in *.gro file, chimera takes CL atom as C (in compound) and gives it wrong color
Dear users, Could I ask a question on chimera? Thanks! I tried to open a gro file (small compound) using chimera. Like below: ... ... 1 LIG CL 18 x.xxx x.xxx x.xxx 1 LIG CL1 19 x.xxx x.xxx x.xxx ... ... Although chimera shows the CL name "CL" when the cursor is above the atom, but the CL atom color is incorrect: the same as Carbon. I tried to change the "CL" to "BR", and the chimera shows the correct color: dark red. It seems weird to me. Could you please give me any suggestions? Thanks! Best, Lei
Hi Lei, There is no explicit indication of the chemical element type in a .gro file, so it's all guesswork. Chimera assumes that atom names that begin with any of the letters C, O, P, S, H, or N are the corresponding single letter element type. This prevents atom names like CA and HG from being interpreted as calcium and mercury, rather than carbon and hydrogen. There aren't any great solutions. One option is to read in the .gro file, write it out as a .mol2 file, then edit that file to change the atom type of the CL atoms to Cl, then read that back in. Another is to select your CL atoms and use the "Modify Structure" tab of the Build Structure tool to change their element to Cl. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Feb 18, 2021, at 8:30 PM, Lei Qian <tuk04130@temple.edu> wrote:
Dear users, Could I ask a question on chimera? Thanks! I tried to open a gro file (small compound) using chimera. Like below: ... ... 1 LIG CL 18 x.xxx x.xxx x.xxx 1 LIG CL1 19 x.xxx x.xxx x.xxx ... ... Although chimera shows the CL name "CL" when the cursor is above the atom, but the CL atom color is incorrect: the same as Carbon. I tried to change the "CL" to "BR", and the chimera shows the correct color: dark red. It seems weird to me. Could you please give me any suggestions? Thanks! Best, Lei
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Hi Eric, Thank you very much for your thorough explanation! I really appreciate it. I tried to do some test. I found: Chimera recognizes CL when CL shown as solvent in gro file: 1000CL CL2000 x.xxx x.xxx x.xxx But it cannot recognize CL when CL shown as "LIG" in gro file: 1000LIG CL2000 x.xxx x.xxx x.xxx And in LIG case, "Cl" or "CL" may not have much difference. Thanks again for your kind reply! Best, Lei ________________________________ From: Eric Pettersen <pett@cgl.ucsf.edu> Sent: Tuesday, February 23, 2021 5:04 AM To: Lei Qian <tuk04130@temple.edu> Cc: chimera-users@cgl.ucsf.edu BB <chimera-users@cgl.ucsf.edu> Subject: [External] Re: [Chimera-users] in *.gro file, chimera takes CL atom as C (in compound) and gives it wrong color Hi Lei, There is no explicit indication of the chemical element type in a .gro file, so it's all guesswork. Chimera assumes that atom names that begin with any of the letters C, O, P, S, H, or N are the corresponding single letter element type. This prevents atom names like CA and HG from being interpreted as calcium and mercury, rather than carbon and hydrogen. There aren't any great solutions. One option is to read in the .gro file, write it out as a .mol2 file, then edit that file to change the atom type of the CL atoms to Cl, then read that back in. Another is to select your CL atoms and use the "Modify Structure" tab of the Build Structure tool to change their element to Cl. --Eric Eric Pettersen UCSF Computer Graphics Lab On Feb 18, 2021, at 8:30 PM, Lei Qian <tuk04130@temple.edu<mailto:tuk04130@temple.edu>> wrote: Dear users, Could I ask a question on chimera? Thanks! I tried to open a gro file (small compound) using chimera. Like below: ... ... 1 LIG CL 18 x.xxx x.xxx x.xxx 1 LIG CL1 19 x.xxx x.xxx x.xxx ... ... Although chimera shows the CL name "CL" when the cursor is above the atom, but the CL atom color is incorrect: the same as Carbon. I tried to change the "CL" to "BR", and the chimera shows the correct color: dark red. It seems weird to me. Could you please give me any suggestions? Thanks! Best, Lei _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Lei, AFAIK, the Chimera .gro reader treats all atom records the same, so I would be somewhat surprised if it actually identified a CL as chlorine ever. Do you have an example file? --Eric
On Feb 26, 2021, at 7:53 PM, Lei Qian <leiqian-temple2@outlook.com> wrote:
Hi Eric, Thank you very much for your thorough explanation! I really appreciate it.
I tried to do some test. I found: Chimera recognizes CL when CL shown as solvent in gro file: 1000CL CL2000 x.xxx x.xxx x.xxx But it cannot recognize CL when CL shown as "LIG" in gro file: 1000LIG CL2000 x.xxx x.xxx x.xxx And in LIG case, "Cl" or "CL" may not have much difference.
Thanks again for your kind reply! Best, Lei
From: Eric Pettersen <pett@cgl.ucsf.edu> Sent: Tuesday, February 23, 2021 5:04 AM To: Lei Qian <tuk04130@temple.edu> Cc: chimera-users@cgl.ucsf.edu BB <chimera-users@cgl.ucsf.edu> Subject: [External] Re: [Chimera-users] in *.gro file, chimera takes CL atom as C (in compound) and gives it wrong color
Hi Lei, There is no explicit indication of the chemical element type in a .gro file, so it's all guesswork. Chimera assumes that atom names that begin with any of the letters C, O, P, S, H, or N are the corresponding single letter element type. This prevents atom names like CA and HG from being interpreted as calcium and mercury, rather than carbon and hydrogen. There aren't any great solutions. One option is to read in the .gro file, write it out as a .mol2 file, then edit that file to change the atom type of the CL atoms to Cl, then read that back in. Another is to select your CL atoms and use the "Modify Structure" tab of the Build Structure tool to change their element to Cl.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Feb 18, 2021, at 8:30 PM, Lei Qian <tuk04130@temple.edu <mailto:tuk04130@temple.edu>> wrote:
Dear users, Could I ask a question on chimera? Thanks! I tried to open a gro file (small compound) using chimera. Like below: ... ... 1 LIG CL 18 x.xxx x.xxx x.xxx 1 LIG CL1 19 x.xxx x.xxx x.xxx ... ... Although chimera shows the CL name "CL" when the cursor is above the atom, but the CL atom color is incorrect: the same as Carbon. I tried to change the "CL" to "BR", and the chimera shows the correct color: dark red. It seems weird to me. Could you please give me any suggestions? Thanks! Best, Lei
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Hi Eric, Sorry for my late reply. Yes you are right. I tried it again: I made a new gro file containing only CL and K as ions, and opened it using chimera. I found chimera colored K as violet, which is good; but it colored CL as the same color as Carbon: yellow. Thank you again for your help! Best, Lei On Tue, Feb 23, 2021 at 5:04 AM Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Hi Lei, There is no explicit indication of the chemical element type in a .gro file, so it's all guesswork. Chimera assumes that atom names that begin with any of the letters C, O, P, S, H, or N are the corresponding single letter element type. This prevents atom names like CA and HG from being interpreted as calcium and mercury, rather than carbon and hydrogen. There aren't any great solutions. One option is to read in the .gro file, write it out as a .mol2 file, then edit that file to change the atom type of the CL atoms to Cl, then read that back in. Another is to select your CL atoms and use the "Modify Structure" tab of the Build Structure tool to change their element to Cl.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Feb 18, 2021, at 8:30 PM, Lei Qian <tuk04130@temple.edu> wrote:
Dear users, Could I ask a question on chimera? Thanks! I tried to open a gro file (small compound) using chimera. Like below: ... ... 1 LIG CL 18 x.xxx x.xxx x.xxx 1 LIG CL1 19 x.xxx x.xxx x.xxx ... ... Although chimera shows the CL name "CL" when the cursor is above the atom, but the CL atom color is incorrect: the same as Carbon. I tried to change the "CL" to "BR", and the chimera shows the correct color: dark red. It seems weird to me. Could you please give me any suggestions? Thanks! Best, Lei
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Hi Lei, If all your chlorine atom names start with the characters "CL", you can change them all to chlorine after you open the .gro file with this command (Favorites→Command Line): setattr a element Cl @CL= --Eric Eric Pettersen UCSF Computer Graphics Lab
On Mar 21, 2021, at 7:54 PM, Lei Qian <tuk04130@temple.edu> wrote:
Hi Eric, Sorry for my late reply. Yes you are right. I tried it again: I made a new gro file containing only CL and K as ions, and opened it using chimera. I found chimera colored K as violet, which is good; but it colored CL as the same color as Carbon: yellow. Thank you again for your help! Best, Lei
On Tue, Feb 23, 2021 at 5:04 AM Eric Pettersen <pett@cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> wrote: Hi Lei, There is no explicit indication of the chemical element type in a .gro file, so it's all guesswork. Chimera assumes that atom names that begin with any of the letters C, O, P, S, H, or N are the corresponding single letter element type. This prevents atom names like CA and HG from being interpreted as calcium and mercury, rather than carbon and hydrogen. There aren't any great solutions. One option is to read in the .gro file, write it out as a .mol2 file, then edit that file to change the atom type of the CL atoms to Cl, then read that back in. Another is to select your CL atoms and use the "Modify Structure" tab of the Build Structure tool to change their element to Cl.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Feb 18, 2021, at 8:30 PM, Lei Qian <tuk04130@temple.edu <mailto:tuk04130@temple.edu>> wrote:
Dear users, Could I ask a question on chimera? Thanks! I tried to open a gro file (small compound) using chimera. Like below: ... ... 1 LIG CL 18 x.xxx x.xxx x.xxx 1 LIG CL1 19 x.xxx x.xxx x.xxx ... ... Although chimera shows the CL name "CL" when the cursor is above the atom, but the CL atom color is incorrect: the same as Carbon. I tried to change the "CL" to "BR", and the chimera shows the correct color: dark red. It seems weird to me. Could you please give me any suggestions? Thanks! Best, Lei
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Hi Eric, Thanks for your information! I tried the command, saved this gro to pdb file, opened new pdb, and it worked! BTW, it seems chimera cannot write new gro file (It can write these four files: 'pdb', 'pqr', 'mol2' or 'sph', but not gro) Could I ask you another question? In chimera I can manually change Carbon with 4 bonds to Nitrogen with 3 bonds using Tools/StructureEditing/BuildStructure/ModifyStructure. But I cannot find corresponding command line to do the same thing in chimera tutorial. So, is it possible that we can use command line to modify atom/element, its bonds and its geometry? Thanks! Best, Lei ________________________________ From: Eric Pettersen <pett@cgl.ucsf.edu> Sent: Tuesday, March 23, 2021 1:52 AM To: Lei Qian <tuk04130@temple.edu> Cc: chimera-users@cgl.ucsf.edu BB <chimera-users@cgl.ucsf.edu> Subject: [External] Re: [Chimera-users] [External] Re: in *.gro file, chimera takes CL atom as C (in compound) and gives it wrong color Hi Lei, If all your chlorine atom names start with the characters "CL", you can change them all to chlorine after you open the .gro file with this command (Favorites→Command Line): setattr a element Cl @CL= --Eric Eric Pettersen UCSF Computer Graphics Lab On Mar 21, 2021, at 7:54 PM, Lei Qian <tuk04130@temple.edu<mailto:tuk04130@temple.edu>> wrote: Hi Eric, Sorry for my late reply. Yes you are right. I tried it again: I made a new gro file containing only CL and K as ions, and opened it using chimera. I found chimera colored K as violet, which is good; but it colored CL as the same color as Carbon: yellow. Thank you again for your help! Best, Lei On Tue, Feb 23, 2021 at 5:04 AM Eric Pettersen <pett@cgl.ucsf.edu<mailto:pett@cgl.ucsf.edu>> wrote: Hi Lei, There is no explicit indication of the chemical element type in a .gro file, so it's all guesswork. Chimera assumes that atom names that begin with any of the letters C, O, P, S, H, or N are the corresponding single letter element type. This prevents atom names like CA and HG from being interpreted as calcium and mercury, rather than carbon and hydrogen. There aren't any great solutions. One option is to read in the .gro file, write it out as a .mol2 file, then edit that file to change the atom type of the CL atoms to Cl, then read that back in. Another is to select your CL atoms and use the "Modify Structure" tab of the Build Structure tool to change their element to Cl. --Eric Eric Pettersen UCSF Computer Graphics Lab On Feb 18, 2021, at 8:30 PM, Lei Qian <tuk04130@temple.edu<mailto:tuk04130@temple.edu>> wrote: Dear users, Could I ask a question on chimera? Thanks! I tried to open a gro file (small compound) using chimera. Like below: ... ... 1 LIG CL 18 x.xxx x.xxx x.xxx 1 LIG CL1 19 x.xxx x.xxx x.xxx ... ... Although chimera shows the CL name "CL" when the cursor is above the atom, but the CL atom color is incorrect: the same as Carbon. I tried to change the "CL" to "BR", and the chimera shows the correct color: dark red. It seems weird to me. Could you please give me any suggestions? Thanks! Best, Lei _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: https://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: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Lei, Chimera does not have a command equivalent for that function. If you know how to program in Python, you could write a Python script to call the method that Chimera is using: BuildStructure.changeAtom(). That method is in <your Chimera installation>/share/BuildStructure/__init__.py if you want to see the arguments it takes. Alternatively you could use ChimeraX, which does have a command equivalent ("build modify") for this. You would use Chimera to write out your .gro structures as something ChimeraX can read (e.g. PDB) and go from there. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Mar 22, 2021, at 7:24 PM, Lei Qian <leiqian-temple2@outlook.com> wrote:
Hi Eric, Thanks for your information!
I tried the command, saved this gro to pdb file, opened new pdb, and it worked! BTW, it seems chimera cannot write new gro file (It can write these four files: 'pdb', 'pqr', 'mol2' or 'sph', but not gro)
Could I ask you another question? In chimera I can manually change Carbon with 4 bonds to Nitrogen with 3 bonds using Tools/StructureEditing/BuildStructure/ModifyStructure. But I cannot find corresponding command line to do the same thing in chimera tutorial. So, is it possible that we can use command line to modify atom/element, its bonds and its geometry?
Thanks!
Best, Lei
From: Eric Pettersen <pett@cgl.ucsf.edu> Sent: Tuesday, March 23, 2021 1:52 AM To: Lei Qian <tuk04130@temple.edu> Cc: chimera-users@cgl.ucsf.edu BB <chimera-users@cgl.ucsf.edu> Subject: [External] Re: [Chimera-users] [External] Re: in *.gro file, chimera takes CL atom as C (in compound) and gives it wrong color
Hi Lei, If all your chlorine atom names start with the characters "CL", you can change them all to chlorine after you open the .gro file with this command (Favorites→Command Line):
setattr a element Cl @CL=
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Mar 21, 2021, at 7:54 PM, Lei Qian <tuk04130@temple.edu <mailto:tuk04130@temple.edu>> wrote:
Hi Eric, Sorry for my late reply. Yes you are right. I tried it again: I made a new gro file containing only CL and K as ions, and opened it using chimera. I found chimera colored K as violet, which is good; but it colored CL as the same color as Carbon: yellow. Thank you again for your help! Best, Lei
On Tue, Feb 23, 2021 at 5:04 AM Eric Pettersen <pett@cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> wrote: Hi Lei, There is no explicit indication of the chemical element type in a .gro file, so it's all guesswork. Chimera assumes that atom names that begin with any of the letters C, O, P, S, H, or N are the corresponding single letter element type. This prevents atom names like CA and HG from being interpreted as calcium and mercury, rather than carbon and hydrogen. There aren't any great solutions. One option is to read in the .gro file, write it out as a .mol2 file, then edit that file to change the atom type of the CL atoms to Cl, then read that back in. Another is to select your CL atoms and use the "Modify Structure" tab of the Build Structure tool to change their element to Cl.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Feb 18, 2021, at 8:30 PM, Lei Qian <tuk04130@temple.edu <mailto:tuk04130@temple.edu>> wrote:
Dear users, Could I ask a question on chimera? Thanks! I tried to open a gro file (small compound) using chimera. Like below: ... ... 1 LIG CL 18 x.xxx x.xxx x.xxx 1 LIG CL1 19 x.xxx x.xxx x.xxx ... ... Although chimera shows the CL name "CL" when the cursor is above the atom, but the CL atom color is incorrect: the same as Carbon. I tried to change the "CL" to "BR", and the chimera shows the correct color: dark red. It seems weird to me. Could you please give me any suggestions? Thanks! Best, Lei
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Hi Eric, Thanks for your information! Could I ask a new question on the method you mentioned? Thanks! In previous python scripts, I used chimera module and runCommand method to perform the regular chimera commands smoothly. Because I am not familiar with BuildStructure.changeAtom(), I tried to write a color-change python script trial according to "Chimera Program Guide": import Midas modellist = Midas.open("lig.pdb") Midas.color('red', '@/element=F') out_path = 'test.pdb' Midas.write(modellist, None, out_path) However, this did not work. Actually, I am not sure if I can use the above similar strategy to perform the changeAtom() method. Could you please give me a hint or recommend a tutorial? Thanks! Best, Lei ________________________________ From: Eric Pettersen <pett@cgl.ucsf.edu> Sent: Wednesday, March 24, 2021 6:42 AM To: Lei Qian <leiqian-temple2@outlook.com> Cc: chimera-users@cgl.ucsf.edu BB <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] [External] Re: [External] Re: in *.gro file, chimera takes CL atom as C (in compound) and gives it wrong color Hi Lei, Chimera does not have a command equivalent for that function. If you know how to program in Python, you could write a Python script to call the method that Chimera is using: BuildStructure.changeAtom(). That method is in <your Chimera installation>/share/BuildStructure/__init__.py if you want to see the arguments it takes. Alternatively you could use ChimeraX, which does have a command equivalent ("build modify") for this. You would use Chimera to write out your .gro structures as something ChimeraX can read (e.g. PDB) and go from there. --Eric Eric Pettersen UCSF Computer Graphics Lab On Mar 22, 2021, at 7:24 PM, Lei Qian <leiqian-temple2@outlook.com<mailto:leiqian-temple2@outlook.com>> wrote: Hi Eric, Thanks for your information! I tried the command, saved this gro to pdb file, opened new pdb, and it worked! BTW, it seems chimera cannot write new gro file (It can write these four files: 'pdb', 'pqr', 'mol2' or 'sph', but not gro) Could I ask you another question? In chimera I can manually change Carbon with 4 bonds to Nitrogen with 3 bonds using Tools/StructureEditing/BuildStructure/ModifyStructure. But I cannot find corresponding command line to do the same thing in chimera tutorial. So, is it possible that we can use command line to modify atom/element, its bonds and its geometry? Thanks! Best, Lei ________________________________ From: Eric Pettersen <pett@cgl.ucsf.edu<mailto:pett@cgl.ucsf.edu>> Sent: Tuesday, March 23, 2021 1:52 AM To: Lei Qian <tuk04130@temple.edu<mailto:tuk04130@temple.edu>> Cc: chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> BB <chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>> Subject: [External] Re: [Chimera-users] [External] Re: in *.gro file, chimera takes CL atom as C (in compound) and gives it wrong color Hi Lei, If all your chlorine atom names start with the characters "CL", you can change them all to chlorine after you open the .gro file with this command (Favorites→Command Line): setattr a element Cl @CL= --Eric Eric Pettersen UCSF Computer Graphics Lab On Mar 21, 2021, at 7:54 PM, Lei Qian <tuk04130@temple.edu<mailto:tuk04130@temple.edu>> wrote: Hi Eric, Sorry for my late reply. Yes you are right. I tried it again: I made a new gro file containing only CL and K as ions, and opened it using chimera. I found chimera colored K as violet, which is good; but it colored CL as the same color as Carbon: yellow. Thank you again for your help! Best, Lei On Tue, Feb 23, 2021 at 5:04 AM Eric Pettersen <pett@cgl.ucsf.edu<mailto:pett@cgl.ucsf.edu>> wrote: Hi Lei, There is no explicit indication of the chemical element type in a .gro file, so it's all guesswork. Chimera assumes that atom names that begin with any of the letters C, O, P, S, H, or N are the corresponding single letter element type. This prevents atom names like CA and HG from being interpreted as calcium and mercury, rather than carbon and hydrogen. There aren't any great solutions. One option is to read in the .gro file, write it out as a .mol2 file, then edit that file to change the atom type of the CL atoms to Cl, then read that back in. Another is to select your CL atoms and use the "Modify Structure" tab of the Build Structure tool to change their element to Cl. --Eric Eric Pettersen UCSF Computer Graphics Lab On Feb 18, 2021, at 8:30 PM, Lei Qian <tuk04130@temple.edu<mailto:tuk04130@temple.edu>> wrote: Dear users, Could I ask a question on chimera? Thanks! I tried to open a gro file (small compound) using chimera. Like below: ... ... 1 LIG CL 18 x.xxx x.xxx x.xxx 1 LIG CL1 19 x.xxx x.xxx x.xxx ... ... Although chimera shows the CL name "CL" when the cursor is above the atom, but the CL atom color is incorrect: the same as Carbon. I tried to change the "CL" to "BR", and the chimera shows the correct color: dark red. It seems weird to me. Could you please give me any suggestions? Thanks! Best, Lei _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: https://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: https://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: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Lei, Your script was pretty close to correct. The problem is that Midas.open() returns a list of models (using containing only one model, but in the case of an NMR ensemble it could be more) and Midas.write() expects to be given a single model, not a list of models. So something like: modellist = Midas.open("lig.pdb") model = modellist[0] ... Midas.write(model, None, out_path) As for changeAtom(), let's say you've selected some sp3 carbons that you want to change to sp2 nitrogen by whatever means (such as runCommand("select something")). You would change them (one by one) with: from BuildStructure import changeAtom from chimera.selection import currentAtoms for a in currentAtoms(): changeAtom(a, 'N', 3, 3) If the carbons had 4 bonds, you would have to delete one first. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Mar 28, 2021, at 9:54 AM, Lei Qian <leiqian-temple2@outlook.com> wrote:
Hi Eric, Thanks for your information! Could I ask a new question on the method you mentioned? Thanks!
In previous python scripts, I used chimera module and runCommand method to perform the regular chimera commands smoothly. Because I am not familiar with BuildStructure.changeAtom(), I tried to write a color-change python script trial according to "Chimera Program Guide": import Midas modellist = Midas.open("lig.pdb") Midas.color('red', '@/element=F') out_path = 'test.pdb' Midas.write(modellist, None, out_path) However, this did not work. Actually, I am not sure if I can use the above similar strategy to perform the changeAtom() method. Could you please give me a hint or recommend a tutorial? Thanks! Best,
Lei
From: Eric Pettersen <pett@cgl.ucsf.edu> Sent: Wednesday, March 24, 2021 6:42 AM To: Lei Qian <leiqian-temple2@outlook.com> Cc: chimera-users@cgl.ucsf.edu BB <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] [External] Re: [External] Re: in *.gro file, chimera takes CL atom as C (in compound) and gives it wrong color
Hi Lei, Chimera does not have a command equivalent for that function. If you know how to program in Python, you could write a Python script to call the method that Chimera is using: BuildStructure.changeAtom(). That method is in <your Chimera installation>/share/BuildStructure/__init__.py if you want to see the arguments it takes. Alternatively you could use ChimeraX, which does have a command equivalent ("build modify") for this. You would use Chimera to write out your .gro structures as something ChimeraX can read (e.g. PDB) and go from there.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Mar 22, 2021, at 7:24 PM, Lei Qian <leiqian-temple2@outlook.com <mailto:leiqian-temple2@outlook.com>> wrote:
Hi Eric, Thanks for your information!
I tried the command, saved this gro to pdb file, opened new pdb, and it worked! BTW, it seems chimera cannot write new gro file (It can write these four files: 'pdb', 'pqr', 'mol2' or 'sph', but not gro)
Could I ask you another question? In chimera I can manually change Carbon with 4 bonds to Nitrogen with 3 bonds using Tools/StructureEditing/BuildStructure/ModifyStructure. But I cannot find corresponding command line to do the same thing in chimera tutorial. So, is it possible that we can use command line to modify atom/element, its bonds and its geometry?
Thanks!
Best, Lei
From: Eric Pettersen <pett@cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> Sent: Tuesday, March 23, 2021 1:52 AM To: Lei Qian <tuk04130@temple.edu <mailto:tuk04130@temple.edu>> Cc: chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> BB <chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> Subject: [External] Re: [Chimera-users] [External] Re: in *.gro file, chimera takes CL atom as C (in compound) and gives it wrong color
Hi Lei, If all your chlorine atom names start with the characters "CL", you can change them all to chlorine after you open the .gro file with this command (Favorites→Command Line):
setattr a element Cl @CL=
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Mar 21, 2021, at 7:54 PM, Lei Qian <tuk04130@temple.edu <mailto:tuk04130@temple.edu>> wrote:
Hi Eric, Sorry for my late reply. Yes you are right. I tried it again: I made a new gro file containing only CL and K as ions, and opened it using chimera. I found chimera colored K as violet, which is good; but it colored CL as the same color as Carbon: yellow. Thank you again for your help! Best, Lei
On Tue, Feb 23, 2021 at 5:04 AM Eric Pettersen <pett@cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> wrote: Hi Lei, There is no explicit indication of the chemical element type in a .gro file, so it's all guesswork. Chimera assumes that atom names that begin with any of the letters C, O, P, S, H, or N are the corresponding single letter element type. This prevents atom names like CA and HG from being interpreted as calcium and mercury, rather than carbon and hydrogen. There aren't any great solutions. One option is to read in the .gro file, write it out as a .mol2 file, then edit that file to change the atom type of the CL atoms to Cl, then read that back in. Another is to select your CL atoms and use the "Modify Structure" tab of the Build Structure tool to change their element to Cl.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Feb 18, 2021, at 8:30 PM, Lei Qian <tuk04130@temple.edu <mailto:tuk04130@temple.edu>> wrote:
Dear users, Could I ask a question on chimera? Thanks! I tried to open a gro file (small compound) using chimera. Like below: ... ... 1 LIG CL 18 x.xxx x.xxx x.xxx 1 LIG CL1 19 x.xxx x.xxx x.xxx ... ... Although chimera shows the CL name "CL" when the cursor is above the atom, but the CL atom color is incorrect: the same as Carbon. I tried to change the "CL" to "BR", and the chimera shows the correct color: dark red. It seems weird to me. Could you please give me any suggestions? Thanks! Best, Lei
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Hi Eric, I tried the changeAtom method from your email, and it worked. Many Thanks! BTW, regarding the color-change method, I found even if I changed the color for one atom (e.g., from white to red for Hydrogen) and saved it to a new file, when I opened the new file, the Hydrogen color was still white. It seems chimera insists the correct color in which it believes :-) Lei ________________________________ From: Eric Pettersen <pett@cgl.ucsf.edu> Sent: Tuesday, March 30, 2021 2:19 AM To: Lei Qian <leiqian-temple2@outlook.com> Cc: chimera-users@cgl.ucsf.edu BB <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] [External] Re: [External] Re: in *.gro file, chimera takes CL atom as C (in compound) and gives it wrong color Hi Lei, Your script was pretty close to correct. The problem is that Midas.open() returns a list of models (using containing only one model, but in the case of an NMR ensemble it could be more) and Midas.write() expects to be given a single model, not a list of models. So something like: modellist = Midas.open("lig.pdb") model = modellist[0] ... Midas.write(model, None, out_path) As for changeAtom(), let's say you've selected some sp3 carbons that you want to change to sp2 nitrogen by whatever means (such as runCommand("select something")). You would change them (one by one) with: from BuildStructure import changeAtom from chimera.selection import currentAtoms for a in currentAtoms(): changeAtom(a, 'N', 3, 3) If the carbons had 4 bonds, you would have to delete one first. --Eric Eric Pettersen UCSF Computer Graphics Lab On Mar 28, 2021, at 9:54 AM, Lei Qian <leiqian-temple2@outlook.com<mailto:leiqian-temple2@outlook.com>> wrote: Hi Eric, Thanks for your information! Could I ask a new question on the method you mentioned? Thanks! In previous python scripts, I used chimera module and runCommand method to perform the regular chimera commands smoothly. Because I am not familiar with BuildStructure.changeAtom(), I tried to write a color-change python script trial according to "Chimera Program Guide": import Midas modellist = Midas.open("lig.pdb") Midas.color('red', '@/element=F') out_path = 'test.pdb' Midas.write(modellist, None, out_path) However, this did not work. Actually, I am not sure if I can use the above similar strategy to perform the changeAtom() method. Could you please give me a hint or recommend a tutorial? Thanks! Best, Lei ________________________________ From: Eric Pettersen <pett@cgl.ucsf.edu<mailto:pett@cgl.ucsf.edu>> Sent: Wednesday, March 24, 2021 6:42 AM To: Lei Qian <leiqian-temple2@outlook.com<mailto:leiqian-temple2@outlook.com>> Cc: chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> BB <chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>> Subject: Re: [Chimera-users] [External] Re: [External] Re: in *.gro file, chimera takes CL atom as C (in compound) and gives it wrong color Hi Lei, Chimera does not have a command equivalent for that function. If you know how to program in Python, you could write a Python script to call the method that Chimera is using: BuildStructure.changeAtom(). That method is in <your Chimera installation>/share/BuildStructure/__init__.py if you want to see the arguments it takes. Alternatively you could use ChimeraX, which does have a command equivalent ("build modify") for this. You would use Chimera to write out your .gro structures as something ChimeraX can read (e.g. PDB) and go from there. --Eric Eric Pettersen UCSF Computer Graphics Lab On Mar 22, 2021, at 7:24 PM, Lei Qian <leiqian-temple2@outlook.com<mailto:leiqian-temple2@outlook.com>> wrote: Hi Eric, Thanks for your information! I tried the command, saved this gro to pdb file, opened new pdb, and it worked! BTW, it seems chimera cannot write new gro file (It can write these four files: 'pdb', 'pqr', 'mol2' or 'sph', but not gro) Could I ask you another question? In chimera I can manually change Carbon with 4 bonds to Nitrogen with 3 bonds using Tools/StructureEditing/BuildStructure/ModifyStructure. But I cannot find corresponding command line to do the same thing in chimera tutorial. So, is it possible that we can use command line to modify atom/element, its bonds and its geometry? Thanks! Best, Lei ________________________________ From: Eric Pettersen <pett@cgl.ucsf.edu<mailto:pett@cgl.ucsf.edu>> Sent: Tuesday, March 23, 2021 1:52 AM To: Lei Qian <tuk04130@temple.edu<mailto:tuk04130@temple.edu>> Cc: chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> BB <chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>> Subject: [External] Re: [Chimera-users] [External] Re: in *.gro file, chimera takes CL atom as C (in compound) and gives it wrong color Hi Lei, If all your chlorine atom names start with the characters "CL", you can change them all to chlorine after you open the .gro file with this command (Favorites→Command Line): setattr a element Cl @CL= --Eric Eric Pettersen UCSF Computer Graphics Lab On Mar 21, 2021, at 7:54 PM, Lei Qian <tuk04130@temple.edu<mailto:tuk04130@temple.edu>> wrote: Hi Eric, Sorry for my late reply. Yes you are right. I tried it again: I made a new gro file containing only CL and K as ions, and opened it using chimera. I found chimera colored K as violet, which is good; but it colored CL as the same color as Carbon: yellow. Thank you again for your help! Best, Lei On Tue, Feb 23, 2021 at 5:04 AM Eric Pettersen <pett@cgl.ucsf.edu<mailto:pett@cgl.ucsf.edu>> wrote: Hi Lei, There is no explicit indication of the chemical element type in a .gro file, so it's all guesswork. Chimera assumes that atom names that begin with any of the letters C, O, P, S, H, or N are the corresponding single letter element type. This prevents atom names like CA and HG from being interpreted as calcium and mercury, rather than carbon and hydrogen. There aren't any great solutions. One option is to read in the .gro file, write it out as a .mol2 file, then edit that file to change the atom type of the CL atoms to Cl, then read that back in. Another is to select your CL atoms and use the "Modify Structure" tab of the Build Structure tool to change their element to Cl. --Eric Eric Pettersen UCSF Computer Graphics Lab On Feb 18, 2021, at 8:30 PM, Lei Qian <tuk04130@temple.edu<mailto:tuk04130@temple.edu>> wrote: Dear users, Could I ask a question on chimera? Thanks! I tried to open a gro file (small compound) using chimera. Like below: ... ... 1 LIG CL 18 x.xxx x.xxx x.xxx 1 LIG CL1 19 x.xxx x.xxx x.xxx ... ... Although chimera shows the CL name "CL" when the cursor is above the atom, but the CL atom color is incorrect: the same as Carbon. I tried to change the "CL" to "BR", and the chimera shows the correct color: dark red. It seems weird to me. Could you please give me any suggestions? Thanks! Best, Lei _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: https://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: https://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: https://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: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Lei, Glad you got it working! Most output file types (e.g. PDB, mol2) do not support color information, and therefore color information is neither saved nor restored when using such files. Chimera simply colors such structures in a standard informative way when you open such a file. --Eric
On Mar 31, 2021, at 7:38 AM, Lei Qian <leiqian-temple2@outlook.com> wrote:
Hi Eric, I tried the changeAtom method from your email, and it worked. Many Thanks! BTW, regarding the color-change method, I found even if I changed the color for one atom (e.g., from white to red for Hydrogen) and saved it to a new file, when I opened the new file, the Hydrogen color was still white. It seems chimera insists the correct color in which it believes :-) Lei
From: Eric Pettersen <pett@cgl.ucsf.edu> Sent: Tuesday, March 30, 2021 2:19 AM To: Lei Qian <leiqian-temple2@outlook.com> Cc: chimera-users@cgl.ucsf.edu BB <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] [External] Re: [External] Re: in *.gro file, chimera takes CL atom as C (in compound) and gives it wrong color
Hi Lei, Your script was pretty close to correct. The problem is that Midas.open() returns a list of models (using containing only one model, but in the case of an NMR ensemble it could be more) and Midas.write() expects to be given a single model, not a list of models. So something like:
modellist = Midas.open("lig.pdb") model = modellist[0] ... Midas.write(model, None, out_path)
As for changeAtom(), let's say you've selected some sp3 carbons that you want to change to sp2 nitrogen by whatever means (such as runCommand("select something")). You would change them (one by one) with:
from BuildStructure import changeAtom from chimera.selection import currentAtoms for a in currentAtoms(): changeAtom(a, 'N', 3, 3)
If the carbons had 4 bonds, you would have to delete one first.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Mar 28, 2021, at 9:54 AM, Lei Qian <leiqian-temple2@outlook.com <mailto:leiqian-temple2@outlook.com>> wrote:
Hi Eric, Thanks for your information! Could I ask a new question on the method you mentioned? Thanks!
In previous python scripts, I used chimera module and runCommand method to perform the regular chimera commands smoothly. Because I am not familiar with BuildStructure.changeAtom(), I tried to write a color-change python script trial according to "Chimera Program Guide": import Midas modellist = Midas.open("lig.pdb") Midas.color('red', '@/element=F') out_path = 'test.pdb' Midas.write(modellist, None, out_path) However, this did not work. Actually, I am not sure if I can use the above similar strategy to perform the changeAtom() method. Could you please give me a hint or recommend a tutorial? Thanks! Best,
Lei
From: Eric Pettersen <pett@cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> Sent: Wednesday, March 24, 2021 6:42 AM To: Lei Qian <leiqian-temple2@outlook.com <mailto:leiqian-temple2@outlook.com>> Cc: chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> BB <chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> Subject: Re: [Chimera-users] [External] Re: [External] Re: in *.gro file, chimera takes CL atom as C (in compound) and gives it wrong color
Hi Lei, Chimera does not have a command equivalent for that function. If you know how to program in Python, you could write a Python script to call the method that Chimera is using: BuildStructure.changeAtom(). That method is in <your Chimera installation>/share/BuildStructure/__init__.py if you want to see the arguments it takes. Alternatively you could use ChimeraX, which does have a command equivalent ("build modify") for this. You would use Chimera to write out your .gro structures as something ChimeraX can read (e.g. PDB) and go from there.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Mar 22, 2021, at 7:24 PM, Lei Qian <leiqian-temple2@outlook.com <mailto:leiqian-temple2@outlook.com>> wrote:
Hi Eric, Thanks for your information!
I tried the command, saved this gro to pdb file, opened new pdb, and it worked! BTW, it seems chimera cannot write new gro file (It can write these four files: 'pdb', 'pqr', 'mol2' or 'sph', but not gro)
Could I ask you another question? In chimera I can manually change Carbon with 4 bonds to Nitrogen with 3 bonds using Tools/StructureEditing/BuildStructure/ModifyStructure. But I cannot find corresponding command line to do the same thing in chimera tutorial. So, is it possible that we can use command line to modify atom/element, its bonds and its geometry?
Thanks!
Best, Lei
From: Eric Pettersen <pett@cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> Sent: Tuesday, March 23, 2021 1:52 AM To: Lei Qian <tuk04130@temple.edu <mailto:tuk04130@temple.edu>> Cc: chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> BB <chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> Subject: [External] Re: [Chimera-users] [External] Re: in *.gro file, chimera takes CL atom as C (in compound) and gives it wrong color
Hi Lei, If all your chlorine atom names start with the characters "CL", you can change them all to chlorine after you open the .gro file with this command (Favorites→Command Line):
setattr a element Cl @CL=
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Mar 21, 2021, at 7:54 PM, Lei Qian <tuk04130@temple.edu <mailto:tuk04130@temple.edu>> wrote:
Hi Eric, Sorry for my late reply. Yes you are right. I tried it again: I made a new gro file containing only CL and K as ions, and opened it using chimera. I found chimera colored K as violet, which is good; but it colored CL as the same color as Carbon: yellow. Thank you again for your help! Best, Lei
On Tue, Feb 23, 2021 at 5:04 AM Eric Pettersen <pett@cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> wrote: Hi Lei, There is no explicit indication of the chemical element type in a .gro file, so it's all guesswork. Chimera assumes that atom names that begin with any of the letters C, O, P, S, H, or N are the corresponding single letter element type. This prevents atom names like CA and HG from being interpreted as calcium and mercury, rather than carbon and hydrogen. There aren't any great solutions. One option is to read in the .gro file, write it out as a .mol2 file, then edit that file to change the atom type of the CL atoms to Cl, then read that back in. Another is to select your CL atoms and use the "Modify Structure" tab of the Build Structure tool to change their element to Cl.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Feb 18, 2021, at 8:30 PM, Lei Qian <tuk04130@temple.edu <mailto:tuk04130@temple.edu>> wrote:
Dear users, Could I ask a question on chimera? Thanks! I tried to open a gro file (small compound) using chimera. Like below: ... ... 1 LIG CL 18 x.xxx x.xxx x.xxx 1 LIG CL1 19 x.xxx x.xxx x.xxx ... ... Although chimera shows the CL name "CL" when the cursor is above the atom, but the CL atom color is incorrect: the same as Carbon. I tried to change the "CL" to "BR", and the chimera shows the correct color: dark red. It seems weird to me. Could you please give me any suggestions? Thanks! Best, Lei
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participants (3)
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Eric Pettersen -
Lei Qian -
Lei Qian