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View Full Version : Does the PDB importer actually work?



Turner
09-12-2004, 06:54 AM
I can't seem to find a file that it will import.

thx
Andrew

Lynx3d
09-12-2004, 11:02 AM
Hm i just tried one from http://www.rcsb.org/pdb/index.html
some 130 info-messages later i got a bunch grey spheres that maybe could be the ricin i searched for.
Perhaps it doesn't like poison... :D
LW 8.01 on Windows that is.

Turner
09-12-2004, 01:15 PM
Bummer.

I hope this thing works... doesn't seem to, yet.

Andrew


Hm i just tried one from http://www.rcsb.org/pdb/index.html
some 130 info-messages later i got a bunch grey spheres that maybe could be the ricin i searched for.
Perhaps it doesn't like poison... :D
LW 8.01 on Windows that is.

yazan
09-15-2004, 09:46 AM
I did this a while back.

Turner
09-15-2004, 12:32 PM
Nice!

Mind telling us how you got the thing in there? I've tried a bunch of sources but none seem to work..

Thanks,
Andrew

ingersol
09-15-2004, 03:00 PM
I've found that you have to convert the line breaks -- most PDB files are unix text files, which use "newline" for the line break character. Mac uses "carriage return" for line breaks, dos uses both. To get PDB files to import, I open them in BBEdit, then resave with DOS linebreaks. Then PDBreader will recognize them and do it's thing. (Any other linebreak-aware text editor should work.)

Now, I haven't ever gotten anything like that secondary-structure image to show up. Just the points.

Oh -- I find that the PDBreader 2.85 plugin has a lot more options than the 3.0 version bundled with LW8. You can still download 2.85, check Flay.

But really, yazan -- how'd you do that??!?

Evan

yazan
09-18-2004, 03:32 AM
this was a long while ago and I was on PC then. I'll have to dive back and try to get the files for you guys and find exactly what I did. Back then I was in Science animation, talking about 3 years ago. I'll try my best. hope you can wait a bit till I unfold the process again. But to get you started, I remember using a middle software to get the ribbony structure, and it may have been either weblab viewer (http://old.medric.or.kr/educateNews/popup/chapter10/weblabviewer/) or ViewerLab (http://www.accelrys.com/download/), put in the PDB and then export to something usable in Lightwave. I appologize, looking back at my thread I might have mislead you that its possible to do it straight in Lightwave, but I was just thinking of the whole process. Hope this helps, Ill try to go back and get my old files if you guys are still interested.
Yazan

Turner
09-18-2004, 04:57 AM
Thanks Yazan.

Still, it -would- be pretty nice if LW's built-in whatever did what it was supposed to do.

Andrew

Turner
09-22-2004, 05:26 AM
This thing is not working...

I can't seem to import a single PDB from any source I've found.

Please help.

Andrew

ingersol
09-22-2004, 08:14 AM
Hey, Turner -- are you getting any informative error messages, or is it just failing silently? If you're getting the "no ATOM or HETATOM data found" message, that's likely the line-break problem I mentioned above.

Also, I still recommend getting the 2.85 plugin -- you can have them both installed, and the older plug has many more options and much better documentation. See the Lscript section at Chromecow (http://www.chromecow.com/downloads.htm) for the download.

Evan

Turner
09-22-2004, 05:03 PM
Cool!

Actually, yes, that's the error. I'll try your method.

thx
Andrew