I was wondering if there is a way for Houdini 9 to read .PDB (Protein Database) data. I know lightwave has a plugin available called PDB Reader and it was used heavily by XVIVO lead animator John Liebler in the creation of The Inner Life of a Cell. If you haven't seen it it is worth the time. Here is the link: www.youtube.com/watch?v=kxSLw1LMvgk

Here is a sample of the data contained in the Chlorotriflouride(LP).pdb file

COMPND Chlorotriflouride(LP).pdb
HETATM 1 Cl -0.3136 0.3145 0.0966
HETATM 2 F -1.9557 0.0544 0.0378
HETATM 3 F -0.1257 -1.3145 -0.1830
HETATM 4 F 1.3369 0.4039 0.2987
HETATM 5 Lp -0.3836 0.4942 1.2249
HETATM 6 Lp -0.2574 0.8438 -0.8225
CONECT 1 2 3 4 5
CONECT 1 6
CONECT 2 1
CONECT 3 1
CONECT 4 1
CONECT 5 1
CONECT 6 1
END

The HETATM lines suggest XYZ transform values for the individual molecules and if that were true then, hey, that's just peachy! Now how would I get Houdini to read this data and build me a set of points representing the Chlorotriflouride molecule?

Any help in this regard would be appreciated. Thank you

Barad

From what I understand you'll need to build a custom plugin to read special file formats inside Houdini. I've played with it a bit. It's not too bad.

There's also hscript which can be run independently of Houdini and can generate geometry files that can later be loaded into Houdini.
This is pretty handy for building procedural geometry simply.
Check out the hscript tutorials and docs. Perhaps it could help.

looks like a pretty basic format you could probably easy write something in python to turn it into a geo file (that's a ascii version of Houdini's bgeo format)

Thanks guys. I am looking into your respective suggestions now. It's just that I am not much of a programmer right now. Guess I get to have a crash course. Thanks again.

David

I am currently working with PDB files and was thinking about the same thing about a week ago.

I finaly decided that i didnt have enough time to start experimenting with Hscript and to cheat and work with pointclouds exported from LW…
(there is an older but really good PDB reader or LW @ chromecow.com)

there are a few Maya PDB readers tho @highend3d.com
so if you know anyone that can handle MEL and use the same technique
i dont think it would be too difficult…
U can also use Chimera and export RIBs
(Even blender has a PDB importer i u want)
(not to mention POVray)

cheers
J.

In H9, one could use a Python-based SOP.

and PDB has it's XML incarnation…. that would help also. What about using Blander as a conversion tool?

Barad_Dur
I was wondering if there is a way for Houdini 9 to read .PDB (Protein Database) data. I know lightwave has a plugin available called PDB Reader and it was used heavily by XVIVO lead animator John Liebler in the creation of The Inner Life of a Cell. If you haven't seen it it is worth the time. Here is the link: www.youtube.com/watch?v=kxSLw1LMvgk

Here is a sample of the data contained in the Chlorotriflouride(LP).pdb file

COMPND Chlorotriflouride(LP).pdb
HETATM 1 Cl -0.3136 0.3145 0.0966
HETATM 2 F -1.9557 0.0544 0.0378
HETATM 3 F -0.1257 -1.3145 -0.1830
HETATM 4 F 1.3369 0.4039 0.2987
HETATM 5 Lp -0.3836 0.4942 1.2249
HETATM 6 Lp -0.2574 0.8438 -0.8225
CONECT 1 2 3 4 5
CONECT 1 6
CONECT 2 1
CONECT 3 1
CONECT 4 1
CONECT 5 1
CONECT 6 1
END

The HETATM lines suggest XYZ transform values for the individual molecules and if that were true then, hey, that's just peachy! Now how would I get Houdini to read this data and build me a set of points representing the Chlorotriflouride molecule?

Any help in this regard would be appreciated. Thank you

Barad

It would be pretty trivial to write a Perl filter to turn this into a .geo format file; then you modify the GEOio file to have the Perl translator convert this on the fly to .geo format, and presto, Houdini will be able to natively understand this format.

What's not clear to me is what to do with each of the Chlorine, Fluorine, or Lp elements (is Lp lone-pair?) You could set a string attribute, or a point group with the appropriate name. But at some point, all the constituent elements need to be dereferenced, e.g. with a copy/stamp operation, else you'll just have a bunch of points with some connecting edges.

Is the spec for the format available somewhere?

– Antoine

Antoine,

I looked for specs over at http://www.wwpdb.org/docs.html [wwpdb.org] and i think I found a piece of the puzzle but it was like accidently bashing a huge wasp nest. I do think that this is where descriptions and acceptable formats for PDB files will be found - or at least a start. Thanks for getting me to look in the right direction.

David

http://www.rcsb.org/ [rcsb.org]

u ll find tons of info here..

J.

http://www.wwpdb.org/docs.html [wwpdb.org]
(file format info among others)

http://cvcweb.ices.utexas.edu/software/ [cvcweb.ices.utexas.edu]
(these guys @CVC work alot with Pdb format ..)

http://www.chromecow.com/index.php?s=PDB&submit=Go [chromecow.com]
(for LW)

http://www.highend3d.com/maya/downloads/mel_scripts/modeling/misc/pdbReader-1641.html [highend3d.com]
(For Maya)

http://www.highend3d.com/3dsmax/downloads/scripts/utility_external/import/Molecule-Importer-4407.html [highend3d.com]
(for 3DSMax)

or here :

http://www.mtco.com/~cwtooley/Molecule/ [mtco.com]
(ouch ..my eyes)

http://www.malte-reimold.de/blender/pdb2blend.html [malte-reimold.de]
(for blender
)

Hey people

I know you guys posted this a while ago but you may still be interested in the subject . sidefx have a standalone executable now that converts some PDB files into native BGEO format .
Cheers

John

Hello John I just found this post because I need to import a pdb file, can you tell me where it is possible to find the executable you were talking about ?
Thank you

madrenderman
I just found this post because I need to import a pdb file

Houdini supports .pdb files since H14.5.120, so just use File SOP

Thank you, just found it

Hey signore madrenderman

you might find this thread interesting

https://www.sidefx.com/forum/topic/34137/ [www.sidefx.com]

It might be a bit old now though and I went about connecting them in a very convoluted way. learned a lot though.

When I revisited this a few years later I found that using the ‘connectadjacentpieces’ sop and connecting by points was the quickest way to bond them. Just scale up and down the search radi until they connect correctly .

your probably beyond this but for the sake of the thread - modelling the sop way would be to use ‘group’ and ‘colour’ sops to colour them.
And ‘create attribute’ sops to set Pscale.
Or use ‘VOP’ or ‘wrangle’ nodes to set these attributes.

Then feed them all of those coloured and scaled points into a ‘copy to points’ sop, with a ‘metaball’ or ‘sphere’ plugged in the other side.

I got a bit stuck with mantra and rendering transparency and colour with objects inside objects, which you are likely to do for rendering molecular models. You can set the surface priority - look up absorption and nested dielectrics for this.
After revisiting this I think the problems I was having with nested dialetrics might have been caused by my scene scale.
Please let me know if you get some nice renders working with this look.

Also data wise - look out for miscellaneous water atoms H and O, and sometimes the data provides alternative configurations.
you might have to group and delete a few things to clean up before modeling the points.

Cheers

John

John, thank you for these informations, very useful, in this moment I was trying to understand how to connect all those points using add testing all the attributes available after importing. I'm going to read the post you are telling me, it's exactly what I was looking for.

P.S. It was funny because I started to research online how to open these pdb files, I tried to see if Rhino, polytrans or Maya could open them, I tested a Maya mel script … crash, I was looking for an xml importer … then I thought … let me try … Houdini/import … all the points imported with complete list of attributes, noooo

Thank you

Ray

It would be nice to understand how to create this visualization of the pdb points

https://www.rcsb.org/3d-view/3J83?fbclid=IwAR0gZjqdEnIu-EJu9fUEaQGZFJlHR2qdfKvYOkCDdJWl3rdQn5y22JQK4RQ [www.rcsb.org]