Hi I am learning Chimera and I have gone through soe online tutorials. The tutorials showed how to introduce point mutation by Rotamers command. But it only allows to replace 1 ammino acid residue at a time. I want to insert 4-5 ammino acid residues in a gap of a sequence. Is there any standard procedure, command in Chimera that will let me do this type of residue insertion? This is really crucial for my research work. Thanks Tanzila Islam Graduate Student Washington State University
Hi Tanzila Islam, To add more residues instead of just changing the residues that are already in the structure, probably the best way is to use the Modeller interface of Chimera. This runs a Modeller web service, for which you have to register to get a “license key” to enter into the dialog … this is free for noncommercial users, but it may take a while for them to respond with the key. To get the key, see: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html#modeller-license> After you get the key, then the steps would be: (1) make a sequence file (plain text file in FASTA format) containing the sequence that you want, including the insertion, and open it in Chimera. The filename should end in “.fa” to indicate the format. The sequence will appear in a separate Chimera window. (2) make sure the sequence is associated with your starting structure. It will probably happen automatically when both the sequence and structure are opened in Chimera. You can check by seeing if the sequence window menu: "Structure… Modeller (loops/refinement)” is grayed out. If it is grayed out, use sequence window menu: “Structure… Associations” to manually associate the structure with the sequence. (3) Choose sequence window menu: "Structure… Modeller (loops/refinement)” and in the resulting dialog choose to model “non-terminal missing structure” or “all missing structure” … doesn’t matter which one of those since you are modeling an insertion. For information on the options in that dialog, see: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html#building> 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 Nov 17, 2016, at 10:59 AM, Islam, Tanzila <tanzila.islam@wsu.edu> wrote:
Hi I am learning Chimera and I have gone through soe online tutorials. The tutorials showed how to introduce point mutation by Rotamers command. But it only allows to replace 1 ammino acid residue at a time.
I want to insert 4-5 ammino acid residues in a gap of a sequence. Is there any standard procedure, command in Chimera that will let me do this type of residue insertion? This is really crucial for my research work. Thanks Tanzila Islam Graduate Student Washington State University
Thanks a lot for your email. But the 2 links you gave are not working and leading to the same page named 'Red Angus Society'. Is this the correct site? Tanzila Islam Graduate Student Washington State University ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Thursday, November 17, 2016 2:08:16 PM To: Islam, Tanzila Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Mutation in Chimera Hi Tanzila Islam, To add more residues instead of just changing the residues that are already in the structure, probably the best way is to use the Modeller interface of Chimera. This runs a Modeller web service, for which you have to register to get a “license key” to enter into the dialog … this is free for noncommercial users, but it may take a while for them to respond with the key. To get the key, see: <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chimer... > After you get the key, then the steps would be: (1) make a sequence file (plain text file in FASTA format) containing the sequence that you want, including the insertion, and open it in Chimera. The filename should end in “.fa” to indicate the format. The sequence will appear in a separate Chimera window. (2) make sure the sequence is associated with your starting structure. It will probably happen automatically when both the sequence and structure are opened in Chimera. You can check by seeing if the sequence window menu: "Structure… Modeller (loops/refinement)” is grayed out. If it is grayed out, use sequence window menu: “Structure… Associations” to manually associate the structure with the sequence. (3) Choose sequence window menu: "Structure… Modeller (loops/refinement)” and in the resulting dialog choose to model “non-terminal missing structure” or “all missing structure” … doesn’t matter which one of those since you are modeling an insertion. For information on the options in that dialog, see: <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chimer... > 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 Nov 17, 2016, at 10:59 AM, Islam, Tanzila <tanzila.islam@wsu.edu> wrote:
Hi I am learning Chimera and I have gone through soe online tutorials. The tutorials showed how to introduce point mutation by Rotamers command. But it only allows to replace 1 ammino acid residue at a time.
I want to insert 4-5 ammino acid residues in a gap of a sequence. Is there any standard procedure, command in Chimera that will let me do this type of residue insertion? This is really crucial for my research work. Thanks Tanzila Islam Graduate Student Washington State University
What???? those are not the links I sent…. I have no idea what is wrong with your email, but the links were fine in the copy of the mail that I received. I was about to send another link that contains the original posting from me, but now I’m afraid something will go crazy along the way. Hmm. OK, try this, how to get the page with that original posting. Go to UCSF Chimera homepage (you can google “ucsf chimera". Then near the bottom of the lefthand Quick Links section, click the “Contact Us” link. Then click the link to “view” the whole archive of chimera-users. Then click Thread in the November 2016 row, then scroll down to my first reply to you, and click to view it. In that page, I see the links just as I sent them, and when I click them they go to the correct places. Elaine
On Nov 17, 2016, at 2:46 PM, Islam, Tanzila <tanzila.islam@wsu.edu> wrote:
Thanks a lot for your email. But the 2 links you gave are not working and leading to the same page named 'Red Angus Society'. Is this the correct site?
Tanzila Islam Graduate Student Washington State University From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Thursday, November 17, 2016 2:08:16 PM To: Islam, Tanzila Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Mutation in Chimera
Hi Tanzila Islam, To add more residues instead of just changing the residues that are already in the structure, probably the best way is to use the Modeller interface of Chimera. This runs a Modeller web service, for which you have to register to get a “license key” to enter into the dialog … this is free for noncommercial users, but it may take a while for them to respond with the key. To get the key, see: <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chimer... >
After you get the key, then the steps would be:
(1) make a sequence file (plain text file in FASTA format) containing the sequence that you want, including the insertion, and open it in Chimera. The filename should end in “.fa” to indicate the format. The sequence will appear in a separate Chimera window.
(2) make sure the sequence is associated with your starting structure. It will probably happen automatically when both the sequence and structure are opened in Chimera. You can check by seeing if the sequence window menu: "Structure… Modeller (loops/refinement)” is grayed out. If it is grayed out, use sequence window menu: “Structure… Associations” to manually associate the structure with the sequence.
(3) Choose sequence window menu: "Structure… Modeller (loops/refinement)” and in the resulting dialog choose to model “non-terminal missing structure” or “all missing structure” … doesn’t matter which one of those since you are modeling an insertion. For information on the options in that dialog, see: <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chimer... >
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 Nov 17, 2016, at 10:59 AM, Islam, Tanzila <tanzila.islam@wsu.edu> wrote:
Hi I am learning Chimera and I have gone through soe online tutorials. The tutorials showed how to introduce point mutation by Rotamers command. But it only allows to replace 1 ammino acid residue at a time.
I want to insert 4-5 ammino acid residues in a gap of a sequence. Is there any standard procedure, command in Chimera that will let me do this type of residue insertion? This is really crucial for my research work. Thanks Tanzila Islam Graduate Student Washington State University
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Thanks a lot. I have got the product key and installed modeller. I will try the way you suggested. It was really helpful. Tanzila Islam Graduate Student Washington State University ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Thursday, November 17, 2016 3:38:12 PM To: Islam, Tanzila Cc: chimera-users@cgl.ucsf.edu BB Subject: Re: [Chimera-users] Mutation in Chimera What???? those are not the links I sent…. I have no idea what is wrong with your email, but the links were fine in the copy of the mail that I received. I was about to send another link that contains the original posting from me, but now I’m afraid something will go crazy along the way. Hmm. OK, try this, how to get the page with that original posting. Go to UCSF Chimera homepage (you can google “ucsf chimera". Then near the bottom of the lefthand Quick Links section, click the “Contact Us” link. Then click the link to “view” the whole archive of chimera-users. Then click Thread in the November 2016 row, then scroll down to my first reply to you, and click to view it. In that page, I see the links just as I sent them, and when I click them they go to the correct places. Elaine
On Nov 17, 2016, at 2:46 PM, Islam, Tanzila <tanzila.islam@wsu.edu> wrote:
Thanks a lot for your email. But the 2 links you gave are not working and leading to the same page named 'Red Angus Society'. Is this the correct site?
Tanzila Islam Graduate Student Washington State University From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Thursday, November 17, 2016 2:08:16 PM To: Islam, Tanzila Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Mutation in Chimera
Hi Tanzila Islam, To add more residues instead of just changing the residues that are already in the structure, probably the best way is to use the Modeller interface of Chimera. This runs a Modeller web service, for which you have to register to get a “license key” to enter into the dialog … this is free for noncommercial users, but it may take a while for them to respond with the key. To get the key, see: <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chimera_docs_ContributedSoftware_multalignviewer_modeller.html-23modeller-2Dlicense&d=DgIF-g&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=zA9st_jbqMZ-6qaduW-fZ6ZgnxlqIQlkWFNGnI1qgus&m=qnzukRr71oE5Ot_xJugoDK0hgwfxK0qI7QPmc0Xates&s=V51J9advE8qkJUtFSQ9Yx1k6yK_iOdgZx6gREEKVuIs&e=>
After you get the key, then the steps would be:
(1) make a sequence file (plain text file in FASTA format) containing the sequence that you want, including the insertion, and open it in Chimera. The filename should end in “.fa” to indicate the format. The sequence will appear in a separate Chimera window.
(2) make sure the sequence is associated with your starting structure. It will probably happen automatically when both the sequence and structure are opened in Chimera. You can check by seeing if the sequence window menu: "Structure… Modeller (loops/refinement)” is grayed out. If it is grayed out, use sequence window menu: “Structure… Associations” to manually associate the structure with the sequence.
(3) Choose sequence window menu: "Structure… Modeller (loops/refinement)” and in the resulting dialog choose to model “non-terminal missing structure” or “all missing structure” … doesn’t matter which one of those since you are modeling an insertion. For information on the options in that dialog, see: <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chimera_docs_ContributedSoftware_multalignviewer_modeller.html-23building&d=DgIF-g&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=zA9st_jbqMZ-6qaduW-fZ6ZgnxlqIQlkWFNGnI1qgus&m=qnzukRr71oE5Ot_xJugoDK0hgwfxK0qI7QPmc0Xates&s=CVGkyCc5pUx7kCxie2lSflYKg3LlbbIxPJcq_oOL5OY&e=>
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 Nov 17, 2016, at 10:59 AM, Islam, Tanzila <tanzila.islam@wsu.edu> wrote:
Hi I am learning Chimera and I have gone through soe online tutorials. The tutorials showed how to introduce point mutation by Rotamers command. But it only allows to replace 1 ammino acid residue at a time.
I want to insert 4-5 ammino acid residues in a gap of a sequence. Is there any standard procedure, command in Chimera that will let me do this type of residue insertion? This is really crucial for my research work. Thanks Tanzila Islam Graduate Student Washington State University
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://urldefense.proofpoint.com/v2/url?u=http-3A__plato.cgl.ucsf.edu_mailm...
Hello Elaine How is everything going? I need a little help regarding modeller service with Chimera. I was able to perform some insertions to the protein structure using your methods. Your emails were very helpful. But the modeller is not working properly for last 2 days. Its showing error- But liiks like the service is down for last couple of days. ......................................................................................... ...................................................................................... NonChimeraError: Web service appears to be down. See Reply Log for more details. Service 'opal:Modeller9v8Service' is unavailable. See Reply Log for more details. Is there any problem with the web service that you know of? Will that be resolved soon? If you can tell me when I will be able to use the service, that will be very helpful. Thanks Tanzila Islam Graduate Student Washington State University ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Thursday, November 17, 2016 2:08:16 PM To: Islam, Tanzila Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Mutation in Chimera Hi Tanzila Islam, To add more residues instead of just changing the residues that are already in the structure, probably the best way is to use the Modeller interface of Chimera. This runs a Modeller web service, for which you have to register to get a “license key” to enter into the dialog … this is free for noncommercial users, but it may take a while for them to respond with the key. To get the key, see: <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chimer... > After you get the key, then the steps would be: (1) make a sequence file (plain text file in FASTA format) containing the sequence that you want, including the insertion, and open it in Chimera. The filename should end in “.fa” to indicate the format. The sequence will appear in a separate Chimera window. (2) make sure the sequence is associated with your starting structure. It will probably happen automatically when both the sequence and structure are opened in Chimera. You can check by seeing if the sequence window menu: "Structure… Modeller (loops/refinement)” is grayed out. If it is grayed out, use sequence window menu: “Structure… Associations” to manually associate the structure with the sequence. (3) Choose sequence window menu: "Structure… Modeller (loops/refinement)” and in the resulting dialog choose to model “non-terminal missing structure” or “all missing structure” … doesn’t matter which one of those since you are modeling an insertion. For information on the options in that dialog, see: <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chimer... > 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 Nov 17, 2016, at 10:59 AM, Islam, Tanzila <tanzila.islam@wsu.edu> wrote:
Hi I am learning Chimera and I have gone through soe online tutorials. The tutorials showed how to introduce point mutation by Rotamers command. But it only allows to replace 1 ammino acid residue at a time.
I want to insert 4-5 ammino acid residues in a gap of a sequence. Is there any standard procedure, command in Chimera that will let me do this type of residue insertion? This is really crucial for my research work. Thanks Tanzila Islam Graduate Student Washington State University
Hello Tanzila, Yes, the RBVI web services (running Modeller, Blast Protein and others from Chimera) are currently down. We are actively working to fix this problem, but I don’t know how soon it will be resolved. Best, 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 Jan 5, 2017, at 12:12 PM, Islam, Tanzila <tanzila.islam@wsu.edu> wrote:
Hello Elaine
How is everything going? I need a little help regarding modeller service with Chimera. I was able to perform some insertions to the protein structure using your methods. Your emails were very helpful.
But the modeller is not working properly for last 2 days. Its showing error-
But liiks like the service is down for last couple of days. ......................................................................................... ...................................................................................... NonChimeraError: Web service appears to be down. See Reply Log for more details. Service 'opal:Modeller9v8Service' is unavailable. See Reply Log for more details.
Is there any problem with the web service that you know of? Will that be resolved soon? If you can tell me when I will be able to use the service, that will be very helpful.
Thanks
Tanzila Islam Graduate Student Washington State University
participants (2)
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Elaine Meng -
Islam, Tanzila