[Chimera-users] ribbon problem
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.
> On 9/23/2010 12:30 PM, Francesco Oteri wrote:
>> I've supposed the problem resides in the pdb, for this reason i
>> 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.
>>> Elaine C. Meng, Ph.D.
>>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>>> Department of Pharmaceutical Chemistry
>>> University of California, San Francisco
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
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