[Chimera-users] ribbon problem

Francesco Oteri francesco.oteri at gmail.com
Wed Sep 29 14:16:13 PDT 2010

  OK, I will try and I will report on mailing-list the result!!!

Il 29/09/2010 21:04, Conrad Huang ha scritto:
> 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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