I am trying to work with a data set that has three copies of a protein complex per asymetric unit in the cell. It is a rather large complex. I can delete two of the copies and work with only one complex. There are 9 chains in each complex. 3 oligonucleotide sequences, and 6 proteins of different sizes, the largest having about 1400 residues. The way in which I selected only one complex to visualize was to delete the other 18 chains one at a time. There must be a way of deleting each of the other two copies all at once but I did not try to find it in the Chimera tutorial list. The deletion only eliminates the image of each complex. Both complexes are still there in the total data set. The result is that saving a session takes about three minutes because it saving all the coordinates of the three copies of the complex. How can I make the process more efficient and delete two copies from the coordinate data set. Thank you Arthur G. Szabo
Hi Arthur, It’s mostly impossible to answer without knowing the model number and chain IDs. Also if you say the structures are still there, you were not really deleting them, you were only hiding them. To delete you can use the command “delete” with a specification of which atoms to delete. The “atom specification” page explains how to specify chain ID, etc. in commands. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> Here is one simple example to delete chains A-C and F: delete :.a-c:.f Or, if you can select all the parts you want to delete, you can then use command “delete sel” or menu: Actions… Atoms/Bonds… delete. If it is easier to select the parts you want to keep, then do that first, but then use the Select menu to invert the selection to make it the parts you want to delete. One way to see what chains you have is to look in the Select… Chain menu, and you can even use it to highlight each chain and see where in the structure it is. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 7, 2017, at 6:37 AM, Arthur Szabo <agszabo@outlook.com> wrote:
I am trying to work with a data set that has three copies of a protein complex per asymetric unit in the cell. It is a rather large complex. I can delete two of the copies and work with only one complex.
There are 9 chains in each complex. 3 oligonucleotide sequences, and 6 proteins of different sizes, the largest having about 1400 residues.
The way in which I selected only one complex to visualize was to delete the other 18 chains one at a time. There must be a way of deleting each of the other two copies all at once but I did not try to find it in the Chimera tutorial list.
The deletion only eliminates the image of each complex. Both complexes are still there in the total data set. The result is that saving a session takes about three minutes because it saving all the coordinates of the three copies of the complex.
How can I make the process more efficient and delete two copies from the coordinate data set.
Thank you
Arthur G. Szabo
Elaine Thanks once again. I will try that. The PDB file is 4YLN Regards art -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Friday, July 07, 2017 11:16 AM To: Arthur Szabo <agszabo@outlook.com> Cc: chimera-users@cgl.ucsf.edu BB <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] large datasets Hi Arthur, It’s mostly impossible to answer without knowing the model number and chain IDs. Also if you say the structures are still there, you were not really deleting them, you were only hiding them. To delete you can use the command “delete” with a specification of which atoms to delete. The “atom specification” page explains how to specify chain ID, etc. in commands. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> Here is one simple example to delete chains A-C and F: delete :.a-c:.f Or, if you can select all the parts you want to delete, you can then use command “delete sel” or menu: Actions… Atoms/Bonds… delete. If it is easier to select the parts you want to keep, then do that first, but then use the Select menu to invert the selection to make it the parts you want to delete. One way to see what chains you have is to look in the Select… Chain menu, and you can even use it to highlight each chain and see where in the structure it is. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 7, 2017, at 6:37 AM, Arthur Szabo <agszabo@outlook.com> wrote:
I am trying to work with a data set that has three copies of a protein complex per asymetric unit in the cell. It is a rather large complex. I can delete two of the copies and work with only one complex.
There are 9 chains in each complex. 3 oligonucleotide sequences, and 6 proteins of different sizes, the largest having about 1400 residues.
The way in which I selected only one complex to visualize was to delete the other 18 chains one at a time. There must be a way of deleting each of the other two copies all at once but I did not try to find it in the Chimera tutorial list.
The deletion only eliminates the image of each complex. Both complexes are still there in the total data set. The result is that saving a session takes about three minutes because it saving all the coordinates of the three copies of the complex.
How can I make the process more efficient and delete two copies from the coordinate data set.
Thank you
Arthur G. Szabo
Elaine I used the command Delete:,g-r:.4-9 And those chains no longer show up in the list of chains. However, what is left has lost all definition of secondary structure, showing only the chain as a spaghetti noodle. I couldn't seem to restore the secondary structure for chains 1 - 3, and A - F. Over to you Thanks art -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Friday, July 07, 2017 11:16 AM To: Arthur Szabo <agszabo@outlook.com> Cc: chimera-users@cgl.ucsf.edu BB <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] large datasets Hi Arthur, It’s mostly impossible to answer without knowing the model number and chain IDs. Also if you say the structures are still there, you were not really deleting them, you were only hiding them. To delete you can use the command “delete” with a specification of which atoms to delete. The “atom specification” page explains how to specify chain ID, etc. in commands. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> Here is one simple example to delete chains A-C and F: delete :.a-c:.f Or, if you can select all the parts you want to delete, you can then use command “delete sel” or menu: Actions… Atoms/Bonds… delete. If it is easier to select the parts you want to keep, then do that first, but then use the Select menu to invert the selection to make it the parts you want to delete. One way to see what chains you have is to look in the Select… Chain menu, and you can even use it to highlight each chain and see where in the structure it is. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 7, 2017, at 6:37 AM, Arthur Szabo <agszabo@outlook.com> wrote:
I am trying to work with a data set that has three copies of a protein complex per asymetric unit in the cell. It is a rather large complex. I can delete two of the copies and work with only one complex.
There are 9 chains in each complex. 3 oligonucleotide sequences, and 6 proteins of different sizes, the largest having about 1400 residues.
The way in which I selected only one complex to visualize was to delete the other 18 chains one at a time. There must be a way of deleting each of the other two copies all at once but I did not try to find it in the Chimera tutorial list.
The deletion only eliminates the image of each complex. Both complexes are still there in the total data set. The result is that saving a session takes about three minutes because it saving all the coordinates of the three copies of the complex.
How can I make the process more efficient and delete two copies from the coordinate data set.
Thank you
Arthur G. Szabo
Hi Arthur, You must have typed something wrong. You need a space after the “delete” and no commas, only colon and dot. If I do this open 4yln delete :.g-r:.4-9 … the remaining chains look fine to me, the same as when I opened the structure. Best, Elaine
On Jul 7, 2017, at 9:45 AM, Arthur Szabo <agszabo@outlook.com> wrote:
Elaine
I used the command
Delete:,g-r:.4-9
And those chains no longer show up in the list of chains.
However, what is left has lost all definition of secondary structure, showing only the chain as a spaghetti noodle.
I couldn't seem to restore the secondary structure for chains 1 - 3, and A - F.
Over to you
Thanks
art
-----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Friday, July 07, 2017 11:16 AM To: Arthur Szabo <agszabo@outlook.com> Cc: chimera-users@cgl.ucsf.edu BB <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] large datasets
Hi Arthur, It’s mostly impossible to answer without knowing the model number and chain IDs. Also if you say the structures are still there, you were not really deleting them, you were only hiding them.
To delete you can use the command “delete” with a specification of which atoms to delete. The “atom specification” page explains how to specify chain ID, etc. in commands. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>
Here is one simple example to delete chains A-C and F:
delete :.a-c:.f
Or, if you can select all the parts you want to delete, you can then use command “delete sel” or menu: Actions… Atoms/Bonds… delete. If it is easier to select the parts you want to keep, then do that first, but then use the Select menu to invert the selection to make it the parts you want to delete.
One way to see what chains you have is to look in the Select… Chain menu, and you can even use it to highlight each chain and see where in the structure it is.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 7, 2017, at 6:37 AM, Arthur Szabo <agszabo@outlook.com> wrote:
I am trying to work with a data set that has three copies of a protein complex per asymetric unit in the cell. It is a rather large complex. I can delete two of the copies and work with only one complex.
There are 9 chains in each complex. 3 oligonucleotide sequences, and 6 proteins of different sizes, the largest having about 1400 residues.
The way in which I selected only one complex to visualize was to delete the other 18 chains one at a time. There must be a way of deleting each of the other two copies all at once but I did not try to find it in the Chimera tutorial list.
The deletion only eliminates the image of each complex. Both complexes are still there in the total data set. The result is that saving a session takes about three minutes because it saving all the coordinates of the three copies of the complex.
How can I make the process more efficient and delete two copies from the coordinate data set.
Thank you
Arthur G. Szabo
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Elaine Thanks, that worked. art -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Friday, July 07, 2017 1:25 PM To: Arthur Szabo <agszabo@outlook.com> Cc: Chimera - users <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] large datasets Hi Arthur, You must have typed something wrong. You need a space after the “delete” and no commas, only colon and dot. If I do this open 4yln delete :.g-r:.4-9 … the remaining chains look fine to me, the same as when I opened the structure. Best, Elaine
On Jul 7, 2017, at 9:45 AM, Arthur Szabo <agszabo@outlook.com> wrote:
Elaine
I used the command
Delete:,g-r:.4-9
And those chains no longer show up in the list of chains.
However, what is left has lost all definition of secondary structure, showing only the chain as a spaghetti noodle.
I couldn't seem to restore the secondary structure for chains 1 - 3, and A - F.
Over to you
Thanks
art
-----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Friday, July 07, 2017 11:16 AM To: Arthur Szabo <agszabo@outlook.com> Cc: chimera-users@cgl.ucsf.edu BB <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] large datasets
Hi Arthur, It’s mostly impossible to answer without knowing the model number and chain IDs. Also if you say the structures are still there, you were not really deleting them, you were only hiding them.
To delete you can use the command “delete” with a specification of which atoms to delete. The “atom specification” page explains how to specify chain ID, etc. in commands. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec .html>
Here is one simple example to delete chains A-C and F:
delete :.a-c:.f
Or, if you can select all the parts you want to delete, you can then use command “delete sel” or menu: Actions… Atoms/Bonds… delete. If it is easier to select the parts you want to keep, then do that first, but then use the Select menu to invert the selection to make it the parts you want to delete.
One way to see what chains you have is to look in the Select… Chain menu, and you can even use it to highlight each chain and see where in the structure it is.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 7, 2017, at 6:37 AM, Arthur Szabo <agszabo@outlook.com> wrote:
I am trying to work with a data set that has three copies of a protein complex per asymetric unit in the cell. It is a rather large complex. I can delete two of the copies and work with only one complex.
There are 9 chains in each complex. 3 oligonucleotide sequences, and 6 proteins of different sizes, the largest having about 1400 residues.
The way in which I selected only one complex to visualize was to delete the other 18 chains one at a time. There must be a way of deleting each of the other two copies all at once but I did not try to find it in the Chimera tutorial list.
The deletion only eliminates the image of each complex. Both complexes are still there in the total data set. The result is that saving a session takes about three minutes because it saving all the coordinates of the three copies of the complex.
How can I make the process more efficient and delete two copies from the coordinate data set.
Thank you
Arthur G. Szabo
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
-
Arthur Szabo -
Elaine Meng