello, I load 3 protein models into Chimera and enter several "move" commands. The structures change their positions. Then, I save them as a PDB file, and immediately open the PDB file. The structures are not overlapping (screenshot: http://i.imgur.com/gtGBN.png ). Why does it work like this and what can I do to obtain accurate coordinates on my screen without re-opening the model (after I finish my sequence of translations)? Mateusz
Maybe I'm not understanding the question. You could make a Chimera command file (just a text file, filename ending in .com or .cmd) that has the move commands in it. You could first open the original structures and then open the Chimera command file, which would execute the commands. If you are making an animation with a script, those commands could be at the beginning of the script before the recording. My only other idea is to just save a Chimera session, which can later be restored. Elaine On Sep 14, 2012, at 11:26 AM, Mateusz Dobrychłop wrote:
Hi Elaine,
Thank you for your reply!
I'm trying to recreate the components' moves from another software (in order to record it and export it to a movie file). The software generates a text "history" file with a list of all the moves the components make and a PDB file which is a result of those transformations. After applying all the transformations listed in the history file using Chimera, the stuff that's displayed on screen does not match the "result" model from this other software. Hovewer, if I save the result of my Chimera transformations into a PDB file, it perfectly matches the result file from the other software.
What I'm trying to say is that the PDB file that I create is actually okay, but I'm trying to generate an animation so I much more care about the things that are displayed in Chimera window.
Is there maybe a way to move (not save) the structures relatively to one of them?
Mateusz
2012/9/14 Elaine Meng <meng@cgl.ucsf.edu> Hi Mateusz, To retain the spatial relationships between the structures when you have moved them independently, you need to save the PDBs "relative to" the same model. For example, save models 0,1,2 all relative to 0. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 13, 2012, at 6:26 PM, Mateusz Dobrychłop wrote:
Hello, I load 3 protein models into Chimera and enter several "move" commands. The structures change their positions. Then, I save them as a PDB file, and immediately open the PDB file. The structures are not overlapping (screenshot: http://i.imgur.com/gtGBN.png ). Why does it work like this and what can I do to obtain accurate coordinates on my screen without re-opening the model (after I finish my sequence of translations)? Mateusz
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Hi Mateusz, I don't understand exactly what is going wrong for you. But maybe an example will help. If you have two models #0 and #1 you can move #1 relative to #0 in 100 steps each 0.5 Angstrom along the x axis with a command move x 0.5 100 model #1 coord #0 The "coord #0" option is important here. It says move along the x-axis of the model #0 coordinate system. If you leave off that option it moves along the horizontal axis displayed on the screen. That is different from the x-axis of model #0 if you have rotated the models. The "turn" command also accepts the coordinate system option. Here is documentation for the move command http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/move.html and examples of other commands useful in movie making http://www.cgl.ucsf.edu/chimera/data/movie-howto-mar2012/movie_examples.html Tom -------- Original Message -------- Subject: Re: [Chimera-users] Difference between atoms' coordinates on screen and in a PDB file From: Mateusz Dobrychłop To: UCSF Chimera Mailing List <chimera-users@cgl.ucsf.edu> Date: 9/14/12 11:26 AM
Hi Elaine,
Thank you for your reply!
I'm trying to recreate the components' moves from another software (in order to record it and export it to a movie file). The software generates a text "history" file with a list of all the moves the components make and a PDB file which is a result of those transformations. After applying all the transformations listed in the history file using Chimera, the stuff that's displayed on screen does not match the "result" model from this other software. Hovewer, if I save the result of my Chimera transformations into a PDB file, it perfectly matches the result file from the other software.
What I'm trying to say is that the PDB file that I create is actually okay, but I'm trying to generate an animation so I much more care about the things that are displayed in Chimera window.
Is there maybe a way to move (not save) the structures relatively to one of them?
Mateusz
2012/9/14 Elaine Meng
Hi Mateusz, To retain the spatial relationships between the structures when you have moved them independently, you need to save the PDBs "relative to" the same model. For example, save models 0,1,2 all relative to 0. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 13, 2012, at 6:26 PM, Mateusz Dobrychłop wrote:
> Hello, > I load 3 protein models into Chimera and enter several "move" commands. The structures change their positions. Then, I save them as a PDB file, and immediately open the PDB file. The structures are not overlapping (screenshot: http://i.imgur.com/gtGBN.png ). Why does it work like this and what can I do to obtain accurate coordinates on my screen without re-opening the model (after I finish my sequence of translations)? > Mateusz
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participants (3)
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Elaine Meng -
Mateusz Dobrychłop -
Tom Goddard