VMD-L Mailing List
From: Mario Valle (mvalle_at_cscs.ch)
Date: Wed Oct 04 2006 - 00:31:50 CDT
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Perfect!
Exactly the problem Prof. Eric Martz told me. So the problem is in the
terminal residues. I'll try to understand why they are unusual.
Thanks!
mario
John Stone wrote:
> Mario,
> I'll have to look at this more closely, but to make a long story shorter,
> VMD 1.8.5 is a bit pickier with nucleic acid structures than VMD 1.8.4 was,
> as a result of changes I made that allow it to do a better job drawing
> nucleic acid structures. A side effect of these changes is that structures
> with unusual terminal residues that were accepted by the older versions of
> VMD will not be marked as nucleic acid fragments, and will thus be skipped
> when secondary structure representations such as tube/ribbon/cartoon etc are
> drawn. This is essentially the same issue that occurs with some of the new
> RNA structures, and I'm working on making VMD 1.8.6 more flexible so it will
> do the right thing even when it encounters unusual residues.
>
> John
>
> On Mon, Oct 02, 2006 at 09:59:08AM +0200, Mario Valle wrote:
>
>> I'm trying to determine if the following error is due to VMD or is the data erroneous.
>> To reproduce:
>> 1) download PDB 1D66
>> 2) load it in VMD (tried in 1.8.5 on Linux)
>> 3) select: "chain D E"
>> 4) select representation "New Tube". Nothing will be draw and the following error appears
>> on the console:
>>
>> ERROR) Internal error in draw_tube for P atoms: last_resid = 1 but no first atom was added.
>> ERROR) Tubes may be incomplete.
>>
>> Instead the tube appears correctly on Windows under 1.8.4
>> I suspect the data contains some error that makes VMD misbehave. Prof. Eric Martz told me
>> this file is a good example of erroneous data in a public repository, but my chemistry is
>> not at the level to understand and find the error...
>>
>> Thanks for your help!
>> mario
>>
>> --
>> Ing. Mario Valle
>> Visualization Group | http://www.cscs.ch/~mvalle
>> Swiss National Supercomputing Centre (CSCS) | Tel: +41 (91) 610.82.60
>> v. Cantonale Galleria 2, 6928 Manno, Switzerland | Fax: +41 (91) 610.82.82
>>
>
>
-- Ing. Mario Valle Visualization Group | http://www.cscs.ch/~mvalle Swiss National Supercomputing Centre (CSCS) | Tel: +41 (91) 610.82.60 v. Cantonale Galleria 2, 6928 Manno, Switzerland | Fax: +41 (91) 610.82.82
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