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Author Topic: x3dna-v2.3 no backbone ribbon  (Read 571 times)

Offline cllawson

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x3dna-v2.3 no backbone ribbon
« on: July 31, 2018, 12:28:39 pm »
Hi Xiang-Jun,

I have been trying to replicate the images that appear on NDB using your latest x3dna package (v2.3) on Mac OS. 

When i run blocview filename.pdb, I get the message:

cannot find 'render'
no image output; 'blocview.r3d' -- to be fed into render/pymol

Which is fine because I have MacPymol so I can view/snap images of the r3d file. 

However, the images I get do not include the backbone ribbon, even though it seems it should be the default to include it (blocview --help states that --no-ds turns it off), so this seems like a bug.

I've attached an example image.

Thanks in advance for your help!

Offline cllawson

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Re: x3dna-v2.3 no backbone ribbon
« Reply #1 on: July 31, 2018, 12:36:21 pm »
also, for structures with both protein and nucleic acid, no ribbon is appearing for the protein.

Offline xiangjun

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Re: x3dna-v2.3 no backbone ribbon
« Reply #2 on: July 31, 2018, 12:42:59 pm »
Are you sure you have MolScript installed and in your path? The 3DNA v2.x version of 'blocview' relies on MolScript for the backbone ribbon, be it for nucleic acids or proteins.

You may well consider switching to the DSSR --blocview option which relies ONLY on PyMOL.

Best regards,

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline cllawson

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Re: x3dna-v2.3 no backbone ribbon
« Reply #3 on: July 31, 2018, 02:51:08 pm »
Thanks for the quick reply.
I don't have MolScript installed so that would explain the issue. 
I did find a relatively easy "workaround" though with pymol-- If I load the file "pmiview1" and have pymol create a cartoon with it, it overlays nicely with the r3d file. 
Thanks also for the tip about  DSSR --blocview option, I'll try that as well.

Offline xiangjun

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Re: x3dna-v2.3 no backbone ribbon
« Reply #4 on: July 31, 2018, 03:02:10 pm »
Quote
I did find a relatively easy "workaround" though with pymol-- If I load the file "pmiview1" and have pymol create a cartoon with it, it overlays nicely with the r3d file.

That's true. That's also the tricks the DSSR --blocview option depends on. When 3DNA was initially released around the beginning of the century, MolScript/Raster3D (and RasMol) were very popular. Nowadays, these earlier software programs are virtually gone and PyMOL (among others) become the dominant players. DSSR takes advantages of what PyMOL has to offer and it greatly simplifies the user-interface to creation of the characteristic cartoon-block images.

Best regards,

Xiang-Jun


 
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.