Dear Sir/Madam,
I am using Chimara to display large proteins. It is very nice. 6DHO(PDB structure, see attachment) is a very recent PSII structure consisting both S2 and S3(richer) states, which are highly overlapped in the raw data. I am urgently wondering how can I separate S3 out from the S2/S3 mixture by Chimera, especially the OEY? cluster and all its ligands? Thank you very much!
Best wishes
Dear Yu,
Since I don’t know what S2 and S3 richer state is… I don’t know if this is going to help. but, you can open, select and save pdb chains in chimera command line and view only the selected subunits:
Example: 1) View only the selected chain ~display ~ribbon disp :.A-B
2) saving only selected PDB files open 6DHO select :.A-B write selected 0 test.pdb
then follow step 1.
if you don’t like cif file formats you can convert them in Phenix package (PDB tools).
Hope this helps, David
On Nov 24, 2018, at 11:28 AM, Yu Guo yg2@kth.se wrote:
Dear Sir/Madam, I am using Chimara to display large proteins. It is very nice. 6DHO(PDB structure, see attachment) is a very recent PSII structure consisting both S2 and S3(richer) states, which are highly overlapped in the raw data. I am urgently wondering how can I separate S3 out from the S2/S3 mixture by Chimera, especially the OEY cluster and all its ligands? Thank you very much! Best wishes
<6dho.cif>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu mailto:Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Yu Guo, Well, it all depends on how these two states are described in the file. I took a look at the associated paper in Nature and they don’t really say exactly how they described the two states, but they do mention modeling them at reduced occupancy. So my best guess if one structure has more than one state, they are described in the file is with “alternate locations” for some atoms (i.e. multiple positions for a given atom) with reduced occupancy values. For me, it is harder to figure out with mmCIF file than PDB because I’m more familiar with looking at PDB files in a text editor.
Usually when there are alternate locations, they are A and B. So, you could select (or “delete” instead of “select” but then there is no going back other than by re-opening the original file) all atoms with alternate locations A with command:
select @.A
… and similarly for alternate location B. In my tests, it looks like A has the lower occupancy than B, and selecting alternate location A or B will each select 2188 atoms. You could also select by occupancy value; however, I get different numbers depending on the value I choose, presumably omitting some atoms with alternate locations or including some of the atoms that do NOT have alternate locations, so be careful using that method:
select @/occupancy<0.4 … I avoid using “=“ because rounding issues may prevent exact match select @/occupancy<0.45 … or you can use a range, e.g. select @/occupancy>0.5 and occupancy<0.75
Because they did not clearly state in the paper (or at least I didn’t see it), I could not be sure, but guessing that alternate location A is the minority state and alternate location B is the majority state, and atoms without alternate locations were the same in both states.
How I figured out that alternate location A appears to have lower occupancy than B is with these commands: ~disp ~ribbon disp :ala labelopt info occupancy label :ala@.A ~label label :ala@.B
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. ChimeraX is much faster reading mmCIF than Chimera. Also it automatically only uses the alternate location set with average higher occupancy (in this case B). However, if you want to show the altloc set with lower occupancy, there is no easy/convenient method for it yet, although it can be done with a setattr command.
On Nov 24, 2018, at 11:28 AM, Yu Guo yg2@kth.se wrote:
Dear Sir/Madam, I am using Chimara to display large proteins. It is very nice. 6DHO(PDB structure, see attachment) is a very recent PSII structure consisting both S2 and S3(richer) states, which are highly overlapped in the raw data. I am urgently wondering how can I separate S3 out from the S2/S3 mixture by Chimera, especially the OEY cluster and all its ligands? Thank you very much! Best wishes
<6dho.cif>
Dear Elaine, Thank you very much for help. Here I attach 6dho.pdb which has been converted from the original 6dho.cif by Openbabel. Since I am not very familar with the Chimera command, I hope you could make it easier with this .pdb file. Best wishes ________________________________________ 发件人: Elaine Meng meng@cgl.ucsf.edu 发送时间: 2018年11月26日 20:28 收件人: Yu Guo 抄送: chimera-users@cgl.ucsf.edu 主题: Re: [Chimera-users] needing help for separating structures
Hi Yu Guo, Well, it all depends on how these two states are described in the file. I took a look at the associated paper in Nature and they don’t really say exactly how they described the two states, but they do mention modeling them at reduced occupancy. So my best guess if one structure has more than one state, they are described in the file is with “alternate locations” for some atoms (i.e. multiple positions for a given atom) with reduced occupancy values. For me, it is harder to figure out with mmCIF file than PDB because I’m more familiar with looking at PDB files in a text editor.
Usually when there are alternate locations, they are A and B. So, you could select (or “delete” instead of “select” but then there is no going back other than by re-opening the original file) all atoms with alternate locations A with command:
select @.A
… and similarly for alternate location B. In my tests, it looks like A has the lower occupancy than B, and selecting alternate location A or B will each select 2188 atoms. You could also select by occupancy value; however, I get different numbers depending on the value I choose, presumably omitting some atoms with alternate locations or including some of the atoms that do NOT have alternate locations, so be careful using that method:
select @/occupancy<0.4 … I avoid using “=“ because rounding issues may prevent exact match select @/occupancy<0.45 … or you can use a range, e.g. select @/occupancy>0.5 and occupancy<0.75
Because they did not clearly state in the paper (or at least I didn’t see it), I could not be sure, but guessing that alternate location A is the minority state and alternate location B is the majority state, and atoms without alternate locations were the same in both states.
How I figured out that alternate location A appears to have lower occupancy than B is with these commands: ~disp ~ribbon disp :ala labelopt info occupancy label :ala@.A ~label label :ala@.B
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. ChimeraX is much faster reading mmCIF than Chimera. Also it automatically only uses the alternate location set with average higher occupancy (in this case B). However, if you want to show the altloc set with lower occupancy, there is no easy/convenient method for it yet, although it can be done with a setattr command.
On Nov 24, 2018, at 11:28 AM, Yu Guo yg2@kth.se wrote:
Dear Sir/Madam, I am using Chimara to display large proteins. It is very nice. 6DHO(PDB structure, see attachment) is a very recent PSII structure consisting both S2 and S3(richer) states, which are highly overlapped in the raw data. I am urgently wondering how can I separate S3 out from the S2/S3 mixture by Chimera, especially the OEY cluster and all its ligands? Thank you very much! Best wishes
<6dho.cif>
Hi Yu Guo, The PDB file is not needed, since I already spent the time to investigate what was in the mmCIF file, and gave you several example commands to select parts of the structure. If you have selected atoms, you can use the Actions menu to hide, show, or delete them. Please see the rest of the previous reply. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 26, 2018, at 12:31 PM, Yu Guo yg2@kth.se wrote:
Dear Elaine, Thank you very much for help. Here I attach 6dho.pdb which has been converted from the original 6dho.cif by Openbabel. Since I am not very familar with the Chimera command, I hope you could make it easier with this .pdb file. Best wishes ________________________________________ 发件人: Elaine Meng meng@cgl.ucsf.edu 发送时间: 2018年11月26日 20:28 收件人: Yu Guo 抄送: chimera-users@cgl.ucsf.edu 主题: Re: [Chimera-users] needing help for separating structures
Hi Yu Guo, Well, it all depends on how these two states are described in the file. I took a look at the associated paper in Nature and they don’t really say exactly how they described the two states, but they do mention modeling them at reduced occupancy. So my best guess if one structure has more than one state, they are described in the file is with “alternate locations” for some atoms (i.e. multiple positions for a given atom) with reduced occupancy values. For me, it is harder to figure out with mmCIF file than PDB because I’m more familiar with looking at PDB files in a text editor.
Usually when there are alternate locations, they are A and B. So, you could select (or “delete” instead of “select” but then there is no going back other than by re-opening the original file) all atoms with alternate locations A with command:
select @.A
… and similarly for alternate location B. In my tests, it looks like A has the lower occupancy than B, and selecting alternate location A or B will each select 2188 atoms. You could also select by occupancy value; however, I get different numbers depending on the value I choose, presumably omitting some atoms with alternate locations or including some of the atoms that do NOT have alternate locations, so be careful using that method:
select @/occupancy<0.4 … I avoid using “=“ because rounding issues may prevent exact match select @/occupancy<0.45 … or you can use a range, e.g. select @/occupancy>0.5 and occupancy<0.75
Because they did not clearly state in the paper (or at least I didn’t see it), I could not be sure, but guessing that alternate location A is the minority state and alternate location B is the majority state, and atoms without alternate locations were the same in both states.
How I figured out that alternate location A appears to have lower occupancy than B is with these commands: ~disp ~ribbon disp :ala labelopt info occupancy label :ala@.A ~label label :ala@.B
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. ChimeraX is much faster reading mmCIF than Chimera. Also it automatically only uses the alternate location set with average higher occupancy (in this case B). However, if you want to show the altloc set with lower occupancy, there is no easy/convenient method for it yet, although it can be done with a setattr command.
On Nov 24, 2018, at 11:28 AM, Yu Guo yg2@kth.se wrote:
Dear Sir/Madam, I am using Chimara to display large proteins. It is very nice. 6DHO(PDB structure, see attachment) is a very recent PSII structure consisting both S2 and S3(richer) states, which are highly overlapped in the raw data. I am urgently wondering how can I separate S3 out from the S2/S3 mixture by Chimera, especially the OEY cluster and all its ligands? Thank you very much! Best wishes
<6dho.cif>
<6dho.pdb>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Dear Elaine, Many thanks for your help! Yes, it is B that I need! Your way works! By the way, what are the main differences in functions between Chimera and ChimeraX? Regards ________________________________________ 发件人: Elaine Meng meng@cgl.ucsf.edu 发送时间: 2018年11月26日 23:56 收件人: Yu Guo 抄送: chimera-users 主题: Re: [Chimera-users] 答复: needing help for separating structures
Hi Yu Guo, The PDB file is not needed, since I already spent the time to investigate what was in the mmCIF file, and gave you several example commands to select parts of the structure. If you have selected atoms, you can use the Actions menu to hide, show, or delete them. Please see the rest of the previous reply. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 26, 2018, at 12:31 PM, Yu Guo yg2@kth.se wrote:
Dear Elaine, Thank you very much for help. Here I attach 6dho.pdb which has been converted from the original 6dho.cif by Openbabel. Since I am not very familar with the Chimera command, I hope you could make it easier with this .pdb file. Best wishes ________________________________________ 发件人: Elaine Meng meng@cgl.ucsf.edu 发送时间: 2018年11月26日 20:28 收件人: Yu Guo 抄送: chimera-users@cgl.ucsf.edu 主题: Re: [Chimera-users] needing help for separating structures
Hi Yu Guo, Well, it all depends on how these two states are described in the file. I took a look at the associated paper in Nature and they don’t really say exactly how they described the two states, but they do mention modeling them at reduced occupancy. So my best guess if one structure has more than one state, they are described in the file is with “alternate locations” for some atoms (i.e. multiple positions for a given atom) with reduced occupancy values. For me, it is harder to figure out with mmCIF file than PDB because I’m more familiar with looking at PDB files in a text editor.
Usually when there are alternate locations, they are A and B. So, you could select (or “delete” instead of “select” but then there is no going back other than by re-opening the original file) all atoms with alternate locations A with command:
select @.A
… and similarly for alternate location B. In my tests, it looks like A has the lower occupancy than B, and selecting alternate location A or B will each select 2188 atoms. You could also select by occupancy value; however, I get different numbers depending on the value I choose, presumably omitting some atoms with alternate locations or including some of the atoms that do NOT have alternate locations, so be careful using that method:
select @/occupancy<0.4 … I avoid using “=“ because rounding issues may prevent exact match select @/occupancy<0.45 … or you can use a range, e.g. select @/occupancy>0.5 and occupancy<0.75
Because they did not clearly state in the paper (or at least I didn’t see it), I could not be sure, but guessing that alternate location A is the minority state and alternate location B is the majority state, and atoms without alternate locations were the same in both states.
How I figured out that alternate location A appears to have lower occupancy than B is with these commands: ~disp ~ribbon disp :ala labelopt info occupancy label :ala@.A ~label label :ala@.B
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. ChimeraX is much faster reading mmCIF than Chimera. Also it automatically only uses the alternate location set with average higher occupancy (in this case B). However, if you want to show the altloc set with lower occupancy, there is no easy/convenient method for it yet, although it can be done with a setattr command.
On Nov 24, 2018, at 11:28 AM, Yu Guo yg2@kth.se wrote:
Dear Sir/Madam, I am using Chimara to display large proteins. It is very nice. 6DHO(PDB structure, see attachment) is a very recent PSII structure consisting both S2 and S3(richer) states, which are highly overlapped in the raw data. I am urgently wondering how can I separate S3 out from the S2/S3 mixture by Chimera, especially the OEY cluster and all its ligands? Thank you very much! Best wishes
<6dho.cif>
<6dho.pdb>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Dear Yu Guo, Well, ChimeraX is changing every day because it is actively under development. It is faster and better at handling large structures, and has some fancier display options… it is the “next generation” software that we intend will eventually replace Chimera. However, it will be some time before it reaches that goal; Chimera has several analysis or modeling tools that are not (yet) in ChimeraX, and currently ChimeraX features are nearly all commands and very few GUIs. However, ChimeraX has some new features that were never in Chimera, like support for VR and more robust/reliable molecular surface calculations, and improvements of features that were also in Chimera, like morphing molecules.
See ChimeraX advantages summary: http://www.rbvi.ucsf.edu/chimerax/docs/user/advantages.html
...ChimeraX feature highlights: http://www.rbvi.ucsf.edu/chimerax/features.html
...and the “missing features” list in the ChimeraX download page: http://www.rbvi.ucsf.edu/chimerax/download.html
Regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 27, 2018, at 1:54 AM, Yu Guo yg2@kth.se wrote:
Dear Elaine, Many thanks for your help! Yes, it is B that I need! Your way works! By the way, what are the main differences in functions between Chimera and ChimeraX? Regards ________________________________________ 发件人: Elaine Meng meng@cgl.ucsf.edu 发送时间: 2018年11月26日 23:56 收件人: Yu Guo 抄送: chimera-users 主题: Re: [Chimera-users] 答复: needing help for separating structures
Hi Yu Guo, The PDB file is not needed, since I already spent the time to investigate what was in the mmCIF file, and gave you several example commands to select parts of the structure. If you have selected atoms, you can use the Actions menu to hide, show, or delete them. Please see the rest of the previous reply. Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 26, 2018, at 12:31 PM, Yu Guo yg2@kth.se wrote:
Dear Elaine, Thank you very much for help. Here I attach 6dho.pdb which has been converted from the original 6dho.cif by Openbabel. Since I am not very familar with the Chimera command, I hope you could make it easier with this .pdb file. Best wishes ________________________________________ 发件人: Elaine Meng meng@cgl.ucsf.edu 发送时间: 2018年11月26日 20:28 收件人: Yu Guo 抄送: chimera-users@cgl.ucsf.edu 主题: Re: [Chimera-users] needing help for separating structures
Hi Yu Guo, Well, it all depends on how these two states are described in the file. I took a look at the associated paper in Nature and they don’t really say exactly how they described the two states, but they do mention modeling them at reduced occupancy. So my best guess if one structure has more than one state, they are described in the file is with “alternate locations” for some atoms (i.e. multiple positions for a given atom) with reduced occupancy values. For me, it is harder to figure out with mmCIF file than PDB because I’m more familiar with looking at PDB files in a text editor.
Usually when there are alternate locations, they are A and B. So, you could select (or “delete” instead of “select” but then there is no going back other than by re-opening the original file) all atoms with alternate locations A with command:
select @.A
… and similarly for alternate location B. In my tests, it looks like A has the lower occupancy than B, and selecting alternate location A or B will each select 2188 atoms. You could also select by occupancy value; however, I get different numbers depending on the value I choose, presumably omitting some atoms with alternate locations or including some of the atoms that do NOT have alternate locations, so be careful using that method:
select @/occupancy<0.4 … I avoid using “=“ because rounding issues may prevent exact match select @/occupancy<0.45 … or you can use a range, e.g. select @/occupancy>0.5 and occupancy<0.75
Because they did not clearly state in the paper (or at least I didn’t see it), I could not be sure, but guessing that alternate location A is the minority state and alternate location B is the majority state, and atoms without alternate locations were the same in both states.
How I figured out that alternate location A appears to have lower occupancy than B is with these commands: ~disp ~ribbon disp :ala labelopt info occupancy label :ala@.A ~label label :ala@.B
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. ChimeraX is much faster reading mmCIF than Chimera. Also it automatically only uses the alternate location set with average higher occupancy (in this case B). However, if you want to show the altloc set with lower occupancy, there is no easy/convenient method for it yet, although it can be done with a setattr command.
On Nov 24, 2018, at 11:28 AM, Yu Guo yg2@kth.se wrote:
Dear Sir/Madam, I am using Chimara to display large proteins. It is very nice. 6DHO(PDB structure, see attachment) is a very recent PSII structure consisting both S2 and S3(richer) states, which are highly overlapped in the raw data. I am urgently wondering how can I separate S3 out from the S2/S3 mixture by Chimera, especially the OEY cluster and all its ligands? Thank you very much! Best wishes
<6dho.cif>
<6dho.pdb>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Dear Elaine, How can I use Chimera/ChimeraX to make a reaction movie for Gaussian16's IRC trajectory? ________________________________________ 发件人: Elaine Meng meng@cgl.ucsf.edu 发送时间: 2018年11月27日 17:57 收件人: Yu Guo 抄送: chimera-users 主题: Re: [Chimera-users] 答复: 答复: needing help for separating structures
Dear Yu Guo, Well, ChimeraX is changing every day because it is actively under development. It is faster and better at handling large structures, and has some fancier display options… it is the “next generation” software that we intend will eventually replace Chimera. However, it will be some time before it reaches that goal; Chimera has several analysis or modeling tools that are not (yet) in ChimeraX, and currently ChimeraX features are nearly all commands and very few GUIs. However, ChimeraX has some new features that were never in Chimera, like support for VR and more robust/reliable molecular surface calculations, and improvements of features that were also in Chimera, like morphing molecules.
See ChimeraX advantages summary: http://www.rbvi.ucsf.edu/chimerax/docs/user/advantages.html
...ChimeraX feature highlights: http://www.rbvi.ucsf.edu/chimerax/features.html
...and the “missing features” list in the ChimeraX download page: http://www.rbvi.ucsf.edu/chimerax/download.html
Regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 27, 2018, at 1:54 AM, Yu Guo yg2@kth.se wrote:
Dear Elaine, Many thanks for your help! Yes, it is B that I need! Your way works! By the way, what are the main differences in functions between Chimera and ChimeraX? Regards ________________________________________ 发件人: Elaine Meng meng@cgl.ucsf.edu 发送时间: 2018年11月26日 23:56 收件人: Yu Guo 抄送: chimera-users 主题: Re: [Chimera-users] 答复: needing help for separating structures
Hi Yu Guo, The PDB file is not needed, since I already spent the time to investigate what was in the mmCIF file, and gave you several example commands to select parts of the structure. If you have selected atoms, you can use the Actions menu to hide, show, or delete them. Please see the rest of the previous reply. Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 26, 2018, at 12:31 PM, Yu Guo yg2@kth.se wrote:
Dear Elaine, Thank you very much for help. Here I attach 6dho.pdb which has been converted from the original 6dho.cif by Openbabel. Since I am not very familar with the Chimera command, I hope you could make it easier with this .pdb file. Best wishes ________________________________________ 发件人: Elaine Meng meng@cgl.ucsf.edu 发送时间: 2018年11月26日 20:28 收件人: Yu Guo 抄送: chimera-users@cgl.ucsf.edu 主题: Re: [Chimera-users] needing help for separating structures
Hi Yu Guo, Well, it all depends on how these two states are described in the file. I took a look at the associated paper in Nature and they don’t really say exactly how they described the two states, but they do mention modeling them at reduced occupancy. So my best guess if one structure has more than one state, they are described in the file is with “alternate locations” for some atoms (i.e. multiple positions for a given atom) with reduced occupancy values. For me, it is harder to figure out with mmCIF file than PDB because I’m more familiar with looking at PDB files in a text editor.
Usually when there are alternate locations, they are A and B. So, you could select (or “delete” instead of “select” but then there is no going back other than by re-opening the original file) all atoms with alternate locations A with command:
select @.A
… and similarly for alternate location B. In my tests, it looks like A has the lower occupancy than B, and selecting alternate location A or B will each select 2188 atoms. You could also select by occupancy value; however, I get different numbers depending on the value I choose, presumably omitting some atoms with alternate locations or including some of the atoms that do NOT have alternate locations, so be careful using that method:
select @/occupancy<0.4 … I avoid using “=“ because rounding issues may prevent exact match select @/occupancy<0.45 … or you can use a range, e.g. select @/occupancy>0.5 and occupancy<0.75
Because they did not clearly state in the paper (or at least I didn’t see it), I could not be sure, but guessing that alternate location A is the minority state and alternate location B is the majority state, and atoms without alternate locations were the same in both states.
How I figured out that alternate location A appears to have lower occupancy than B is with these commands: ~disp ~ribbon disp :ala labelopt info occupancy label :ala@.A ~label label :ala@.B
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. ChimeraX is much faster reading mmCIF than Chimera. Also it automatically only uses the alternate location set with average higher occupancy (in this case B). However, if you want to show the altloc set with lower occupancy, there is no easy/convenient method for it yet, although it can be done with a setattr command.
On Nov 24, 2018, at 11:28 AM, Yu Guo yg2@kth.se wrote:
Dear Sir/Madam, I am using Chimara to display large proteins. It is very nice. 6DHO(PDB structure, see attachment) is a very recent PSII structure consisting both S2 and S3(richer) states, which are highly overlapped in the raw data. I am urgently wondering how can I separate S3 out from the S2/S3 mixture by Chimera, especially the OEY cluster and all its ligands? Thank you very much! Best wishes
<6dho.cif>
<6dho.pdb>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Dear Yu Guo, ChimeraX has no capability to show a “reaction” trajectory where bonds break and form. Chimera does have the capability to do this, but you actually have to make a slight modification to the Chimera code to turn on the capability. First, you would need to get the Gaussian trajectory into one of the formats that Chimera can read. The trajectory formats that Chimera supports are listed here:
https://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/movie/fram... https://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/movie/framemovie.html
Then, to turn on the “dynamic bonds” capability you would need to edit the file <your Chimera installation>/share/Trajectory/__init__.py and after line 26, which looks like this:
solventResNames = set(["HOH", "WAT", "H2O", "D2O", "SOL", "TIP3”])
add this line:
dynamicBonds = True
Use the same indentation as for the solventResNames line — indentation is important in Python [on a Mac, <your Chimera installation> is Chimera.app/Contents/Resources]. Then save the file and start Chimera. Chimera should be able to play the trajectory and show bonds breaking and forming. The change you made causes Chimera to recompute the bonds every frame, so it may slow down your first play through of the trajectory and might slow it down a little on subsequent play throughs (it remembers the bonds after the first play through) — so you might want to undo the change after you are completely done. The link I gave above also has a section on “Recording a Movie” that you should read through, and probably follow some of the links in that, such as the “making movies” and “tips on preparing images” links.
—Eric
Eric Pettersen UCSF Computer Graphics Lab
On Nov 30, 2018, at 6:23 AM, Yu Guo yg2@kth.se wrote:
Dear Elaine, How can I use Chimera/ChimeraX to make a reaction movie for Gaussian16's IRC trajectory? ________________________________________ 发件人: Elaine Meng meng@cgl.ucsf.edu 发送时间: 2018年11月27日 17:57 收件人: Yu Guo 抄送: chimera-users 主题: Re: [Chimera-users] 答复: 答复: needing help for separating structures
Dear Yu Guo, Well, ChimeraX is changing every day because it is actively under development. It is faster and better at handling large structures, and has some fancier display options… it is the “next generation” software that we intend will eventually replace Chimera. However, it will be some time before it reaches that goal; Chimera has several analysis or modeling tools that are not (yet) in ChimeraX, and currently ChimeraX features are nearly all commands and very few GUIs. However, ChimeraX has some new features that were never in Chimera, like support for VR and more robust/reliable molecular surface calculations, and improvements of features that were also in Chimera, like morphing molecules.
See ChimeraX advantages summary: http://www.rbvi.ucsf.edu/chimerax/docs/user/advantages.html
...ChimeraX feature highlights: http://www.rbvi.ucsf.edu/chimerax/features.html
...and the “missing features” list in the ChimeraX download page: http://www.rbvi.ucsf.edu/chimerax/download.html
Regards, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 27, 2018, at 1:54 AM, Yu Guo yg2@kth.se wrote:
Dear Elaine, Many thanks for your help! Yes, it is B that I need! Your way works! By the way, what are the main differences in functions between Chimera and ChimeraX? Regards ________________________________________ 发件人: Elaine Meng meng@cgl.ucsf.edu 发送时间: 2018年11月26日 23:56 收件人: Yu Guo 抄送: chimera-users 主题: Re: [Chimera-users] 答复: needing help for separating structures
Hi Yu Guo, The PDB file is not needed, since I already spent the time to investigate what was in the mmCIF file, and gave you several example commands to select parts of the structure. If you have selected atoms, you can use the Actions menu to hide, show, or delete them. Please see the rest of the previous reply. Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 26, 2018, at 12:31 PM, Yu Guo yg2@kth.se wrote:
Dear Elaine, Thank you very much for help. Here I attach 6dho.pdb which has been converted from the original 6dho.cif by Openbabel. Since I am not very familar with the Chimera command, I hope you could make it easier with this .pdb file. Best wishes ________________________________________ 发件人: Elaine Meng meng@cgl.ucsf.edu 发送时间: 2018年11月26日 20:28 收件人: Yu Guo 抄送: chimera-users@cgl.ucsf.edu 主题: Re: [Chimera-users] needing help for separating structures
Hi Yu Guo, Well, it all depends on how these two states are described in the file. I took a look at the associated paper in Nature and they don’t really say exactly how they described the two states, but they do mention modeling them at reduced occupancy. So my best guess if one structure has more than one state, they are described in the file is with “alternate locations” for some atoms (i.e. multiple positions for a given atom) with reduced occupancy values. For me, it is harder to figure out with mmCIF file than PDB because I’m more familiar with looking at PDB files in a text editor.
Usually when there are alternate locations, they are A and B. So, you could select (or “delete” instead of “select” but then there is no going back other than by re-opening the original file) all atoms with alternate locations A with command:
select @.A
… and similarly for alternate location B. In my tests, it looks like A has the lower occupancy than B, and selecting alternate location A or B will each select 2188 atoms. You could also select by occupancy value; however, I get different numbers depending on the value I choose, presumably omitting some atoms with alternate locations or including some of the atoms that do NOT have alternate locations, so be careful using that method:
select @/occupancy<0.4 … I avoid using “=“ because rounding issues may prevent exact match select @/occupancy<0.45 … or you can use a range, e.g. select @/occupancy>0.5 and occupancy<0.75
Because they did not clearly state in the paper (or at least I didn’t see it), I could not be sure, but guessing that alternate location A is the minority state and alternate location B is the majority state, and atoms without alternate locations were the same in both states.
How I figured out that alternate location A appears to have lower occupancy than B is with these commands: ~disp ~ribbon disp :ala labelopt info occupancy label :ala@.A ~label label :ala@.B
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. ChimeraX is much faster reading mmCIF than Chimera. Also it automatically only uses the alternate location set with average higher occupancy (in this case B). However, if you want to show the altloc set with lower occupancy, there is no easy/convenient method for it yet, although it can be done with a setattr command.
On Nov 24, 2018, at 11:28 AM, Yu Guo yg2@kth.se wrote:
Dear Sir/Madam, I am using Chimara to display large proteins. It is very nice. 6DHO(PDB structure, see attachment) is a very recent PSII structure consisting both S2 and S3(richer) states, which are highly overlapped in the raw data. I am urgently wondering how can I separate S3 out from the S2/S3 mixture by Chimera, especially the OEY cluster and all its ligands? Thank you very much! Best wishes
<6dho.cif>
<6dho.pdb>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Dear Eric,
I have done according to you, but seems not work. maybe something is wrong with my modification. Could you correct it ? See the attachment.
________________________________ 发件人: Eric Pettersen pett@cgl.ucsf.edu 发送时间: 2018年11月30日 19:35 收件人: Yu Guo 抄送: chimera-users 主题: Re: [Chimera-users] 答复: 答复: 答复: needing help for separating structures
Dear Yu Guo, ChimeraX has no capability to show a “reaction” trajectory where bonds break and form. Chimera does have the capability to do this, but you actually have to make a slight modification to the Chimera code to turn on the capability. First, you would need to get the Gaussian trajectory into one of the formats that Chimera can read. The trajectory formats that Chimera supports are listed here:
https://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/movie/fram...
Then, to turn on the “dynamic bonds” capability you would need to edit the file <your Chimera installation>/share/Trajectory/__init__.py and after line 26, which looks like this:
solventResNames = set(["HOH", "WAT", "H2O", "D2O", "SOL", "TIP3”])
add this line:
dynamicBonds = True
Use the same indentation as for the solventResNames line — indentation is important in Python [on a Mac, <your Chimera installation> is Chimera.app/Contents/Resources]. Then save the file and start Chimera. Chimera should be able to play the trajectory and show bonds breaking and forming. The change you made causes Chimera to recompute the bonds every frame, so it may slow down your first play through of the trajectory and might slow it down a little on subsequent play throughs (it remembers the bonds after the first play through) — so you might want to undo the change after you are completely done. The link I gave above also has a section on “Recording a Movie” that you should read through, and probably follow some of the links in that, such as the “making movies” and “tips on preparing images” links.
—Eric
Eric Pettersen UCSF Computer Graphics Lab
On Nov 30, 2018, at 6:23 AM, Yu Guo <yg2@kth.semailto:yg2@kth.se> wrote:
Dear Elaine, How can I use Chimera/ChimeraX to make a reaction movie for Gaussian16's IRC trajectory? ________________________________________ 发件人: Elaine Meng <meng@cgl.ucsf.edumailto:meng@cgl.ucsf.edu> 发送时间: 2018年11月27日 17:57 收件人: Yu Guo 抄送: chimera-users 主题: Re: [Chimera-users] 答复: 答复: needing help for separating structures
Dear Yu Guo, Well, ChimeraX is changing every day because it is actively under development. It is faster and better at handling large structures, and has some fancier display options… it is the “next generation” software that we intend will eventually replace Chimera. However, it will be some time before it reaches that goal; Chimera has several analysis or modeling tools that are not (yet) in ChimeraX, and currently ChimeraX features are nearly all commands and very few GUIs. However, ChimeraX has some new features that were never in Chimera, like support for VR and more robust/reliable molecular surface calculations, and improvements of features that were also in Chimera, like morphing molecules.
See ChimeraX advantages summary: http://www.rbvi.ucsf.edu/chimerax/docs/user/advantages.html
...ChimeraX feature highlights: http://www.rbvi.ucsf.edu/chimerax/features.html
...and the “missing features” list in the ChimeraX download page: http://www.rbvi.ucsf.edu/chimerax/download.html
Regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 27, 2018, at 1:54 AM, Yu Guo <yg2@kth.semailto:yg2@kth.se> wrote:
Dear Elaine, Many thanks for your help! Yes, it is B that I need! Your way works! By the way, what are the main differences in functions between Chimera and ChimeraX? Regards ________________________________________ 发件人: Elaine Meng <meng@cgl.ucsf.edumailto:meng@cgl.ucsf.edu> 发送时间: 2018年11月26日 23:56 收件人: Yu Guo 抄送: chimera-users 主题: Re: [Chimera-users] 答复: needing help for separating structures
Hi Yu Guo, The PDB file is not needed, since I already spent the time to investigate what was in the mmCIF file, and gave you several example commands to select parts of the structure. If you have selected atoms, you can use the Actions menu to hide, show, or delete them. Please see the rest of the previous reply. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 26, 2018, at 12:31 PM, Yu Guo <yg2@kth.semailto:yg2@kth.se> wrote:
Dear Elaine, Thank you very much for help. Here I attach 6dho.pdb which has been converted from the original 6dho.cif by Openbabel. Since I am not very familar with the Chimera command, I hope you could make it easier with this .pdb file. Best wishes ________________________________________ 发件人: Elaine Meng <meng@cgl.ucsf.edumailto:meng@cgl.ucsf.edu> 发送时间: 2018年11月26日 20:28 收件人: Yu Guo 抄送: chimera-users@cgl.ucsf.edumailto:chimera-users@cgl.ucsf.edu 主题: Re: [Chimera-users] needing help for separating structures
Hi Yu Guo, Well, it all depends on how these two states are described in the file. I took a look at the associated paper in Nature and they don’t really say exactly how they described the two states, but they do mention modeling them at reduced occupancy. So my best guess if one structure has more than one state, they are described in the file is with “alternate locations” for some atoms (i.e. multiple positions for a given atom) with reduced occupancy values. For me, it is harder to figure out with mmCIF file than PDB because I’m more familiar with looking at PDB files in a text editor.
Usually when there are alternate locations, they are A and B. So, you could select (or “delete” instead of “select” but then there is no going back other than by re-opening the original file) all atoms with alternate locations A with command:
select @.A
… and similarly for alternate location B. In my tests, it looks like A has the lower occupancy than B, and selecting alternate location A or B will each select 2188 atoms. You could also select by occupancy value; however, I get different numbers depending on the value I choose, presumably omitting some atoms with alternate locations or including some of the atoms that do NOT have alternate locations, so be careful using that method:
select @/occupancy<0.4 … I avoid using “=“ because rounding issues may prevent exact match select @/occupancy<0.45 … or you can use a range, e.g. select @/occupancy>0.5 and occupancy<0.75
Because they did not clearly state in the paper (or at least I didn’t see it), I could not be sure, but guessing that alternate location A is the minority state and alternate location B is the majority state, and atoms without alternate locations were the same in both states.
How I figured out that alternate location A appears to have lower occupancy than B is with these commands: ~disp ~ribbon disp :ala labelopt info occupancy label :ala@.A ~label label :ala@.B
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. ChimeraX is much faster reading mmCIF than Chimera. Also it automatically only uses the alternate location set with average higher occupancy (in this case B). However, if you want to show the altloc set with lower occupancy, there is no easy/convenient method for it yet, although it can be done with a setattr command.
On Nov 24, 2018, at 11:28 AM, Yu Guo <yg2@kth.semailto:yg2@kth.se> wrote:
Dear Sir/Madam, I am using Chimara to display large proteins. It is very nice. 6DHO(PDB structure, see attachment) is a very recent PSII structure consisting both S2 and S3(richer) states, which are highly overlapped in the raw data. I am urgently wondering how can I separate S3 out from the S2/S3 mixture by Chimera, especially the OEY cluster and all its ligands? Thank you very much! Best wishes
<6dho.cif> <6dho.pdb>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edumailto:Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edumailto:Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edumailto:Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
I guess my instructions weren’t quite detailed enough in that the type of indentation also has to be the same. The indentation in the rest of the file uses tabs, but you used spaces. Here’s a corrected version that uses just tabs.
—Eric
On Nov 30, 2018, at 11:47 AM, Yu Guo yg2@kth.se wrote:
Dear Eric, I have done according to you, but seems not work. maybe something is wrong with my modification. Could you correct it ? See the attachment. 发件人: Eric Pettersen pett@cgl.ucsf.edu 发送时间: 2018年11月30日 19:35 收件人: Yu Guo 抄送: chimera-users 主题: Re: [Chimera-users] 答复: 答复: 答复: needing help for separating structures
Dear Yu Guo, ChimeraX has no capability to show a “reaction” trajectory where bonds break and form. Chimera does have the capability to do this, but you actually have to make a slight modification to the Chimera code to turn on the capability. First, you would need to get the Gaussian trajectory into one of the formats that Chimera can read. The trajectory formats that Chimera supports are listed here:
https://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/movie/fram... https://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/movie/framemovie.html
Then, to turn on the “dynamic bonds” capability you would need to edit the file <your Chimera installation>/share/Trajectory/__init__.py and after line 26, which looks like this:
solventResNames = set(["HOH", "WAT", "H2O", "D2O", "SOL", "TIP3”])
add this line:
dynamicBonds = True
Use the same indentation as for the solventResNames line — indentation is important in Python [on a Mac, <your Chimera installation> is Chimera.app/Contents/Resources]. Then save the file and start Chimera. Chimera should be able to play the trajectory and show bonds breaking and forming. The change you made causes Chimera to recompute the bonds every frame, so it may slow down your first play through of the trajectory and might slow it down a little on subsequent play throughs (it remembers the bonds after the first play through) — so you might want to undo the change after you are completely done. The link I gave above also has a section on “Recording a Movie” that you should read through, and probably follow some of the links in that, such as the “making movies” and “tips on preparing images” links.
—Eric
Eric Pettersen UCSF Computer Graphics Lab
On Nov 30, 2018, at 6:23 AM, Yu Guo <yg2@kth.se mailto:yg2@kth.se> wrote:
Dear Elaine, How can I use Chimera/ChimeraX to make a reaction movie for Gaussian16's IRC trajectory? ________________________________________ 发件人: Elaine Meng <meng@cgl.ucsf.edu mailto:meng@cgl.ucsf.edu> 发送时间: 2018年11月27日 17:57 收件人: Yu Guo 抄送: chimera-users 主题: Re: [Chimera-users] 答复: 答复: needing help for separating structures
Dear Yu Guo, Well, ChimeraX is changing every day because it is actively under development. It is faster and better at handling large structures, and has some fancier display options… it is the “next generation” software that we intend will eventually replace Chimera. However, it will be some time before it reaches that goal; Chimera has several analysis or modeling tools that are not (yet) in ChimeraX, and currently ChimeraX features are nearly all commands and very few GUIs. However, ChimeraX has some new features that were never in Chimera, like support for VR and more robust/reliable molecular surface calculations, and improvements of features that were also in Chimera, like morphing molecules.
See ChimeraX advantages summary: <http://www.rbvi.ucsf.edu/chimerax/docs/user/advantages.html http://www.rbvi.ucsf.edu/chimerax/docs/user/advantages.html>
...ChimeraX feature highlights: <http://www.rbvi.ucsf.edu/chimerax/features.html http://www.rbvi.ucsf.edu/chimerax/features.html>
...and the “missing features” list in the ChimeraX download page: <http://www.rbvi.ucsf.edu/chimerax/download.html http://www.rbvi.ucsf.edu/chimerax/download.html>
Regards, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 27, 2018, at 1:54 AM, Yu Guo <yg2@kth.se mailto:yg2@kth.se> wrote:
Dear Elaine, Many thanks for your help! Yes, it is B that I need! Your way works! By the way, what are the main differences in functions between Chimera and ChimeraX? Regards ________________________________________ 发件人: Elaine Meng <meng@cgl.ucsf.edu mailto:meng@cgl.ucsf.edu> 发送时间: 2018年11月26日 23:56 收件人: Yu Guo 抄送: chimera-users 主题: Re: [Chimera-users] 答复: needing help for separating structures
Hi Yu Guo, The PDB file is not needed, since I already spent the time to investigate what was in the mmCIF file, and gave you several example commands to select parts of the structure. If you have selected atoms, you can use the Actions menu to hide, show, or delete them. Please see the rest of the previous reply. Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 26, 2018, at 12:31 PM, Yu Guo <yg2@kth.se mailto:yg2@kth.se> wrote:
Dear Elaine, Thank you very much for help. Here I attach 6dho.pdb which has been converted from the original 6dho.cif by Openbabel. Since I am not very familar with the Chimera command, I hope you could make it easier with this .pdb file. Best wishes ________________________________________ 发件人: Elaine Meng <meng@cgl.ucsf.edu mailto:meng@cgl.ucsf.edu> 发送时间: 2018年11月26日 20:28 收件人: Yu Guo 抄送: chimera-users@cgl.ucsf.edu mailto:chimera-users@cgl.ucsf.edu 主题: Re: [Chimera-users] needing help for separating structures
Hi Yu Guo, Well, it all depends on how these two states are described in the file. I took a look at the associated paper in Nature and they don’t really say exactly how they described the two states, but they do mention modeling them at reduced occupancy. So my best guess if one structure has more than one state, they are described in the file is with “alternate locations” for some atoms (i.e. multiple positions for a given atom) with reduced occupancy values. For me, it is harder to figure out with mmCIF file than PDB because I’m more familiar with looking at PDB files in a text editor.
Usually when there are alternate locations, they are A and B. So, you could select (or “delete” instead of “select” but then there is no going back other than by re-opening the original file) all atoms with alternate locations A with command:
select @.A
… and similarly for alternate location B. In my tests, it looks like A has the lower occupancy than B, and selecting alternate location A or B will each select 2188 atoms. You could also select by occupancy value; however, I get different numbers depending on the value I choose, presumably omitting some atoms with alternate locations or including some of the atoms that do NOT have alternate locations, so be careful using that method:
select @/occupancy<0.4 … I avoid using “=“ because rounding issues may prevent exact match select @/occupancy<0.45 … or you can use a range, e.g. select @/occupancy>0.5 and occupancy<0.75
Because they did not clearly state in the paper (or at least I didn’t see it), I could not be sure, but guessing that alternate location A is the minority state and alternate location B is the majority state, and atoms without alternate locations were the same in both states.
How I figured out that alternate location A appears to have lower occupancy than B is with these commands: ~disp ~ribbon disp :ala labelopt info occupancy label :ala@.A ~label label :ala@.B
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. ChimeraX is much faster reading mmCIF than Chimera. Also it automatically only uses the alternate location set with average higher occupancy (in this case B). However, if you want to show the altloc set with lower occupancy, there is no easy/convenient method for it yet, although it can be done with a setattr command.
On Nov 24, 2018, at 11:28 AM, Yu Guo <yg2@kth.se mailto:yg2@kth.se> wrote:
Dear Sir/Madam, I am using Chimara to display large proteins. It is very nice. 6DHO(PDB structure, see attachment) is a very recent PSII structure consisting both S2 and S3(richer) states, which are highly overlapped in the raw data. I am urgently wondering how can I separate S3 out from the S2/S3 mixture by Chimera, especially the OEY cluster and all its ligands? Thank you very much! Best wishes
<6dho.cif>
<6dho.pdb>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu mailto:Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu mailto:Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu mailto:Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
<__init__.py>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu mailto:Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Dear Eric,
Thank you!
I can generate IRC to .xyz file like in the attachment, I can also separate coordinates into each file. But How can I load all these trajectory .xyz files to Chimera? When I press MD movie, there is 'NoFrameError'. Sorry for that It is a bit hard to see that much information in the link, althought it is very nice.
________________________________ 发件人: Eric Pettersen pett@cgl.ucsf.edu 发送时间: 2018年11月30日 19:35 收件人: Yu Guo 抄送: chimera-users 主题: Re: [Chimera-users] 答复: 答复: 答复: needing help for separating structures
Dear Yu Guo, ChimeraX has no capability to show a “reaction” trajectory where bonds break and form. Chimera does have the capability to do this, but you actually have to make a slight modification to the Chimera code to turn on the capability. First, you would need to get the Gaussian trajectory into one of the formats that Chimera can read. The trajectory formats that Chimera supports are listed here:
https://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/movie/fram...
Then, to turn on the “dynamic bonds” capability you would need to edit the file <your Chimera installation>/share/Trajectory/__init__.py and after line 26, which looks like this:
solventResNames = set(["HOH", "WAT", "H2O", "D2O", "SOL", "TIP3”])
add this line:
dynamicBonds = True
Use the same indentation as for the solventResNames line ― indentation is important in Python [on a Mac, <your Chimera installation> is Chimera.app/Contents/Resources]. Then save the file and start Chimera. Chimera should be able to play the trajectory and show bonds breaking and forming. The change you made causes Chimera to recompute the bonds every frame, so it may slow down your first play through of the trajectory and might slow it down a little on subsequent play throughs (it remembers the bonds after the first play through) ― so you might want to undo the change after you are completely done. The link I gave above also has a section on “Recording a Movie” that you should read through, and probably follow some of the links in that, such as the “making movies” and “tips on preparing images” links.
―Eric
Eric Pettersen UCSF Computer Graphics Lab
On Nov 30, 2018, at 6:23 AM, Yu Guo <yg2@kth.semailto:yg2@kth.se> wrote:
Dear Elaine, How can I use Chimera/ChimeraX to make a reaction movie for Gaussian16's IRC trajectory? ________________________________________ 发件人: Elaine Meng <meng@cgl.ucsf.edumailto:meng@cgl.ucsf.edu> 发送时间: 2018年11月27日 17:57 收件人: Yu Guo 抄送: chimera-users 主题: Re: [Chimera-users] 答复: 答复: needing help for separating structures
Dear Yu Guo, Well, ChimeraX is changing every day because it is actively under development. It is faster and better at handling large structures, and has some fancier display options… it is the “next generation” software that we intend will eventually replace Chimera. However, it will be some time before it reaches that goal; Chimera has several analysis or modeling tools that are not (yet) in ChimeraX, and currently ChimeraX features are nearly all commands and very few GUIs. However, ChimeraX has some new features that were never in Chimera, like support for VR and more robust/reliable molecular surface calculations, and improvements of features that were also in Chimera, like morphing molecules.
See ChimeraX advantages summary: http://www.rbvi.ucsf.edu/chimerax/docs/user/advantages.html
...ChimeraX feature highlights: http://www.rbvi.ucsf.edu/chimerax/features.html
...and the “missing features” list in the ChimeraX download page: http://www.rbvi.ucsf.edu/chimerax/download.html
Regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 27, 2018, at 1:54 AM, Yu Guo <yg2@kth.semailto:yg2@kth.se> wrote:
Dear Elaine, Many thanks for your help! Yes, it is B that I need! Your way works! By the way, what are the main differences in functions between Chimera and ChimeraX? Regards ________________________________________ 发件人: Elaine Meng <meng@cgl.ucsf.edumailto:meng@cgl.ucsf.edu> 发送时间: 2018年11月26日 23:56 收件人: Yu Guo 抄送: chimera-users 主题: Re: [Chimera-users] 答复: needing help for separating structures
Hi Yu Guo, The PDB file is not needed, since I already spent the time to investigate what was in the mmCIF file, and gave you several example commands to select parts of the structure. If you have selected atoms, you can use the Actions menu to hide, show, or delete them. Please see the rest of the previous reply. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 26, 2018, at 12:31 PM, Yu Guo <yg2@kth.semailto:yg2@kth.se> wrote:
Dear Elaine, Thank you very much for help. Here I attach 6dho.pdb which has been converted from the original 6dho.cif by Openbabel. Since I am not very familar with the Chimera command, I hope you could make it easier with this .pdb file. Best wishes ________________________________________ 发件人: Elaine Meng <meng@cgl.ucsf.edumailto:meng@cgl.ucsf.edu> 发送时间: 2018年11月26日 20:28 收件人: Yu Guo 抄送: chimera-users@cgl.ucsf.edumailto:chimera-users@cgl.ucsf.edu 主题: Re: [Chimera-users] needing help for separating structures
Hi Yu Guo, Well, it all depends on how these two states are described in the file. I took a look at the associated paper in Nature and they don’t really say exactly how they described the two states, but they do mention modeling them at reduced occupancy. So my best guess if one structure has more than one state, they are described in the file is with “alternate locations” for some atoms (i.e. multiple positions for a given atom) with reduced occupancy values. For me, it is harder to figure out with mmCIF file than PDB because I’m more familiar with looking at PDB files in a text editor.
Usually when there are alternate locations, they are A and B. So, you could select (or “delete” instead of “select” but then there is no going back other than by re-opening the original file) all atoms with alternate locations A with command:
select @.A
… and similarly for alternate location B. In my tests, it looks like A has the lower occupancy than B, and selecting alternate location A or B will each select 2188 atoms. You could also select by occupancy value; however, I get different numbers depending on the value I choose, presumably omitting some atoms with alternate locations or including some of the atoms that do NOT have alternate locations, so be careful using that method:
select @/occupancy<0.4 … I avoid using “=“ because rounding issues may prevent exact match select @/occupancy<0.45 … or you can use a range, e.g. select @/occupancy>0.5 and occupancy<0.75
Because they did not clearly state in the paper (or at least I didn’t see it), I could not be sure, but guessing that alternate location A is the minority state and alternate location B is the majority state, and atoms without alternate locations were the same in both states.
How I figured out that alternate location A appears to have lower occupancy than B is with these commands: ~disp ~ribbon disp :ala labelopt info occupancy label :ala@.A ~label label :ala@.B
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. ChimeraX is much faster reading mmCIF than Chimera. Also it automatically only uses the alternate location set with average higher occupancy (in this case B). However, if you want to show the altloc set with lower occupancy, there is no easy/convenient method for it yet, although it can be done with a setattr command.
On Nov 24, 2018, at 11:28 AM, Yu Guo <yg2@kth.semailto:yg2@kth.se> wrote:
Dear Sir/Madam, I am using Chimara to display large proteins. It is very nice. 6DHO(PDB structure, see attachment) is a very recent PSII structure consisting both S2 and S3(richer) states, which are highly overlapped in the raw data. I am urgently wondering how can I separate S3 out from the S2/S3 mixture by Chimera, especially the OEY? cluster and all its ligands? Thank you very much! Best wishes
<6dho.cif> <6dho.pdb>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edumailto:Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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Yeah, Chimera does not support single-file XYZ trajectories (nor is there really a standard for that). You would need one XYZ per frame. As per the MD Movie documentation for the XYZ format:
Starting and ending file names must be supplied. The file names must include frame numbers, and the frames will be ordered by increasing number (not necessarily consecutive; missing numbers will be ignored).
i.e. when you start the MD Movie tool and change the “Trajectory format:” to “XYZ”, you put the starting file name in the first field and the ending file name in the second field.
Eric Pettersen UCSF Computer Graphics Lab
On Nov 30, 2018, at 12:32 PM, Yu Guo yg2@kth.se wrote:
Dear Eric, Thank you! I can generate IRC to .xyz file like in the attachment, I can also separate coordinates into each file. But How can I load all these trajectory .xyz files to Chimera? When I press MD movie, there is 'NoFrameError'. Sorry for that It is a bit hard to see that much information in the link, althought it is very nice.
发件人: Eric Pettersen pett@cgl.ucsf.edu 发送时间: 2018年11月30日 19:35 收件人: Yu Guo 抄送: chimera-users 主题: Re: [Chimera-users] 答复: 答复: 答复: needing help for separating structures
Dear Yu Guo, ChimeraX has no capability to show a “reaction” trajectory where bonds break and form. Chimera does have the capability to do this, but you actually have to make a slight modification to the Chimera code to turn on the capability. First, you would need to get the Gaussian trajectory into one of the formats that Chimera can read. The trajectory formats that Chimera supports are listed here:
https://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/movie/fram... https://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/movie/framemovie.html
Then, to turn on the “dynamic bonds” capability you would need to edit the file <your Chimera installation>/share/Trajectory/__init__.py and after line 26, which looks like this:
solventResNames = set(["HOH", "WAT", "H2O", "D2O", "SOL", "TIP3”])
add this line:
dynamicBonds = True
Use the same indentation as for the solventResNames line ― indentation is important in Python [on a Mac, <your Chimera installation> is Chimera.app/Contents/Resources]. Then save the file and start Chimera. Chimera should be able to play the trajectory and show bonds breaking and forming. The change you made causes Chimera to recompute the bonds every frame, so it may slow down your first play through of the trajectory and might slow it down a little on subsequent play throughs (it remembers the bonds after the first play through) ― so you might want to undo the change after you are completely done. The link I gave above also has a section on “Recording a Movie” that you should read through, and probably follow some of the links in that, such as the “making movies” and “tips on preparing images” links.
―Eric
Eric Pettersen UCSF Computer Graphics Lab
On Nov 30, 2018, at 6:23 AM, Yu Guo <yg2@kth.se mailto:yg2@kth.se> wrote:
Dear Elaine, How can I use Chimera/ChimeraX to make a reaction movie for Gaussian16's IRC trajectory? ________________________________________ 发件人: Elaine Meng <meng@cgl.ucsf.edu mailto:meng@cgl.ucsf.edu> 发送时间: 2018年11月27日 17:57 收件人: Yu Guo 抄送: chimera-users 主题: Re: [Chimera-users] 答复: 答复: needing help for separating structures
Dear Yu Guo, Well, ChimeraX is changing every day because it is actively under development. It is faster and better at handling large structures, and has some fancier display options… it is the “next generation” software that we intend will eventually replace Chimera. However, it will be some time before it reaches that goal; Chimera has several analysis or modeling tools that are not (yet) in ChimeraX, and currently ChimeraX features are nearly all commands and very few GUIs. However, ChimeraX has some new features that were never in Chimera, like support for VR and more robust/reliable molecular surface calculations, and improvements of features that were also in Chimera, like morphing molecules.
See ChimeraX advantages summary: <http://www.rbvi.ucsf.edu/chimerax/docs/user/advantages.html http://www.rbvi.ucsf.edu/chimerax/docs/user/advantages.html>
...ChimeraX feature highlights: <http://www.rbvi.ucsf.edu/chimerax/features.html http://www.rbvi.ucsf.edu/chimerax/features.html>
...and the “missing features” list in the ChimeraX download page: <http://www.rbvi.ucsf.edu/chimerax/download.html http://www.rbvi.ucsf.edu/chimerax/download.html>
Regards, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 27, 2018, at 1:54 AM, Yu Guo <yg2@kth.se mailto:yg2@kth.se> wrote:
Dear Elaine, Many thanks for your help! Yes, it is B that I need! Your way works! By the way, what are the main differences in functions between Chimera and ChimeraX? Regards ________________________________________ 发件人: Elaine Meng <meng@cgl.ucsf.edu mailto:meng@cgl.ucsf.edu> 发送时间: 2018年11月26日 23:56 收件人: Yu Guo 抄送: chimera-users 主题: Re: [Chimera-users] 答复: needing help for separating structures
Hi Yu Guo, The PDB file is not needed, since I already spent the time to investigate what was in the mmCIF file, and gave you several example commands to select parts of the structure. If you have selected atoms, you can use the Actions menu to hide, show, or delete them. Please see the rest of the previous reply. Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 26, 2018, at 12:31 PM, Yu Guo <yg2@kth.se mailto:yg2@kth.se> wrote:
Dear Elaine, Thank you very much for help. Here I attach 6dho.pdb which has been converted from the original 6dho.cif by Openbabel. Since I am not very familar with the Chimera command, I hope you could make it easier with this .pdb file. Best wishes ________________________________________ 发件人: Elaine Meng <meng@cgl.ucsf.edu mailto:meng@cgl.ucsf.edu> 发送时间: 2018年11月26日 20:28 收件人: Yu Guo 抄送: chimera-users@cgl.ucsf.edu mailto:chimera-users@cgl.ucsf.edu 主题: Re: [Chimera-users] needing help for separating structures
Hi Yu Guo, Well, it all depends on how these two states are described in the file. I took a look at the associated paper in Nature and they don’t really say exactly how they described the two states, but they do mention modeling them at reduced occupancy. So my best guess if one structure has more than one state, they are described in the file is with “alternate locations” for some atoms (i.e. multiple positions for a given atom) with reduced occupancy values. For me, it is harder to figure out with mmCIF file than PDB because I’m more familiar with looking at PDB files in a text editor.
Usually when there are alternate locations, they are A and B. So, you could select (or “delete” instead of “select” but then there is no going back other than by re-opening the original file) all atoms with alternate locations A with command:
select @.A
… and similarly for alternate location B. In my tests, it looks like A has the lower occupancy than B, and selecting alternate location A or B will each select 2188 atoms. You could also select by occupancy value; however, I get different numbers depending on the value I choose, presumably omitting some atoms with alternate locations or including some of the atoms that do NOT have alternate locations, so be careful using that method:
select @/occupancy<0.4 … I avoid using “=“ because rounding issues may prevent exact match select @/occupancy<0.45 … or you can use a range, e.g. select @/occupancy>0.5 and occupancy<0.75
Because they did not clearly state in the paper (or at least I didn’t see it), I could not be sure, but guessing that alternate location A is the minority state and alternate location B is the majority state, and atoms without alternate locations were the same in both states.
How I figured out that alternate location A appears to have lower occupancy than B is with these commands: ~disp ~ribbon disp :ala labelopt info occupancy label :ala@.A ~label label :ala@.B
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. ChimeraX is much faster reading mmCIF than Chimera. Also it automatically only uses the alternate location set with average higher occupancy (in this case B). However, if you want to show the altloc set with lower occupancy, there is no easy/convenient method for it yet, although it can be done with a setattr command.
On Nov 24, 2018, at 11:28 AM, Yu Guo <yg2@kth.se mailto:yg2@kth.se> wrote:
Dear Sir/Madam, I am using Chimara to display large proteins. It is very nice. 6DHO(PDB structure, see attachment) is a very recent PSII structure consisting both S2 and S3(richer) states, which are highly overlapped in the raw data. I am urgently wondering how can I separate S3 out from the S2/S3 mixture by Chimera, especially the OEY cluster and all its ligands? Thank you very much! Best wishes
<6dho.cif>
<6dho.pdb>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu mailto:Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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participants (4)
-
David Gae -
Elaine Meng -
Eric Pettersen -
Yu Guo