Good evening, I am emailing on behalf of a message that was responded to in 2018. It involved the deleting of CONECT records from a PDB file. I was wondering if there were instructions on how that was done? I look forward to hearing from you. Thank you Justin Prado
Hi Justin, You just open the PDB file in your favorite text editor and then delete all the lines that start with CONECT. It is not something you would do using Chimera or ChimeraX. 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 13, 2023, at 9:52 PM, Justin Prado via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Good evening,
I am emailing on behalf of a message that was responded to in 2018. It involved the deleting of CONECT records from a PDB file. I was wondering if there were instructions on how that was done? I look forward to hearing from you.
Thank you Justin Prado
Thank you so much for getting back to me. I was able to delete those files, but it did not really solve my issue. The thing is, I am trying to add a peptide into a protein but not by the end of the protein. There is a part of the structure that is missing which is about 20 amino acids, so I am trying to fit a peptide inside that section. I keep running into an error that says "Unexpected branching atom ( ) connected to C-terminal carbon. I just assumed it was that pseudo bond that was put to fill that empty space. I deleted those CONECT lines but I still got the same error. Do you have any other suggestions? On Tue, Mar 14, 2023 at 9:43 AM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Justin, You just open the PDB file in your favorite text editor and then delete all the lines that start with CONECT. It is not something you would do using Chimera or ChimeraX. 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 13, 2023, at 9:52 PM, Justin Prado via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
Good evening,
I am emailing on behalf of a message that was responded to in 2018. It involved the deleting of CONECT records from a PDB file. I was wondering if there were instructions on how that was done? I look forward to hearing from you.
Thank you Justin Prado
HI Justin, You could start with a PDB file that has the last part deleted, so you only have the first part and can build the middle part (you could open the last part as another PDB file if you need to see where it is while you are building). Then you can save the PDB file with the first part + middle that you built. Then text-edit it to put the last part back in. That is just one way. Another way if the missing part is not too long is to open the whole sequence from a sequence file (e.g. FASTA format) and open the PDB with the first and last parts in it, and then use Modeller to build the missing loop. See the help: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html> 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 14, 2023, at 6:23 PM, Justin Prado via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Thank you so much for getting back to me. I was able to delete those files, but it did not really solve my issue. The thing is, I am trying to add a peptide into a protein but not by the end of the protein. There is a part of the structure that is missing which is about 20 amino acids, so I am trying to fit a peptide inside that section. I keep running into an error that says "Unexpected branching atom ( ) connected to C-terminal carbon. I just assumed it was that pseudo bond that was put to fill that empty space. I deleted those CONECT lines but I still got the same error. Do you have any other suggestions?
On Tue, Mar 14, 2023 at 9:43 AM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Justin, You just open the PDB file in your favorite text editor and then delete all the lines that start with CONECT. It is not something you would do using Chimera or ChimeraX. 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 13, 2023, at 9:52 PM, Justin Prado via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Good evening,
I am emailing on behalf of a message that was responded to in 2018. It involved the deleting of CONECT records from a PDB file. I was wondering if there were instructions on how that was done? I look forward to hearing from you.
Thank you Justin Prado
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
I did exactly as you instructed and it worked perfectly. Thank you so much for your help, I really appreciate your time. Best Justin Prado On Wed, Mar 15, 2023 at 9:29 AM Elaine Meng <meng@cgl.ucsf.edu> wrote:
HI Justin, You could start with a PDB file that has the last part deleted, so you only have the first part and can build the middle part (you could open the last part as another PDB file if you need to see where it is while you are building). Then you can save the PDB file with the first part + middle that you built. Then text-edit it to put the last part back in. That is just one way.
Another way if the missing part is not too long is to open the whole sequence from a sequence file (e.g. FASTA format) and open the PDB with the first and last parts in it, and then use Modeller to build the missing loop. See the help: < https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m...
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 14, 2023, at 6:23 PM, Justin Prado via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
Thank you so much for getting back to me. I was able to delete those files, but it did not really solve my issue. The thing is, I am trying to add a peptide into a protein but not by the end of the protein. There is a part of the structure that is missing which is about 20 amino acids, so I am trying to fit a peptide inside that section. I keep running into an error that says "Unexpected branching atom ( ) connected to C-terminal carbon. I just assumed it was that pseudo bond that was put to fill that empty space. I deleted those CONECT lines but I still got the same error. Do you have any other suggestions?
On Tue, Mar 14, 2023 at 9:43 AM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Justin, You just open the PDB file in your favorite text editor and then delete all the lines that start with CONECT. It is not something you would do using Chimera or ChimeraX. 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 13, 2023, at 9:52 PM, Justin Prado via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
Good evening,
I am emailing on behalf of a message that was responded to in 2018. It involved the deleting of CONECT records from a PDB file. I was wondering if there were instructions on how that was done? I look forward to hearing from you.
Thank you Justin Prado
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
I am sorry to bother so often, but I had to modify my structure a little more. The only thing I have left is to insert a Arginine. Specifically the residue number is not occupied so my res_numers skips from 142 to 144 and I want to add it to 143. Is there any insert function available or would I have to edit it via some text editor? Sent from my iPhone
On Mar 15, 2023, at 9:29 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
HI Justin, You could start with a PDB file that has the last part deleted, so you only have the first part and can build the middle part (you could open the last part as another PDB file if you need to see where it is while you are building). Then you can save the PDB file with the first part + middle that you built. Then text-edit it to put the last part back in. That is just one way.
Another way if the missing part is not too long is to open the whole sequence from a sequence file (e.g. FASTA format) and open the PDB with the first and last parts in it, and then use Modeller to build the missing loop. See the help: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html>
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 14, 2023, at 6:23 PM, Justin Prado via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Thank you so much for getting back to me. I was able to delete those files, but it did not really solve my issue. The thing is, I am trying to add a peptide into a protein but not by the end of the protein. There is a part of the structure that is missing which is about 20 amino acids, so I am trying to fit a peptide inside that section. I keep running into an error that says "Unexpected branching atom ( ) connected to C-terminal carbon. I just assumed it was that pseudo bond that was put to fill that empty space. I deleted those CONECT lines but I still got the same error. Do you have any other suggestions?
On Tue, Mar 14, 2023 at 9:43 AM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Justin, You just open the PDB file in your favorite text editor and then delete all the lines that start with CONECT. It is not something you would do using Chimera or ChimeraX. 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 13, 2023, at 9:52 PM, Justin Prado via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Good evening,
I am emailing on behalf of a message that was responded to in 2018. It involved the deleting of CONECT records from a PDB file. I was wondering if there were instructions on how that was done? I look forward to hearing from you.
Thank you Justin Prado
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
Hi Justin, Sorry no, there is no insert function. You would have to do something similar to the previous instructions. There is also a Renumber Residues tool (or resrenumber) command that might be useful. <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/renumber.html> See also Build Structure for various features related to atomic-structure building. <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html> 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 16, 2023, at 7:21 PM, Justin Prado via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
I am sorry to bother so often, but I had to modify my structure a little more. The only thing I have left is to insert a Arginine. Specifically the residue number is not occupied so my res_numers skips from 142 to 144 and I want to add it to 143. Is there any insert function available or would I have to edit it via some text editor?
Sent from my iPhone
On Mar 15, 2023, at 9:29 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
HI Justin, You could start with a PDB file that has the last part deleted, so you only have the first part and can build the middle part (you could open the last part as another PDB file if you need to see where it is while you are building). Then you can save the PDB file with the first part + middle that you built. Then text-edit it to put the last part back in. That is just one way.
Another way if the missing part is not too long is to open the whole sequence from a sequence file (e.g. FASTA format) and open the PDB with the first and last parts in it, and then use Modeller to build the missing loop. See the help: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html>
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 14, 2023, at 6:23 PM, Justin Prado via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Thank you so much for getting back to me. I was able to delete those files, but it did not really solve my issue. The thing is, I am trying to add a peptide into a protein but not by the end of the protein. There is a part of the structure that is missing which is about 20 amino acids, so I am trying to fit a peptide inside that section. I keep running into an error that says "Unexpected branching atom ( ) connected to C-terminal carbon. I just assumed it was that pseudo bond that was put to fill that empty space. I deleted those CONECT lines but I still got the same error. Do you have any other suggestions?
On Tue, Mar 14, 2023 at 9:43 AM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Justin, You just open the PDB file in your favorite text editor and then delete all the lines that start with CONECT. It is not something you would do using Chimera or ChimeraX. 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 13, 2023, at 9:52 PM, Justin Prado via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Good evening,
I am emailing on behalf of a message that was responded to in 2018. It involved the deleting of CONECT records from a PDB file. I was wondering if there were instructions on how that was done? I look forward to hearing from you.
Thank you Justin Prado
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
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Elaine Meng -
Justin Prado