[Chimera-users] ribbon problem

Francesco Oteri francesco.oteri at gmail.com
Tue Sep 28 05:47:24 PDT 2010

I've downloaded the latest alpha version, and i saw that for 2kux pdb 
the problem was solves, unfortunately the same is not for my molecule.
I tryed with the amber files and I still see uncorrect viualization. 
Moreover, when I active the ribbon visualizaton, the stick bonds are 
displayed in a wrong  way: it semms that the ribbon change the 
connectivity of the first atom and last atom of the circular structure!!!!
I checked the connectivity with vmd, and it is ok.

I attached the amber files, as a tgz archive, so you can experiance by 
yourself the problem.

In each case, thanks for the speed of your answer.

PS: Is it possible to add the possibility to open topology directly from 
the menu File->Open?

On 28/09/2010 02:39, Conrad Huang wrote:
> I've added some ribbon code to handle circular structures.  Both the 
> original "cycle.pdb" file from bug report #2777 and pdb:2kux are now 
> displayed properly.  I tried your frames2.pdb, but that still showed 
> two ends.  I'm not sure if that is due to the incorrect connectivity 
> in the file.  Can you download the latest daily build and see if it 
> works any better with your trajectory input file?  Thanks.
> Conrad
> On 9/23/2010 12:30 PM, Francesco Oteri wrote:
>>    I've supposed the problem resides in the pdb, for this reason i 
>> tested
>> the amber topology as input.
>> Using amber, in fact, the correct bonds are displayed.
>> Nevertheless, the ribbon is still cutted. I saw that it is a bug and
>> that a new entry in the bugzilla has been opened.
>> Il 23/09/2010 20:31, Elaine Meng ha scritto:
>>> Hi Francesco,
>>> Wow, this is a very pretty structure!  However, the PDB looks 
>>> somewhat messed up.  Perhaps using the AMBER files solves most of 
>>> these problems.
>>> In PDB format, I believe the biopolymer (nucleic acid or protein) 
>>> residues are connected by their order in the file, unless a break is 
>>> enforced with TER.  However, the order in this PDB file seems to be 
>>> quite different than what it should be, for the correct 
>>> connectivity.  Residue 75 is very far from 76, 150 is very far from 
>>> 151, etc. every 75 positions.  I tried just putting TER after every 
>>> 75 residues, which does eliminate the very long bonds.  However, it 
>>> seems like there may be other bonds that are supposed to be there 
>>> that are not, and it would be necessary to do a lot of 
>>> reorganization and renumbering of residues in this file to get the 
>>> correct connectivity.  For example, it looks like maybe 76 is really 
>>> supposed to be connected to 150, 75 is really supposed to be 
>>> connected to 1, etc.
>>> If there were correct ordering in the PDB file (and maybe this is 
>>> already true for when you use the AMBER files as input), the Chimera 
>>> limitation would give you just one break in each circular strand.  
>>> If this DNA is all one big circular strand, there should be only one 
>>> break in the ribbon.
>>> Best,
>>> Elaine
>>> ----------
>>> Elaine C. Meng, Ph.D.
>>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>>> Department of Pharmaceutical Chemistry
>>> University of California, San Francisco
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