Chimeras limited capability to visualize correctly molecular structure

Marek Maly

18 Jun 2013 18 Jun '13

1:55 p.m.

Hello all, recently was sent to the Amber mailing list question about how to proceed here with simulation of the piece of graphene. I was just curious about the molecular structure so I tried to visualize attached PDB file in Chimera which was not able to show correct structure so I visualized it using VMD and also Vega ZZ in both cases without any problem. Then I used Vega ZZ to create MOL2 file and tried again to use Chimera for visualizing graphene saved now in MOL2 format but again without success. So maybe there is still some space for improvement of Chimera visualizing capability. Especially in case of MOL2 format I was surprised that Chimera is not able to show correct molecular structure as in this case all the information (including bonds/connectivity info) is included in the input file. All files are attached. (my version of Chimera is: candidate version 1.8 (build 38694)) Best wishes, Marek -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/

Attachments:

graphene.png (image/png — 28.6 KB)
graphene.pdb (application/octet-stream — 36.7 KB)
graphene.ml2 (application/octet-stream — 72.4 KB)

Show replies by date

R.J. Swett

18 Jun 18 Jun

4:23 p.m.

Marek, I had no problem opening the mol2 file, and displaying the atoms. I simply hid the ribbon structure, displayed the atoms, and saved an image. There are some excellent tutorials on the chimera website on visualization of structures which I'm sure will help you in the future. Chimera makes more guesses on initial display than VMD or VegaZZ, and for protein structures this is very convenient. I have attached an image generated with Chimera which you will see is nearly identical to yours. R.J. Swett Wayne State University 357 Chemistry Detroit, MI 48201 Lab Phone 313-577-0552 Cell Phone 906-235-0768 On 6/18/2013 9:55 AM, Marek Maly wrote:

...

Hello all,

recently was sent to the Amber mailing list question about how to proceed here with simulation of the piece of graphene.

I was just curious about the molecular structure so I tried to visualize attached PDB file in Chimera which was not able to show correct structure so I visualized it using VMD and also Vega ZZ in both cases without any problem. Then I used Vega ZZ to create MOL2 file and tried again to use Chimera for visualizing graphene saved now in MOL2 format but again without success.

So maybe there is still some space for improvement of Chimera visualizing capability. Especially in case of MOL2 format I was surprised that Chimera is not able to show correct molecular structure as in this case all the information (including bonds/connectivity info) is included in the input file.

All files are attached. (my version of Chimera is: candidate version 1.8 (build 38694))

Best wishes,

Marek

_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

Elaine Meng

4:49 p.m.

New subject: Chimeras limited capability to visualize correctly molecular structure

Hi Marek, Just to add to Rebecca's answer, the problem is only that Chimera tries to show the structure as ribbons. You can simply show all atoms, as Rebecca mentioned (for example: Presets… Interactive 2 (all atoms)), or change the preferences to show all atoms when you open a structure (Favorites… Preferences, category: New Molecules, set "smart initial display" to "false", Save if you want it to apply to later uses of Chimera). The smart initial display wasn't smart about this graphene fragment, probably because the carbons are named CA, like amino acid alpha-carbons. However, without smart initial display you will just get (initially) all atoms without any color-coding, so you might prefer to leave it on, especially if you often view macromolecules. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jun 18, 2013, at 9:23 AM, "R.J. Swett" wrote:

...

Marek, I had no problem opening the mol2 file, and displaying the atoms. I simply hid the ribbon structure, displayed the atoms, and saved an image. There are some excellent tutorials on the chimera website on visualization of structures which I'm sure will help you in the future. Chimera makes more guesses on initial display than VMD or VegaZZ, and for protein structures this is very convenient. I have attached an image generated with Chimera which you will see is nearly identical to yours. R.J. Swett Wayne State University 357 Chemistry Detroit, MI 48201

Lab Phone 313-577-0552 Cell Phone 906-235-0768

On 6/18/2013 9:55 AM, Marek Maly wrote:

...
Hello all, recently was sent to the Amber mailing list question about how to proceed here with simulation of the piece of graphene.

I was just curious about the molecular structure so I tried to visualize attached PDB file in Chimera which was not able to show correct structure so I visualized it using VMD and also Vega ZZ in both cases without any problem. Then I used Vega ZZ to create MOL2 file and tried again to use Chimera for visualizing graphene saved now in MOL2 format but again without success.

So maybe there is still some space for improvement of Chimera visualizing capability. Especially in case of MOL2 format I was surprised that Chimera is not able to show correct molecular structure as in this case all the information (including bonds/connectivity info) is included in the input file.

All files are attached. (my version of Chimera is: candidate version 1.8 (build 38694))

Best wishes,

Marek

Marek Maly

4:47 p.m.

Dear Elaine, thanks for the explanation. Now I verified that if the input file is in MOL2 and I use all atom representation Chimera is able to show correct structure although if I try to use the original PDB input file, Chimera still fails to show the right structure perhaps because of the "bond"/connectivity complexity of this structure. Best wishes, Marek Dne Tue, 18 Jun 2013 18:49:39 +0200 Elaine Meng napsal/-a:

...

Hi Marek, Just to add to Rebecca's answer, the problem is only that Chimera tries to show the structure as ribbons. You can simply show all atoms, as Rebecca mentioned (for example: Presets… Interactive 2 (all atoms)), or change the preferences to show all atoms when you open a structure (Favorites… Preferences, category: New Molecules, set "smart initial display" to "false", Save if you want it to apply to later uses of Chimera). The smart initial display wasn't smart about this graphene fragment, probably because the carbons are named CA, like amino acid alpha-carbons.

However, without smart initial display you will just get (initially) all atoms without any color-coding, so you might prefer to leave it on, especially if you often view macromolecules. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

On Jun 18, 2013, at 9:23 AM, "R.J. Swett" wrote:

...
Marek, I had no problem opening the mol2 file, and displaying the atoms. I simply hid the ribbon structure, displayed the atoms, and saved an image. There are some excellent tutorials on the chimera website on visualization of structures which I'm sure will help you in the future. Chimera makes more guesses on initial display than VMD or VegaZZ, and for protein structures this is very convenient. I have attached an image generated with Chimera which you will see is nearly identical to yours. R.J. Swett Wayne State University 357 Chemistry Detroit, MI 48201

Lab Phone 313-577-0552 Cell Phone 906-235-0768

On 6/18/2013 9:55 AM, Marek Maly wrote:

...
Hello all, recently was sent to the Amber mailing list question about how to proceed here with simulation of the piece of graphene.

I was just curious about the molecular structure so I tried to visualize attached PDB file in Chimera which was not able to show correct structure so I visualized it using VMD and also Vega ZZ in both cases without any problem. Then I used Vega ZZ to create MOL2 file and tried again to use Chimera for visualizing graphene saved now in MOL2 format but again without success.

So maybe there is still some space for improvement of Chimera visualizing capability. Especially in case of MOL2 format I was surprised that Chimera is not able to show correct molecular structure as in this case all the information (including bonds/connectivity info) is included in the input file.

All files are attached. (my version of Chimera is: candidate version 1.8 (build 38694))

Best wishes,

Marek

__________ Informace od ESET NOD32 Antivirus, verze databaze 8463 (20130618) __________

Tuto zpravu proveril ESET NOD32 Antivirus.

http://www.eset.cz

-- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/

Eric Pettersen

5:58 p.m.

New subject: Chimeras limited capability to visualize correctly molecular structure

Hi Marek, The reason the PDB doesn't work right is because you are using ATOM records and are also putting each carbon in a separate residue. ATOM records are for standard polymeric residues and therefore Chimera tries to form a "chain", as much as it can, between adjacent "residues". If you change the PDB file to all be one residue, Chimera handles it fine. I've attached such a PDB file. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Jun 18, 2013, at 9:47 AM, "Marek Maly" wrote:

...

Dear Elaine,

thanks for the explanation.

Now I verified that if the input file is in MOL2 and I use all atom representation Chimera is able to show correct structure although if I try to use the original PDB input file, Chimera still fails to show the right structure perhaps because of the "bond"/connectivity complexity of this structure.

Best wishes,

Marek

Dne Tue, 18 Jun 2013 18:49:39 +0200 Elaine Meng napsal/-a:

...
Hi Marek, Just to add to Rebecca's answer, the problem is only that Chimera tries to show the structure as ribbons. You can simply show all atoms, as Rebecca mentioned (for example: Presets… Interactive 2 (all atoms)), or change the preferences to show all atoms when you open a structure (Favorites… Preferences, category: New Molecules, set "smart initial display" to "false", Save if you want it to apply to later uses of Chimera). The smart initial display wasn't smart about this graphene fragment, probably because the carbons are named CA, like amino acid alpha-carbons.

However, without smart initial display you will just get (initially) all atoms without any color-coding, so you might prefer to leave it on, especially if you often view macromolecules. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

On Jun 18, 2013, at 9:23 AM, "R.J. Swett" wrote:

...
Marek, I had no problem opening the mol2 file, and displaying the atoms. I simply hid the ribbon structure, displayed the atoms, and saved an image. There are some excellent tutorials on the chimera website on visualization of structures which I'm sure will help you in the future. Chimera makes more guesses on initial display than VMD or VegaZZ, and for protein structures this is very convenient. I have attached an image generated with Chimera which you will see is nearly identical to yours. R.J. Swett Wayne State University 357 Chemistry Detroit, MI 48201

Lab Phone 313-577-0552 Cell Phone 906-235-0768

On 6/18/2013 9:55 AM, Marek Maly wrote:

...
Hello all, recently was sent to the Amber mailing list question about how to proceed here with simulation of the piece of graphene.

I was just curious about the molecular structure so I tried to visualize attached PDB file in Chimera which was not able to show correct structure so I visualized it using VMD and also Vega ZZ in both cases without any problem. Then I used Vega ZZ to create MOL2 file and tried again to use Chimera for visualizing graphene saved now in MOL2 format but again without success.

So maybe there is still some space for improvement of Chimera visualizing capability. Especially in case of MOL2 format I was surprised that Chimera is not able to show correct molecular structure as in this case all the information (including bonds/connectivity info) is included in the input file.

All files are attached. (my version of Chimera is: candidate version 1.8 (build 38694))

Best wishes,

Marek

__________ Informace od ESET NOD32 Antivirus, verze databaze 8463 (20130618) __________

Tuto zpravu proveril ESET NOD32 Antivirus.

http://www.eset.cz

-- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/ _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

Marek Maly

5:10 p.m.

Thanks, I already confirmed this however as I already answered to Elaine, the problem with PDB input file still persists, but I do not see it as some critical err of course. Best, Marek Dne Tue, 18 Jun 2013 18:23:10 +0200 R.J. Swett napsal/-a:

...

Marek, I had no problem opening the mol2 file, and displaying the atoms. I simply hid the ribbon structure, displayed the atoms, and saved an image. There are some excellent tutorials on the chimera website on visualization of structures which I'm sure will help you in the future. Chimera makes more guesses on initial display than VMD or VegaZZ, and for protein structures this is very convenient. I have attached an image generated with Chimera which you will see is nearly identical to yours.

R.J. Swett Wayne State University 357 Chemistry Detroit, MI 48201

Lab Phone 313-577-0552 Cell Phone 906-235-0768

On 6/18/2013 9:55 AM, Marek Maly wrote:

...
Hello all,

recently was sent to the Amber mailing list question about how to proceed here with simulation of the piece of graphene.

I was just curious about the molecular structure so I tried to visualize attached PDB file in Chimera which was not able to show correct structure so I visualized it using VMD and also Vega ZZ in both cases without any problem. Then I used Vega ZZ to create MOL2 file and tried again to use Chimera for visualizing graphene saved now in MOL2 format but again without success.

So maybe there is still some space for improvement of Chimera visualizing capability. Especially in case of MOL2 format I was surprised that Chimera is not able to show correct molecular structure as in this case all the information (including bonds/connectivity info) is included in the input file.

All files are attached. (my version of Chimera is: candidate version 1.8 (build 38694))

Best wishes,

Marek

_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

__________ Informace od ESET NOD32 Antivirus, verze databaze 8463 (20130618) __________

Tuto zpravu proveril ESET NOD32 Antivirus.

http://www.eset.cz

-- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/

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participants (4)

Elaine Meng
Eric Pettersen
Marek Maly
R.J. Swett