Fwd: [ccp4bb] adding some user-defined graphical objects in a PDB file (and displaying them)
-------- Original Message -------- Subject: [ccp4bb] adding some user-defined graphical objects in a PDB file (and displaying them) Date: Fri, 26 Oct 2012 10:25:10 +0900 From: Francois Berenger <berenger@RIKEN.JP> Reply-To: Francois Berenger <berenger@RIKEN.JP> To: CCP4BB@JISCMAIL.AC.UK Hello, For some new project, I'd like to be able to generate things and store them in PDB format. For example, a triangle, a line segment, a square, a cube, a sphere, an arrow, etc. Being able to change the color and "line width" would be nice. Is there some official recommended way of doing this? Is there some software able to read and display such graphical annotations of PDB files? I'll also need the format description in that case. I want to be able to process a PDB file and store the result of my processing in the same PDB file as some kind of annotation. My current way of doing this is to discretize my objects as H atoms in some other output PDB file, but that's just a temporary workaround. My current search got me this: http://www.cgl.ucsf.edu/eccc1/ So, maybe there is some support for what I am looking for into Chimera. Thanks a lot for your suggestions, Francois.
Hello, PDB format is for atoms/bonds, not graphical objects. Although you could have "fake" atoms and bonds, the display choices would still be just those available for atoms (dots and lines, sticks, ball & stick, spheres). For graphical objects, Chimera understands a few different formats. You could use "Help... Search Documentation" in the Chimera menu, search for "graphical objects," then click link "Input File Types," and in that page see the bottom section: other 3D objects. Probably "Bild" or "VRML" would be the most relevant to you. "Bild" is the simpler format, easy to understand and write. Another possibility is to use the Chimera "shape" command (see instructions using command: help shape). It makes surfaces in different shapes. However, to save those you would probably need to save a Chimera session file. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Oct 25, 2012, at 9:46 PM, Francois Berenger wrote:
-------- Original Message -------- Subject: [ccp4bb] adding some user-defined graphical objects in a PDB file (and displaying them) Date: Fri, 26 Oct 2012 10:25:10 +0900 From: Francois Berenger <berenger@RIKEN.JP> Reply-To: Francois Berenger <berenger@RIKEN.JP> To: CCP4BB@JISCMAIL.AC.UK
Hello,
For some new project, I'd like to be able to generate things and store them in PDB format.
For example, a triangle, a line segment, a square, a cube, a sphere, an arrow, etc. Being able to change the color and "line width" would be nice.
Is there some official recommended way of doing this?
Is there some software able to read and display such graphical annotations of PDB files? I'll also need the format description in that case.
I want to be able to process a PDB file and store the result of my processing in the same PDB file as some kind of annotation.
My current way of doing this is to discretize my objects as H atoms in some other output PDB file, but that's just a temporary workaround.
My current search got me this: http://www.cgl.ucsf.edu/eccc1/ So, maybe there is some support for what I am looking for into Chimera.
Thanks a lot for your suggestions, Francois.
On 10/26/2012 11:56 PM, Elaine Meng wrote:
Hello, PDB format is for atoms/bonds, not graphical objects. Although you could have "fake" atoms and bonds, the display choices would still be just those available for atoms (dots and lines, sticks, ball & stick, spheres).
For graphical objects, Chimera understands a few different formats. You could use "Help... Search Documentation" in the Chimera menu, search for "graphical objects," then click link "Input File Types," and in that page see the bottom section: other 3D objects. Probably "Bild" or "VRML" would be the most relevant to you. "Bild" is the simpler format, easy to understand and write.
I'm amazed to see that Chimera is able to display VRML. Recently, I was looking for a free VRML viewer on Linux and did not find one. Maybe Amaya from w3c could display them, but I don't remember well and it was not very stable. I'll look into the Bild format too. Thanks a lot for these insights, Francois.
Another possibility is to use the Chimera "shape" command (see instructions using command: help shape). It makes surfaces in different shapes. However, to save those you would probably need to save a Chimera session file.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 25, 2012, at 9:46 PM, Francois Berenger wrote:
-------- Original Message -------- Subject: [ccp4bb] adding some user-defined graphical objects in a PDB file (and displaying them) Date: Fri, 26 Oct 2012 10:25:10 +0900 From: Francois Berenger <berenger@RIKEN.JP> Reply-To: Francois Berenger <berenger@RIKEN.JP> To: CCP4BB@JISCMAIL.AC.UK
Hello,
For some new project, I'd like to be able to generate things and store them in PDB format.
For example, a triangle, a line segment, a square, a cube, a sphere, an arrow, etc. Being able to change the color and "line width" would be nice.
Is there some official recommended way of doing this?
Is there some software able to read and display such graphical annotations of PDB files? I'll also need the format description in that case.
I want to be able to process a PDB file and store the result of my processing in the same PDB file as some kind of annotation.
My current way of doing this is to discretize my objects as H atoms in some other output PDB file, but that's just a temporary workaround.
My current search got me this: http://www.cgl.ucsf.edu/eccc1/ So, maybe there is some support for what I am looking for into Chimera.
Thanks a lot for your suggestions, Francois.
On 10/26/2012 11:56 PM, Elaine Meng wrote:
Hello, PDB format is for atoms/bonds, not graphical objects. Although you could have "fake" atoms and bonds, the display choices would still be just those available for atoms (dots and lines, sticks, ball & stick, spheres).
For graphical objects, Chimera understands a few different formats. You could use "Help... Search Documentation" in the Chimera menu, search for "graphical objects," then click link "Input File Types," and in that page see the bottom section: other 3D objects. Probably "Bild" or "VRML" would be the most relevant to you. "Bild" is the simpler format, easy to understand and write.
It's really wonderful this BILD file format support in Chimera. I definitively like its simplicity: it is trivial to generate correctly by programs and read/change by humans if necessary. Best regards, Francois.
Another possibility is to use the Chimera "shape" command (see instructions using command: help shape). It makes surfaces in different shapes. However, to save those you would probably need to save a Chimera session file.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 25, 2012, at 9:46 PM, Francois Berenger wrote:
-------- Original Message -------- Subject: [ccp4bb] adding some user-defined graphical objects in a PDB file (and displaying them) Date: Fri, 26 Oct 2012 10:25:10 +0900 From: Francois Berenger <berenger@RIKEN.JP> Reply-To: Francois Berenger <berenger@RIKEN.JP> To: CCP4BB@JISCMAIL.AC.UK
Hello,
For some new project, I'd like to be able to generate things and store them in PDB format.
For example, a triangle, a line segment, a square, a cube, a sphere, an arrow, etc. Being able to change the color and "line width" would be nice.
Is there some official recommended way of doing this?
Is there some software able to read and display such graphical annotations of PDB files? I'll also need the format description in that case.
I want to be able to process a PDB file and store the result of my processing in the same PDB file as some kind of annotation.
My current way of doing this is to discretize my objects as H atoms in some other output PDB file, but that's just a temporary workaround.
My current search got me this: http://www.cgl.ucsf.edu/eccc1/ So, maybe there is some support for what I am looking for into Chimera.
Thanks a lot for your suggestions, Francois.
Wow, this dredges up ancient memories. The annotated PDB format is known as the PDBRUN format. A draft version of the paper describing the format, that was in the Journal of Molecular Graphics, can be found at: <http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.61.4701>. As you have noticed, embedding graphics objects into PDB files is not common. There is only one program, that I am aware of, that is currently available and implements a subset of the PDBRUN format: the conic program that is distributed as part of UCSF Chimera. However, conic only supports the viewing annotations and not any of the graphical object annotations, so that's not going to help you. So, I'd recommend abandoning the idea of keeping everything in a PDB file. Instead, you could use a Chimera session file and Elaine's suggestion of use Chimera's shape command and/or VRML or bild files. Or you could export all of the graphical data to 3D editor/viewer like Blender or Maya, and manipulate the graphics objects there. HTH, Greg On Fri, 26 Oct 2012, Francois Berenger wrote:
-------- Original Message -------- Subject: [ccp4bb] adding some user-defined graphical objects in a PDB file (and displaying them) Date: Fri, 26 Oct 2012 10:25:10 +0900 From: Francois Berenger <berenger@RIKEN.JP> Reply-To: Francois Berenger <berenger@RIKEN.JP> To: CCP4BB@JISCMAIL.AC.UK
Hello,
For some new project, I'd like to be able to generate things and store them in PDB format.
For example, a triangle, a line segment, a square, a cube, a sphere, an arrow, etc. Being able to change the color and "line width" would be nice.
Is there some official recommended way of doing this?
Is there some software able to read and display such graphical annotations of PDB files? I'll also need the format description in that case.
I want to be able to process a PDB file and store the result of my processing in the same PDB file as some kind of annotation.
My current way of doing this is to discretize my objects as H atoms in some other output PDB file, but that's just a temporary workaround.
My current search got me this: http://www.cgl.ucsf.edu/eccc1/ So, maybe there is some support for what I am looking for into Chimera.
Thanks a lot for your suggestions, Francois.
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On 10/27/2012 08:58 AM, Greg Couch wrote:
Wow, this dredges up ancient memories. The annotated PDB format is known as the PDBRUN format. A draft version of the paper describing the format, that was in the Journal of Molecular Graphics, can be found at: <http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.61.4701>.
As you have noticed, embedding graphics objects into PDB files is not common. There is only one program, that I am aware of, that is currently available and implements a subset of the PDBRUN format: the conic program that is distributed as part of UCSF Chimera. However, conic only supports the viewing annotations and not any of the graphical object annotations, so that's not going to help you.
So, I'd recommend abandoning the idea of keeping everything in a PDB file. Instead, you could use a Chimera session file and Elaine's suggestion of use Chimera's shape command and/or VRML or bild files.
I think I'll go for the .bild files. The example in chimera-1.6.2/share/chimera/helpdir/UsersGuide/bild.html is interesting enough to me. It looks human-readable and easy to generate by programs. Thanks a lot, F.
Or you could export all of the graphical data to 3D editor/viewer like Blender or Maya, and manipulate the graphics objects there.
HTH,
Greg
On Fri, 26 Oct 2012, Francois Berenger wrote:
-------- Original Message -------- Subject: [ccp4bb] adding some user-defined graphical objects in a PDB file (and displaying them) Date: Fri, 26 Oct 2012 10:25:10 +0900 From: Francois Berenger <berenger@RIKEN.JP> Reply-To: Francois Berenger <berenger@RIKEN.JP> To: CCP4BB@JISCMAIL.AC.UK
Hello,
For some new project, I'd like to be able to generate things and store them in PDB format.
For example, a triangle, a line segment, a square, a cube, a sphere, an arrow, etc. Being able to change the color and "line width" would be nice.
Is there some official recommended way of doing this?
Is there some software able to read and display such graphical annotations of PDB files? I'll also need the format description in that case.
I want to be able to process a PDB file and store the result of my processing in the same PDB file as some kind of annotation.
My current way of doing this is to discretize my objects as H atoms in some other output PDB file, but that's just a temporary workaround.
My current search got me this: http://www.cgl.ucsf.edu/eccc1/ So, maybe there is some support for what I am looking for into Chimera.
Thanks a lot for your suggestions, Francois.
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Elaine Meng -
Francois Berenger -
Greg Couch