not showing non-traced amino acids in sequence view after splitting a molecule
Hi all
When I open a cif in chimerax and press the sequence button the window shows up and there is everything within the molecule, including the non-traced amino acids (missing in the structure).
Whereas if I do split the molecule to have just one chain, then the sequence view only shows traced amino acids, but not the non-traced ones anymore... Any ideas on this please?
P.D. With cif files this was a bit confusing in regular chimera for me as well, since when saving the cif it was kind of converted and I guess some info regarding this non-traced aminoacids was missed...
Thank you!!!
Marta
Hi Marta, When you open a structure from PDB or mmCIF format, there is a special part of the file that gives the full sequence of the structure used in the experiment, even if parts of that structure are not visible in the density (and therefore do not have atomic coordinates). This is part of the model information.
However, “split” makes new models, and it currently loses various kinds of information. I believe this is the case in both Chimera and ChimeraX. After splitting, it must only look at the coordinates to get the sequence.
My personal opinion is to avoid using “split” unless it is really necessary.
In Chimera it sometimes helped with molecular surface calculation, but in ChimeraX there is less reason to do it. You can specify chains individually without splitting. The main reason one might split is for separately fitting the chains. However, if having the full sequence is important, you can instead open multiple copies of the original model and just delete the parts of each that you don’t need.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 2, 2020, at 8:30 AM, Marta Perez Illana marta.perez@cnb.csic.es wrote:
Hi all When I open a cif in chimerax and press the sequence button the window shows up and there is everything within the molecule, including the non-traced amino acids (missing in the structure).
Whereas if I do split the molecule to have just one chain, then the sequence view only shows traced amino acids, but not the non-traced ones anymore... Any ideas on this please?
P.D. With cif files this was a bit confusing in regular chimera for me as well, since when saving the cif it was kind of converted and I guess some info regarding this non-traced aminoacids was missed...
Thank you!!! Marta
Hi Elaine
Thanks a lot for the quick reply! I though that maybe there was a way to keep that info of the non-traced amino acids after doing splitting.
I use split because we work with huge molecules, and therefore is really convenient for focusing on a particular chain. And as well for fitting as you mention... I will try the alternatives you proposed! now knowing that making/saving new models implies for sure kind of "loosing that info"...
Regards
Marta
On 02/03/2020 18:05, Elaine Meng wrote:
Hi Marta, When you open a structure from PDB or mmCIF format, there is a special part of the file that gives the full sequence of the structure used in the experiment, even if parts of that structure are not visible in the density (and therefore do not have atomic coordinates). This is part of the model information.
However, “split” makes new models, and it currently loses various kinds of information. I believe this is the case in both Chimera and ChimeraX. After splitting, it must only look at the coordinates to get the sequence.
My personal opinion is to avoid using “split” unless it is really necessary.
In Chimera it sometimes helped with molecular surface calculation, but in ChimeraX there is less reason to do it. You can specify chains individually without splitting. The main reason one might split is for separately fitting the chains. However, if having the full sequence is important, you can instead open multiple copies of the original model and just delete the parts of each that you don’t need.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 2, 2020, at 8:30 AM, Marta Perez Illana marta.perez@cnb.csic.es wrote:
Hi all When I open a cif in chimerax and press the sequence button the window shows up and there is everything within the molecule, including the non-traced amino acids (missing in the structure).
Whereas if I do split the molecule to have just one chain, then the sequence view only shows traced amino acids, but not the non-traced ones anymore... Any ideas on this please?
P.D. With cif files this was a bit confusing in regular chimera for me as well, since when saving the cif it was kind of converted and I guess some info regarding this non-traced aminoacids was missed...
Thank you!!! Marta
Hi Marta, It might be fixed later, but I can’t say for sure.
At least for now, without splitting you can:
- select by chain ID with the select menu
- Ctrl-click to select an atom/residue in the chain and then press keyboard "up arrow" to promote to whole chain
- without selecting, specify chain ID directly in commands, for example: view #1/B
Another possibility is to make easy-to-remember names for individual chains or groups of chains using the “name” command. The names can be used in commands and will also appear in the Select menu. Example:
open 4hhb name alpha #1/A,C name beta #1/B,D color alpha green target r
(color ribbons-only of hemoglobin alpha chains green)
Regards, Elaine
On Mar 2, 2020, at 9:15 AM, Marta Perez Illana marta.perez@cnb.csic.es wrote:
Hi Elaine
Thanks a lot for the quick reply! I though that maybe there was a way to keep that info of the non-traced amino acids after doing splitting.
I use split because we work with huge molecules, and therefore is really convenient for focusing on a particular chain. And as well for fitting as you mention... I will try the alternatives you proposed! now knowing that making/saving new models implies for sure kind of "loosing that info"...
Regards
Marta
On 02/03/2020 18:05, Elaine Meng wrote:
Hi Marta, When you open a structure from PDB or mmCIF format, there is a special part of the file that gives the full sequence of the structure used in the experiment, even if parts of that structure are not visible in the density (and therefore do not have atomic coordinates). This is part of the model information.
However, “split” makes new models, and it currently loses various kinds of information. I believe this is the case in both Chimera and ChimeraX. After splitting, it must only look at the coordinates to get the sequence.
My personal opinion is to avoid using “split” unless it is really necessary.
In Chimera it sometimes helped with molecular surface calculation, but in ChimeraX there is less reason to do it. You can specify chains individually without splitting. The main reason one might split is for separately fitting the chains. However, if having the full sequence is important, you can instead open multiple copies of the original model and just delete the parts of each that you don’t need.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 2, 2020, at 8:30 AM, Marta Perez Illana marta.perez@cnb.csic.es wrote:
Hi all When I open a cif in chimerax and press the sequence button the window shows up and there is everything within the molecule, including the non-traced amino acids (missing in the structure).
Whereas if I do split the molecule to have just one chain, then the sequence view only shows traced amino acids, but not the non-traced ones anymore... Any ideas on this please?
P.D. With cif files this was a bit confusing in regular chimera for me as well, since when saving the cif it was kind of converted and I guess some info regarding this non-traced aminoacids was missed...
Thank you!!! Marta
Hi Marta,
The sequence for the missing structure should be preserved by the split command but it currently is not being preserved. We have opened a request for that
https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/2913 https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/2913
I agree with Elaine, that you should rarely need to use the split command.
Tom
On Mar 2, 2020, at 9:15 AM, Marta Perez Illana wrote:
Hi Elaine
Thanks a lot for the quick reply! I though that maybe there was a way to keep that info of the non-traced amino acids after doing splitting.
I use split because we work with huge molecules, and therefore is really convenient for focusing on a particular chain. And as well for fitting as you mention... I will try the alternatives you proposed! now knowing that making/saving new models implies for sure kind of "loosing that info"...
Regards
Marta
On 02/03/2020 18:05, Elaine Meng wrote:
Hi Marta, When you open a structure from PDB or mmCIF format, there is a special part of the file that gives the full sequence of the structure used in the experiment, even if parts of that structure are not visible in the density (and therefore do not have atomic coordinates). This is part of the model information.
However, “split” makes new models, and it currently loses various kinds of information. I believe this is the case in both Chimera and ChimeraX. After splitting, it must only look at the coordinates to get the sequence.
My personal opinion is to avoid using “split” unless it is really necessary.
In Chimera it sometimes helped with molecular surface calculation, but in ChimeraX there is less reason to do it. You can specify chains individually without splitting. The main reason one might split is for separately fitting the chains. However, if having the full sequence is important, you can instead open multiple copies of the original model and just delete the parts of each that you don’t need.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 2, 2020, at 8:30 AM, Marta Perez Illana wrote:
Hi all When I open a cif in chimerax and press the sequence button the window shows up and there is everything within the molecule, including the non-traced amino acids (missing in the structure).
Whereas if I do split the molecule to have just one chain, then the sequence view only shows traced amino acids, but not the non-traced ones anymore... Any ideas on this please?
P.D. With cif files this was a bit confusing in regular chimera for me as well, since when saving the cif it was kind of converted and I guess some info regarding this non-traced aminoacids was missed...
Thank you!!! Marta
-- Marta Pérez Illana, Ph. D. student Dept. of Macromolecular Structures Lab 15 Centro Nacional de Biotecnología (CNB-CSIC) Darwin, 3 28049-Madrid (SPAIN) http://wwwuser.cnb.csic.es/~sanmartinlab http://wwwuser.cnb.csic.es/~sanmartinlab
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participants (3)
-
Elaine Meng -
Marta Perez Illana -
Tom Goddard