Hello,
I have a structure which I've cut a section out of and I am working on connecting the two loose ends together. I wanted to connect them with two glycine residues - since they are easiest to work with and have no side chains. I am doing this using the Modify Structure option under the Build structure tool and adding one atom at a time. However, when I try to minimize my newly created glycine, I get the error message "No MMTK name for atom "H1" in standard residue "GLY"" (I've attached a picture of my reply log). I'm not sure how to troubleshoot this.
Is there a better way to connect two ends of a peptide, or should I change the way I am using the modify structure tool?
Thank you.
Nicole Ostrovsky
Hi Nicole, (1) If you are adding a whole amino acid residue to the end of a peptide chain, see command "addaa." So maybe you wouldn't need to add it one atom at a time. However, I don't know if "addaa" would work in your specific situation where you are really in the middle of the chain instead of its very beginning or end. https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addaa.html
(2) You would also need to add a bond to connect the two parts. Maybe that is part of the problem... if there is no bond, extra hydrogens will be added to fill the valence(s) of the atom(s) instead.
(3) However, the Reply Log image shows that there are lots of unrecognized atom names. See that long list of residues? So there are lots of unrecognized names, not just in the glycine you added. Usually unrecognized names are for hydrogen atoms, so one thing to try is to delete all hydrogens e.g. command
delete H
... and then try minimization, which will re-add hydrogens, assign charges, etc. If that still doesn't work, then you could use menu Help... Report a Bug and attach your structure PDB file. Make sure to include your e-mail address and a short description so we know that it's this issue we are discussing now. Without seeing your file we can't really say for sure what was wrong with it.
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 26, 2021, at 12:19 PM, Nicole Ostrovsky via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Hello, I have a structure which I've cut a section out of and I am working on connecting the two loose ends together. I wanted to connect them with two glycine residues - since they are easiest to work with and have no side chains. I am doing this using the Modify Structure option under the Build structure tool and adding one atom at a time. However, when I try to minimize my newly created glycine, I get the error message "No MMTK name for atom "H1" in standard residue "GLY"" (I've attached a picture of my reply log). I'm not sure how to troubleshoot this.
Is there a better way to connect two ends of a peptide, or should I change the way I am using the modify structure tool? Thank you. Nicole Ostrovsky <replylog_chimera.png>
Hi Nicole,
you could note the pdb name of the old structure and use the homology modelling tool provided in Chimera (it is based on Modeller then you need a password to access the server) to model the new sequence, using the old one as a template. Check that the alignment is correct (identical alignment except the new region) and let the server prepare your structure.
Hope it helps,
Regards,
Marco
Il 26/07/2021 21:19, Nicole Ostrovsky via Chimera-users ha scritto:
Hello,
I have a structure which I've cut a section out of and I am working on connecting the two loose ends together. I wanted to connect them with two glycine residues - since they are easiest to work with and have no side chains. I am doing this using the Modify Structure option under the Build structure tool and adding one atom at a time. However, when I try to minimize my newly created glycine, I get the error message "No MMTK name for atom "H1" in standard residue "GLY"" (I've attached a picture of my reply log). I'm not sure how to troubleshoot this.
Is there a better way to connect two ends of a peptide, or should I change the way I am using the modify structure tool?
Thank you.
Nicole Ostrovsky
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Thanks, Marco -- good idea! It might give a more reasonable result than manual building + minimization.
Nicole, see: https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html#comparative https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/dor.html
Elaine
On Jul 26, 2021, at 2:58 PM, Marco Sette via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Hi Nicole,
you could note the pdb name of the old structure and use the homology modelling tool provided in Chimera (it is based on Modeller then you need a password to access the server) to model the new sequence, using the old one as a template. Check that the alignment is correct (identical alignment except the new region) and let the server prepare your structure.
Hope it helps,
Regards,
Marco
Il 26/07/2021 21:19, Nicole Ostrovsky via Chimera-users ha scritto:
Hello,
I have a structure which I've cut a section out of and I am working on connecting the two loose ends together. I wanted to connect them with two glycine residues - since they are easiest to work with and have no side chains. I am doing this using the Modify Structure option under the Build structure tool and adding one atom at a time. However, when I try to minimize my newly created glycine, I get the error message "No MMTK name for atom "H1" in standard residue "GLY"" (I've attached a picture of my reply log). I'm not sure how to troubleshoot this.
Is there a better way to connect two ends of a peptide, or should I change the way I am using the modify structure tool?
Thank you.
Nicole Ostrovsky
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu
Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- Dr.Marco Sette, Ph.D. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette@uniroma2.it
e-mail: m77it@yahoo.it
Tel.: +39-0672594424 Fax: +39-0672594328
http://stc.uniroma2.it/?page_id=622&cn-entry-slug=marco-sette
Ai sensi del Regolamento (UE) 2016/679 e dei principi contenuti nelle linee guida del Garante per posta elettronica e interne (artt. 2 e 15 Cost.; Corte cost. 17 luglio 1998, n. 281 e 11 marzo 1993, n. 81; art. 49 Codice dell’amministrazione digitale) si precisa che le informazioni contenute in questo messaggio -come pure i dati esteriori delle comunicazioni e i file allegati- sono riservate e ad uso esclusivo del destinatario. Divulgazione, copia, stampa o qualunque altro uso da parte di altri non è autorizzato. Qualora il messaggio in parola Le fosse pervenuto per errore, La preghiamo di eliminarlo senza copiarlo e di non inoltrarlo a terzi, dandocene gentilmente comunicazione al seguente indirizzo e-mail privacy@uniroma2.it .
On the basis of “(UE) Rules 2016/679 and the codes in general guidelines of Garante for electronic and internal mail (artt. 2 e 15 Cost.; Corte cost. 17 luglio 1998, n. 281 e 11 marzo 1993, n. 81; art. 49 Codice dell’amministrazione digitale) information here contained and any attachments is confidential and intended for the recipient(s) only. Dissemination, copying, printing or use by anybody else is unauthorized. If you are not the intended recipient, please delete this message and any attachments and advise the sender by return e-mail to privacy@uniroma2.it. _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
The modeller tool seems to be working for me, thank you very much! I will email again if any problems arise with it.
One more question - is there a command or a tool I can use to find the internal energy of a peptide? I have been running a 1 DS 0 CGS minimization which means my peptide moves just slightly but I'm wondering if there is a better way to do it.
Nicole Ostrovsky
On Mon, Jul 26, 2021 at 6:24 PM Elaine Meng meng@cgl.ucsf.edu wrote:
Thanks, Marco -- good idea! It might give a more reasonable result than manual building + minimization.
Nicole, see: < https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m...
https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/dor.html
Elaine
On Jul 26, 2021, at 2:58 PM, Marco Sette via Chimera-users <
chimera-users@cgl.ucsf.edu> wrote:
Hi Nicole,
you could note the pdb name of the old structure and use the homology
modelling tool provided in Chimera (it is based on Modeller then you need a password to access the server) to model the new sequence, using the old one as a template. Check that the alignment is correct (identical alignment except the new region) and let the server prepare your structure.
Hope it helps,
Regards,
Marco
Il 26/07/2021 21:19, Nicole Ostrovsky via Chimera-users ha scritto:
Hello,
I have a structure which I've cut a section out of and I am working on
connecting the two loose ends together. I wanted to connect them with two glycine residues - since they are easiest to work with and have no side chains. I am doing this using the Modify Structure option under the Build structure tool and adding one atom at a time. However, when I try to minimize my newly created glycine, I get the error message "No MMTK name for atom "H1" in standard residue "GLY"" (I've attached a picture of my reply log). I'm not sure how to troubleshoot this.
Is there a better way to connect two ends of a peptide, or should I
change the way I am using the modify structure tool?
Thank you.
Nicole Ostrovsky
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu
Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- Dr.Marco Sette, Ph.D. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette@uniroma2.it
e-mail: m77it@yahoo.it
Tel.: +39-0672594424 Fax: +39-0672594328
http://stc.uniroma2.it/?page_id=622&cn-entry-slug=marco-sette
Ai sensi del Regolamento (UE) 2016/679 e dei principi contenuti nelle
linee guida del Garante per posta elettronica e interne (artt. 2 e 15 Cost.; Corte cost. 17 luglio 1998, n. 281 e 11 marzo 1993, n. 81; art. 49 Codice dell’amministrazione digitale) si precisa che le informazioni contenute in questo messaggio -come pure i dati esteriori delle comunicazioni e i file allegati- sono riservate e ad uso esclusivo del destinatario. Divulgazione, copia, stampa o qualunque altro uso da parte di altri non è autorizzato. Qualora il messaggio in parola Le fosse pervenuto per errore, La preghiamo di eliminarlo senza copiarlo e di non inoltrarlo a terzi, dandocene gentilmente comunicazione al seguente indirizzo e-mail
privacy@uniroma2.it .
On the basis of “(UE) Rules 2016/679 and the codes in general guidelines
of Garante for electronic and internal mail (artt. 2 e 15 Cost.; Corte cost. 17 luglio 1998, n. 281 e 11 marzo 1993, n. 81; art. 49 Codice dell’amministrazione digitale) information here contained and any attachments is confidential and intended for the recipient(s) only. Dissemination, copying, printing or use by anybody else is unauthorized. If you are not the intended recipient, please delete this message and any attachments and advise the sender by return e-mail to
privacy@uniroma2.it. _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription:
Hi Nicole, Personally I wouldn't recommend using the total energy values. They are calculated to get a gradient to allow minimization, but the specific total quantities aren't that meaningful. Tiny movements can make a huge difference in the value and you don't know the "shape" of the whole multidimensional energy landscape.
Modeller includes optimization (e.g. see https://salilab.org/archives/modeller_usage/2009/msg00162.html) so you don't need to minimize afterwards, and also various model scores that Modeller and/or the Sali lab Model Evaluation Server gives are probably a more relevant measure of the quality of the result than some energy value.
Model scores that may be reported: https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modbase.html#modellist
Also Modeller puts a confidence value per residue in the bfactor column, so if you color the resulting model by "bfactor" you can see which areas are more or less well modeled. e.g. command
rangecolor bfactor,r min blue mid white max red
would show less reliable parts as red. The value is described here: https://salilab.org/archives/modeller_usage/2003/msg00164.html
However, it may not add more information to what you already know, that the part that you changed is not in the template, so it will be scored as less reliable because less information was used to generate it.
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 27, 2021, at 7:25 AM, Nicole Ostrovsky via Chimera-users chimera-users@cgl.ucsf.edu wrote:
The modeller tool seems to be working for me, thank you very much! I will email again if any problems arise with it.
One more question - is there a command or a tool I can use to find the internal energy of a peptide? I have been running a 1 DS 0 CGS minimization which means my peptide moves just slightly but I'm wondering if there is a better way to do it.
Nicole Ostrovsky
On Mon, Jul 26, 2021 at 6:24 PM Elaine Meng meng@cgl.ucsf.edu wrote: Thanks, Marco -- good idea! It might give a more reasonable result than manual building + minimization.
Nicole, see: https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html#comparative https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/dor.html
Elaine
On Jul 26, 2021, at 2:58 PM, Marco Sette via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Hi Nicole,
you could note the pdb name of the old structure and use the homology modelling tool provided in Chimera (it is based on Modeller then you need a password to access the server) to model the new sequence, using the old one as a template. Check that the alignment is correct (identical alignment except the new region) and let the server prepare your structure.
Hope it helps,
Regards,
Marco
Il 26/07/2021 21:19, Nicole Ostrovsky via Chimera-users ha scritto:
Hello,
I have a structure which I've cut a section out of and I am working on connecting the two loose ends together. I wanted to connect them with two glycine residues - since they are easiest to work with and have no side chains. I am doing this using the Modify Structure option under the Build structure tool and adding one atom at a time. However, when I try to minimize my newly created glycine, I get the error message "No MMTK name for atom "H1" in standard residue "GLY"" (I've attached a picture of my reply log). I'm not sure how to troubleshoot this.
Is there a better way to connect two ends of a peptide, or should I change the way I am using the modify structure tool?
Thank you.
Nicole Ostrovsky
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu
Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- Dr.Marco Sette, Ph.D. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette@uniroma2.it
e-mail: m77it@yahoo.it
Tel.: +39-0672594424 Fax: +39-0672594328
http://stc.uniroma2.it/?page_id=622&cn-entry-slug=marco-sette
Ai sensi del Regolamento (UE) 2016/679 e dei principi contenuti nelle linee guida del Garante per posta elettronica e interne (artt. 2 e 15 Cost.; Corte cost. 17 luglio 1998, n. 281 e 11 marzo 1993, n. 81; art. 49 Codice dell’amministrazione digitale) si precisa che le informazioni contenute in questo messaggio -come pure i dati esteriori delle comunicazioni e i file allegati- sono riservate e ad uso esclusivo del destinatario. Divulgazione, copia, stampa o qualunque altro uso da parte di altri non è autorizzato. Qualora il messaggio in parola Le fosse pervenuto per errore, La preghiamo di eliminarlo senza copiarlo e di non inoltrarlo a terzi, dandocene gentilmente comunicazione al seguente indirizzo e-mail privacy@uniroma2.it .
On the basis of “(UE) Rules 2016/679 and the codes in general guidelines of Garante for electronic and internal mail (artt. 2 e 15 Cost.; Corte cost. 17 luglio 1998, n. 281 e 11 marzo 1993, n. 81; art. 49 Codice dell’amministrazione digitale) information here contained and any attachments is confidential and intended for the recipient(s) only. Dissemination, copying, printing or use by anybody else is unauthorized. If you are not the intended recipient, please delete this message and any attachments and advise the sender by return e-mail to privacy@uniroma2.it.
Hi Elaine,
That makes a lot of sense, thank you very much for your help.
On Tue, Jul 27, 2021 at 11:31 AM Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Nicole, Personally I wouldn't recommend using the total energy values. They are calculated to get a gradient to allow minimization, but the specific total quantities aren't that meaningful. Tiny movements can make a huge difference in the value and you don't know the "shape" of the whole multidimensional energy landscape.
Modeller includes optimization (e.g. see < https://salilab.org/archives/modeller_usage/2009/msg00162.html%3E) so you don't need to minimize afterwards, and also various model scores that Modeller and/or the Sali lab Model Evaluation Server gives are probably a more relevant measure of the quality of the result than some energy value.
Model scores that may be reported: https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modbase.html#modellist
Also Modeller puts a confidence value per residue in the bfactor column, so if you color the resulting model by "bfactor" you can see which areas are more or less well modeled. e.g. command
rangecolor bfactor,r min blue mid white max red
would show less reliable parts as red. The value is described here: https://salilab.org/archives/modeller_usage/2003/msg00164.html
However, it may not add more information to what you already know, that the part that you changed is not in the template, so it will be scored as less reliable because less information was used to generate it.
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 27, 2021, at 7:25 AM, Nicole Ostrovsky via Chimera-users <
chimera-users@cgl.ucsf.edu> wrote:
The modeller tool seems to be working for me, thank you very much! I
will email again if any problems arise with it.
One more question - is there a command or a tool I can use to find the
internal energy of a peptide? I have been running a 1 DS 0 CGS minimization which means my peptide moves just slightly but I'm wondering if there is a better way to do it.
Nicole Ostrovsky
On Mon, Jul 26, 2021 at 6:24 PM Elaine Meng meng@cgl.ucsf.edu wrote: Thanks, Marco -- good idea! It might give a more reasonable result than
manual building + minimization.
Nicole, see: <
https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m...
https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/dor.html
Elaine
On Jul 26, 2021, at 2:58 PM, Marco Sette via Chimera-users <
chimera-users@cgl.ucsf.edu> wrote:
Hi Nicole,
you could note the pdb name of the old structure and use the homology
modelling tool provided in Chimera (it is based on Modeller then you need a password to access the server) to model the new sequence, using the old one as a template. Check that the alignment is correct (identical alignment except the new region) and let the server prepare your structure.
Hope it helps,
Regards,
Marco
Il 26/07/2021 21:19, Nicole Ostrovsky via Chimera-users ha scritto:
Hello,
I have a structure which I've cut a section out of and I am working
on connecting the two loose ends together. I wanted to connect them with two glycine residues - since they are easiest to work with and have no side chains. I am doing this using the Modify Structure option under the Build structure tool and adding one atom at a time. However, when I try to minimize my newly created glycine, I get the error message "No MMTK name for atom "H1" in standard residue "GLY"" (I've attached a picture of my reply log). I'm not sure how to troubleshoot this.
Is there a better way to connect two ends of a peptide, or should I
change the way I am using the modify structure tool?
Thank you.
Nicole Ostrovsky
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu
Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- Dr.Marco Sette, Ph.D. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette@uniroma2.it
e-mail: m77it@yahoo.it
Tel.: +39-0672594424 Fax: +39-0672594328
http://stc.uniroma2.it/?page_id=622&cn-entry-slug=marco-sette
Ai sensi del Regolamento (UE) 2016/679 e dei principi contenuti nelle
linee guida del Garante per posta elettronica e interne (artt. 2 e 15 Cost.; Corte cost. 17 luglio 1998, n. 281 e 11 marzo 1993, n. 81; art. 49 Codice dell’amministrazione digitale) si precisa che le informazioni contenute in questo messaggio -come pure i dati esteriori delle comunicazioni e i file allegati- sono riservate e ad uso esclusivo del destinatario. Divulgazione, copia, stampa o qualunque altro uso da parte di altri non è autorizzato. Qualora il messaggio in parola Le fosse pervenuto per errore, La preghiamo di eliminarlo senza copiarlo e di non inoltrarlo a terzi, dandocene gentilmente comunicazione al seguente indirizzo e-mail
privacy@uniroma2.it .
On the basis of “(UE) Rules 2016/679 and the codes in general
guidelines of Garante for electronic and internal mail (artt. 2 e 15 Cost.; Corte cost. 17 luglio 1998, n. 281 e 11 marzo 1993, n. 81; art. 49 Codice dell’amministrazione digitale) information here contained and any attachments is confidential and intended for the recipient(s) only. Dissemination, copying, printing or use by anybody else is unauthorized. If you are not the intended recipient, please delete this message and any attachments and advise the sender by return e-mail to
privacy@uniroma2.it.
participants (3)
-
Elaine Meng -
Marco Sette -
Nicole Ostrovsky