[Chimera-users] ribbon problem

[Francesco Oteri]

I've tested the last daily build and it works fine for both AMBER files 
and pdb.
In the latter case i've corrected the pdb and chimera read it with the 
correct connectivity.


On 29/09/2010 21:04, Conrad Huang wrote:
> Yup.  My updated code was only updating the last residue ribbon 
> information properly.  I've committed some more changes, and your 
> trajectory file displays properly now with the new code.  These 
> changes should be incorporated in tomorrow's daily build, so can you 
> please give it another try tomorrow?  Thanks.
>
> Conrad
>
> On 9/28/2010 2:29 PM, Eric Pettersen wrote:
>> Hi Francesco,
>> It seems that the new ribbon code for handling circular structures
>> doesn't properly handle models containing multiple circular structures,
>> like yours does. We'll keep working on it and keep you in the "loop" so
>> to speak.
>>
>> --Eric
>>
>> On Sep 28, 2010, at 5:47 AM, Francesco Oteri wrote:
>>
>>> 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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