How to insert a nucleotide to a pdb
Hi, I have a pdb-file of the ribosome and would like to insert two nucleotides to one of the rRNA-chains. How do I do that? I’ve found the addaa command for amino acids, is there a similar one for nucleotides? Best regards, Magdalena När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>.
Hi Magdalena, Sorry, there is no command to add a nucleotide residue on the end of a nucleotide chain. You could still try to do this in Chimera, but it may be tricky and have several steps: (1) find another PDB structure that has those two residues, then open it, delete all the rest of that structure - OR - use the Start Structure section of the Build Structure tool (in menu under Tools... Structure Editing) to build the dinucleotide. This will only build helical conformations, however. (2) use the Join Models section in the Build Structure tool to combine and bond the 2 residues into your original structure. It may be hard to get the right angles/position, so you may have to rotate some bonds after that (see Adjust Torsions section of the Build Structure tool). Click the Help button on the Build Structure tool for details, or see the copy of the same information at our website: <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 Oct 25, 2022, at 4:56 AM, Magdalena Riad via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi, I have a pdb-file of the ribosome and would like to insert two nucleotides to one of the rRNA-chains. How do I do that? I’ve found the addaa command for amino acids, is there a similar one for nucleotides? Best regards, Magdalena
Hi Elaine, Thanks a lot for your answer. I actually want to insert the nucleotides into the middle of an RNA sequence. Then that gets even trickier I guess? Cheers, Magdalena Skickat från Outlook för iOS<https://aka.ms/o0ukef> ________________________________ Från: Elaine Meng <meng@cgl.ucsf.edu> Skickat: Tuesday, October 25, 2022 7:28:13 PM Till: Magdalena Riad <magdalena.riad@ki.se> Kopia: chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu> Ämne: Re: [Chimera-users] How to insert a nucleotide to a pdb [Du får inte e-post ofta från meng@cgl.ucsf.edu. Läs om varför det här är viktigt på https://aka.ms/LearnAboutSenderIdentification ] Hi Magdalena, Sorry, there is no command to add a nucleotide residue on the end of a nucleotide chain. You could still try to do this in Chimera, but it may be tricky and have several steps: (1) find another PDB structure that has those two residues, then open it, delete all the rest of that structure - OR - use the Start Structure section of the Build Structure tool (in menu under Tools... Structure Editing) to build the dinucleotide. This will only build helical conformations, however. (2) use the Join Models section in the Build Structure tool to combine and bond the 2 residues into your original structure. It may be hard to get the right angles/position, so you may have to rotate some bonds after that (see Adjust Torsions section of the Build Structure tool). Click the Help button on the Build Structure tool for details, or see the copy of the same information at our website: <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Fediting%2Fediting.html&data=05%7C01%7Cmagdalena.riad%40ki.se%7C31d4f661cfdc40b8f0d308dab6ae4f02%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C638023157018301548%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=i3FQM%2BQKBpRtum7eZqw8B35f1K2BkuLwbsLMixSmeXA%3D&reserved=0> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 25, 2022, at 4:56 AM, Magdalena Riad via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi, I have a pdb-file of the ribosome and would like to insert two nucleotides to one of the rRNA-chains. How do I do that? I’ve found the addaa command for amino acids, is there a similar one for nucleotides? Best regards, Magdalena
När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>.
Dear all, is there a way in Chimera or ChimeraX to get the unit-cell box being drawn in another colour than white? This forces the background to be dark.... Thanks a lot in advance, Xavier On 26/10/22 08:03, Magdalena Riad via Chimera-users wrote:
Hi Elaine,
Thanks a lot for your answer.
I actually want to insert the nucleotides into the middle of an RNA sequence. Then that gets even trickier I guess?
Cheers, Magdalena
Skickat från Outlook för iOS <https://aka.ms/o0ukef> ------------------------------------------------------------------------ *Från:* Elaine Meng <meng@cgl.ucsf.edu> *Skickat:* Tuesday, October 25, 2022 7:28:13 PM *Till:* Magdalena Riad <magdalena.riad@ki.se> *Kopia:* chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu> *Ämne:* Re: [Chimera-users] How to insert a nucleotide to a pdb [Du får inte e-post ofta från meng@cgl.ucsf.edu. Läs om varför det här är viktigt på https://aka.ms/LearnAboutSenderIdentification ]
Hi Magdalena, Sorry, there is no command to add a nucleotide residue on the end of a nucleotide chain.
You could still try to do this in Chimera, but it may be tricky and have several steps:
(1) find another PDB structure that has those two residues, then open it, delete all the rest of that structure - OR - use the Start Structure section of the Build Structure tool (in menu under Tools... Structure Editing) to build the dinucleotide. This will only build helical conformations, however.
(2) use the Join Models section in the Build Structure tool to combine and bond the 2 residues into your original structure.
It may be hard to get the right angles/position, so you may have to rotate some bonds after that (see Adjust Torsions section of the Build Structure tool).
Click the Help button on the Build Structure tool for details, or see the copy of the same information at our website: <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.u... <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Fediting%2Fediting.html&data=05%7C01%7Cmagdalena.riad%40ki.se%7C31d4f661cfdc40b8f0d308dab6ae4f02%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C638023157018301548%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=i3FQM%2BQKBpRtum7eZqw8B35f1K2BkuLwbsLMixSmeXA%3D&reserved=0>>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 25, 2022, at 4:56 AM, Magdalena Riad via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi, I have a pdb-file of the ribosome and would like to insert two nucleotides to one of the rRNA-chains. How do I do that? I’ve found the addaa command for amino acids, is there a similar one for nucleotides? Best regards, Magdalena
/När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. /Här finns information om hur KI behandlar personuppgifter <https://ki.se/medarbetare/integritetsskyddspolicy>.
/Sending email to Karolinska Institutet (KI) will result in KI processing your personal data./ You can read more about KI’s processing of personal data here <https://ki.se/en/staff/data-protection-policy>.
_______________________________________________ Chimera-users mailing list:Chimera-users@cgl.ucsf.edu Manage subscription:https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
--
Hi Xavier, You can select the box (Ctrl-click on it) and then use menu: Actions... Color... [choose color], then clear selection by Ctrl-click on blank area of window or menu Select... Clear Selection. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 26, 2022, at 1:56 AM, F.Xavier Gomis-Rüth via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear all, is there a way in Chimera or ChimeraX to get the unit-cell box being drawn in another colour than white? This forces the background to be dark.... Thanks a lot in advance, Xavier
Thanks a lot, Elaine! On 26/10/22 17:45, Elaine Meng wrote:
Hi Xavier, You can select the box (Ctrl-click on it) and then use menu: Actions... Color... [choose color], then clear selection by Ctrl-click on blank area of window or menu Select... Clear Selection. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 26, 2022, at 1:56 AM, F.Xavier Gomis-Rüth via Chimera-users<chimera-users@cgl.ucsf.edu> wrote:
Dear all, is there a way in Chimera or ChimeraX to get the unit-cell box being drawn in another colour than white? This forces the background to be dark.... Thanks a lot in advance, Xavier
--
Dear Elaine, I am now trying to get this done in ChimeraX where there is indeed a similar option. Unfortunately, if I proceed as in the instructions I do not get the cell box, in contrast with old Chimera. I also tried through the command line but unsuccessfully. Am I missing something? Thanks a lot in advance, Xavier On 26/10/22 17:45, Elaine Meng wrote:
Hi Xavier, You can select the box (Ctrl-click on it) and then use menu: Actions... Color... [choose color], then clear selection by Ctrl-click on blank area of window or menu Select... Clear Selection. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 26, 2022, at 1:56 AM, F.Xavier Gomis-Rüth via Chimera-users<chimera-users@cgl.ucsf.edu> wrote:
Dear all, is there a way in Chimera or ChimeraX to get the unit-cell box being drawn in another colour than white? This forces the background to be dark.... Thanks a lot in advance, Xavier
--
Hi Xavier, As far as I can tell, it is exactly the same in ChimeraX as in Chimera. First, make sure you aren't using a very old version of ChimeraX. I tried it in ChimeraX 1.5 release candidate (2022-11-08) just now: - open your structure that has unit cell information, e.g. 1fav - in Unit Cell tool (menu: Tools... Higher-Order Structure... Unit Cell) click Outline to show unit cell box - if you want to change box outline color, can use the same method as described below for Chimera. I wasn't able to select it by Ctrl-click, however, so instead use the selection (hand with green dot) checkbox in the Model Panel to select it, then use Actions... Color... [...]. Or, you can just click the color square in the Model Panel and use the system color chooser to change the color interactively. Screenshot: I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco P.S. for ChimeraX questions specifically, you may want to use the other mailing list, chimerax-users@cgl.ucsf.edu
On Nov 18, 2022, at 7:03 AM, F.Xavier Gomis-Rüth via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Elaine, I am now trying to get this done in ChimeraX where there is indeed a similar option. Unfortunately, if I proceed as in the instructions I do not get the cell box, in contrast with old Chimera. I also tried through the command line but unsuccessfully. Am I missing something? Thanks a lot in advance, Xavier
On 26/10/22 17:45, Elaine Meng wrote:
Hi Xavier, You can select the box (Ctrl-click on it) and then use menu: Actions... Color... [choose color], then clear selection by Ctrl-click on blank area of window or menu Select... Clear Selection. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 26, 2022, at 1:56 AM, F.Xavier Gomis-Rüth via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear all, is there a way in Chimera or ChimeraX to get the unit-cell box being drawn in another colour than white? This forces the background to be dark.... Thanks a lot in advance, Xavier
Thanks a lot, Elaine, this worked indeed! Just one final point: how can I make the linewidth larger? When I make a picture, the thin lines of the box disappear. I understand ChimeraX interpretes these lines as a surface, I can change the colour when choosing surface in the colour blow up. On 18/11/22 17:49, Elaine Meng wrote:
Hi Xavier, As far as I can tell, it is exactly the same in ChimeraX as in Chimera. First, make sure you aren't using a very old version of ChimeraX. I tried it in ChimeraX 1.5 release candidate (2022-11-08) just now:
- open your structure that has unit cell information, e.g. 1fav
- in Unit Cell tool (menu: Tools... Higher-Order Structure... Unit Cell) click Outline to show unit cell box
- if you want to change box outline color, can use the same method as described below for Chimera. I wasn't able to select it by Ctrl-click, however, so instead use the selection (hand with green dot) checkbox in the Model Panel to select it, then use Actions... Color... [...]. Or, you can just click the color square in the Model Panel and use the system color chooser to change the color interactively. Screenshot:
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
P.S. for ChimeraX questions specifically, you may want to use the other mailing list, chimerax-users@cgl.ucsf.edu
On Nov 18, 2022, at 7:03 AM, F.Xavier Gomis-Rüth via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Elaine, I am now trying to get this done in ChimeraX where there is indeed a similar option. Unfortunately, if I proceed as in the instructions I do not get the cell box, in contrast with old Chimera. I also tried through the command line but unsuccessfully. Am I missing something? Thanks a lot in advance, Xavier
On 26/10/22 17:45, Elaine Meng wrote:
Hi Xavier, You can select the box (Ctrl-click on it) and then use menu: Actions... Color... [choose color], then clear selection by Ctrl-click on blank area of window or menu Select... Clear Selection. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 26, 2022, at 1:56 AM, F.Xavier Gomis-Rüth via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear all, is there a way in Chimera or ChimeraX to get the unit-cell box being drawn in another colour than white? This forces the background to be dark.... Thanks a lot in advance, Xavier
--
(switching to chimerax-users address since this is all about ChimeraX, not Chimera) Sorry no, there is no linewidth setting on the unit cell outline box. However, you can "fake it" by selecting that model so that there are green outlines to show the selection, and then changing the selection-outline color and width: (1) select the outline box model, e.g. as described in the previous message by checking the selection box in the Model Panel (2) use "graphics selection" command to change the selection-outline color and thickness <https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#selection> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 18, 2022, at 9:12 AM, F.Xavier Gomis-Rüth via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Thanks a lot, Elaine, this worked indeed! Just one final point: how can I make the linewidth larger? When I make a picture, the thin lines of the box disappear. I understand ChimeraX interpretes these lines as a surface, I can change the colour when choosing surface in the colour blow up.
On 18/11/22 17:49, Elaine Meng wrote:
Hi Xavier, As far as I can tell, it is exactly the same in ChimeraX as in Chimera. First, make sure you aren't using a very old version of ChimeraX. I tried it in ChimeraX 1.5 release candidate (2022-11-08) just now:
- open your structure that has unit cell information, e.g. 1fav
- in Unit Cell tool (menu: Tools... Higher-Order Structure... Unit Cell) click Outline to show unit cell box
- if you want to change box outline color, can use the same method as described below for Chimera. I wasn't able to select it by Ctrl-click, however, so instead use the selection (hand with green dot) checkbox in the Model Panel to select it, then use Actions... Color... [...]. Or, you can just click the color square in the Model Panel and use the system color chooser to change the color interactively. Screenshot:
<Screen Shot 2022-11-18 at 8.48.02 AM.png>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
P.S. for ChimeraX questions specifically, you may want to use the other mailing list, chimerax-users@cgl.ucsf.edu
On Nov 18, 2022, at 7:03 AM, F.Xavier Gomis-Rüth via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Elaine, I am now trying to get this done in ChimeraX where there is indeed a similar option. Unfortunately, if I proceed as in the instructions I do not get the cell box, in contrast with old Chimera. I also tried through the command line but unsuccessfully. Am I missing something? Thanks a lot in advance, Xavier
On 26/10/22 17:45, Elaine Meng wrote:
Hi Xavier, You can select the box (Ctrl-click on it) and then use menu: Actions... Color... [choose color], then clear selection by Ctrl-click on blank area of window or menu Select... Clear Selection. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 26, 2022, at 1:56 AM, F.Xavier Gomis-Rüth via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear all, is there a way in Chimera or ChimeraX to get the unit-cell box being drawn in another colour than white? This forces the background to be dark.... Thanks a lot in advance, Xavier
-- <fxgr_signanew.jpg> _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
Hi Magdalena, Chimera does not include tools to insert nucleotides in the middle of a chain. However, take a look at the RNArtist program for RNA modeling -- it has a lot of fancy features and interfaces with Chimera (or ChimeraX) for the display: <https://github.com/fjossinet/RNArtist> There is also the program Assemble2 by the same author, also works with Chimera: <https://www.rbvi.ucsf.edu/chimera/plugins/plugins.html#assemble2> <http://bioinformatics.org/assemble/index.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 Oct 25, 2022, at 11:03 PM, Magdalena Riad via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Elaine,
Thanks a lot for your answer.
I actually want to insert the nucleotides into the middle of an RNA sequence. Then that gets even trickier I guess?
Cheers, Magdalena
Skickat från Outlook för iOS Från: Elaine Meng <meng@cgl.ucsf.edu> Skickat: Tuesday, October 25, 2022 7:28:13 PM Till: Magdalena Riad <magdalena.riad@ki.se> Kopia: chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu> Ämne: Re: [Chimera-users] How to insert a nucleotide to a pdb
[Du får inte e-post ofta från meng@cgl.ucsf.edu. Läs om varför det här är viktigt påhttps://aka.ms/LearnAboutSenderIdentification ]
Hi Magdalena, Sorry, there is no command to add a nucleotide residue on the end of a nucleotide chain.
You could still try to do this in Chimera, but it may be tricky and have several steps:
(1) find another PDB structure that has those two residues, then open it, delete all the rest of that structure - OR - use the Start Structure section of the Build Structure tool (in menu under Tools... Structure Editing) to build the dinucleotide. This will only build helical conformations, however.
(2) use the Join Models section in the Build Structure tool to combine and bond the 2 residues into your original structure.
It may be hard to get the right angles/position, so you may have to rotate some bonds after that (see Adjust Torsions section of the Build Structure tool).
Click the Help button on the Build Structure tool for details, or see the copy of the same information at our website: <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Fediting%2Fediting.html&data=05%7C01%7Cmagdalena.riad%40ki.se%7C31d4f661cfdc40b8f0d308dab6ae4f02%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C638023157018301548%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=i3FQM%2BQKBpRtum7eZqw8B35f1K2BkuLwbsLMixSmeXA%3D&reserved=0>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 25, 2022, at 4:56 AM, Magdalena Riad via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi, I have a pdb-file of the ribosome and would like to insert two nucleotides to one of the rRNA-chains. How do I do that? I’ve found the addaa command for amino acids, is there a similar one for nucleotides? Best regards, Magdalena
När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter.
Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here. _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Elaine Meng -
F.Xavier Gomis-Rüth -
Magdalena Riad