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PostPosted: Mon Oct 24, 2011 11:25 pm 
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Hi,

I've been having some difficulty correctly importing certain PDB files into C4D using ePMV in "Ball + Stick" representation mode.

Please take a look at the attached files:

iBabel (Correct).png: This is what the molecule should look like
C4D (Incorrect).png: This is what I get after importing

If you want to try to recreate the problem on your machine, I've attached TroublesomePDBs.zip

As I see it there are a few issues:
1. On all "Ball + Stick" imports the cylinder reference shape is visible at the center of the scene. I have to manually create a "hider" null in order to hide it while still keeping its instances visible (add a null with editor and render visibility turned off, drop the "Molecule_b_sticks" group into it and you're good to go).

2. Not all chemical bonds are visually represented - sometimes one stick is missing, sometimes both, sometimes the sticks have the wrong orientation.

3. Double bonds are not represented.

Any suggestions on how to avoid these representation issues?
Thanks,

Donovan


Attachments:
File comment: Screenshot of C4D after importing CholineChloride.pdb using ePMV
C4D (Incorrect).png
C4D (Incorrect).png [ 115.42 KiB | Viewed 5367 times ]
File comment: Screenshot of iBabel showing CholineChloride.
iBabel (Correct).png
iBabel (Correct).png [ 68.79 KiB | Viewed 5367 times ]
File comment: PDB Files that don't import correctly.
TroublesomePDBs.zip [1.94 KiB]
Downloaded 235 times
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PostPosted: Tue Oct 25, 2011 1:48 am 
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Hi Donovan,

thanks for the precious feedback. ePMv which is based on PMV intend to be used with proteins. So its possible that errors happens with small unusual chemical compound.
I will look at your file, did you try with another format like mol2 or MMCIF ?

I am sorry about the parent cylinder, this is mostly due to inter compatibility between all 3d software supported by ePMV.

I will let you know If I find some fix.

Did you really need other bond representation such as double bond...would you like it as an option?

Ludovic


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PostPosted: Tue Oct 25, 2011 2:29 am 
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Hi Donovan,
I found the problem. We build the bond by distance bt default, and this function dont gave proper result for you molecule.
In another hand all bonds are not define in the PDB file. Did you have suggestion on how I could modify the build by distance function to be correct with your molecule ?

Ludovic


Attachments:
Screen shot 2011-10-24 at 7.27.15 PM.png
Screen shot 2011-10-24 at 7.27.15 PM.png [ 63.02 KiB | Viewed 5358 times ]
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PostPosted: Tue Oct 25, 2011 3:47 am 
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Ok I got it,

I will provide you a fix tomorow or during the week.
you will be then able to customize the bondBuilding. The Problem was the threshold used for the distance. In your case the threshold was to high and thus created extra bonds...

Ludovic


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PostPosted: Tue Oct 25, 2011 5:21 pm 
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Hello Ludovic,

Thank you for the speedy response, I look forward to the update! The double-bond representation would be nice, but I don't think it's a necessity (bear in mind: I'm something of a novice in this field, so don't let my opinion sway development priorities).

Unfortunately, I can't be of help with how to approach the distance-based bond representation, I'm more of an artist than chemist at this point.
Thanks,

Donovan


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PostPosted: Tue Oct 25, 2011 10:39 pm 
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Hi donovan,

we have an update on our website, you can get it here : http://epmv.scripps.edu/download-install-free/perhost
after this one the update option should work.

After the installation, before loading your molecule, go to Edit->Options
change the fits value from 1.1 to 0.7 or less

For the bonds, you can easily change it manually, the transformation is carried by the instance object, so you can replace the target by a double cylinder...

Let me know if you encounter any problem.

The new version ask you to register..please do so.

Ludovic


Attachments:
Screen shot 2011-10-25 at 3.37.01 PM.png
Screen shot 2011-10-25 at 3.37.01 PM.png [ 193.51 KiB | Viewed 5334 times ]
Screen shot 2011-10-25 at 3.33.46 PM.png
Screen shot 2011-10-25 at 3.33.46 PM.png [ 52.42 KiB | Viewed 5334 times ]
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PostPosted: Wed Oct 26, 2011 12:51 am 
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Fantastic! The atoms are all now correctly bonded and there's no longer an extraneous stick. Thank you for addressing my concerns so quickly.
Sincerely,

Donovan Keith


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PostPosted: Wed Oct 26, 2011 2:29 am 
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Great,

feel free to post rendering in our dedicated post on the forum...
if you got some testimonial feel free too to send me them !


Ludovic


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