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PostPosted: Wed Nov 07, 2012 4:35 pm 
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I'm using ePMV in Cinema4D and have been working ePMV for a few weeks (I'm an animator, not a scientist). I've had great results displaying several complex molecules that my pharmaceutical client has provided, especially with proteins in Ribbon format. I have one molecule that includes a protein which will not display in Ribbon format, though it will display in sphere (atoms), ball & stick, and MSMSurface modes without a problem.

I've gone through all the tutorials I could find, and have a basic understanding of how to select the various molecular components. I can select the portion of the molecule I want to effect (the protein component), but still cannot get it to display as a Ribbon, though my client assures me it is a protein and should display in Ribbon form (and has shown me other renderings, I'm not sure where from, where it appears as a Ribbon).

Is it possible that there are settings that I could adjust that would cause the Ribbon to appear or not appear? I realize this is a vague description, but as the molecule is proprietary, I unfortunately can't include renderings or the pdb file itself.

I appreciate any help or suggestions that anyone can offer.

Thanks.


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PostPosted: Thu Nov 08, 2012 5:48 am 
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Hi,

thanks you for your interest.
without the actual pdb file it is difficult to tell. Is there any secondary structure information inside the PDB file ?
if it is not the case, there is some chance that your pdb file is not "regular" and so it make difficult the assignation/prediction of the secondary structure.
you may need to go through some other software to clean / check the file.
try to open it in pymol, vmd, chimera and then resave it from there. It may help.

another option is to :
compute the secondary structure using stride : http://webclu.bio.wzw.tum.de/cgi-bin/st ... ridecgi.py
then use the stride to pdb server : http://www.canoz.com/sdh/STRIDEtoPDBsecondarystruct.pl
this should gave you a pdb with SS information so you can try again to load it....

I can't tell you much more without the file.

Ludovic


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PostPosted: Thu Nov 08, 2012 4:02 pm 
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Ludovic,

Thanks for the very helpful tips. It turns out that I was able to contact someone in my client's organization who created the pdb file, and he was able to send me a new file with just the protein, which came in and rendered in Ribbon format successfully. So my solution was to combine that in Cinema4D with the non-protein components that were coming in correctly with the original file.

So in the end, my problem was solved, but your tips are going to be very useful to me going forward if I received another pdb file that doesn't respond in ePMV as expected.

Thanks!!

Todd


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PostPosted: Thu Nov 08, 2012 4:29 pm 
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Glad you found a solution

Ludovic


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