VMD-L Mailing List

From: Anurag Sethi (anurag.sethi_at_gmail.com)
Date: Wed Apr 16 2014 - 10:41:02 CDT

Donald,

This is a bug with Qres portion of multiseq - for some reason it is not
recognizing the number of C-alpha atoms in the pdb file correctly. I think
someone from the VMD/Multiseq development group has to correct this bug.

Anurag

Genius is nothing more or less than doing well what anybody can do badly. -
Amelia Barr

On Tue, Apr 8, 2014 at 2:59 PM, Donald Karr <donaldjkarr_at_gmail.com> wrote:

> Sure, it is chain d of 3d9s with base 51 changed from L to R. Thanks for
> the help!
>
>
> MUTATED.pdb<https://docs.google.com/file/d/0B1B1erl0pSFUTmRySUJhTTRQa2c/edit?usp=drive_web>
>
>
>
> On Mon, Apr 7, 2014 at 7:37 PM, Anurag Sethi <anurag.sethi_at_gmail.com>wrote:
>
>> Hi Donald,
>>
>> I suspect that either STAMP or VMD is not recognizing your modified
>> residue and the count of residues between multis and STAMP are getting
>> messed up. Could you send the modified structure?
>>
>> -Anurag
>>
>> Genius is nothing more or less than doing well what anybody can do badly.
>> - Amelia Barr
>>
>>
>>
>> On Thu, Apr 3, 2014 at 11:33 AM, Donald Karr <donaldjkarr_at_gmail.com>wrote:
>>
>>> Dear Users,
>>>
>>> I am trying to compare the structures of several aquaporins (1fqy, 1j4n,
>>> 1lda for reference) to a modified structure from the D chain of the 3d9s
>>> structure. The structures will align using Stamp but when I try to use Qres
>>> an error message appears.
>>>
>>> "An unknown error occurred while processing (residueIndex != num
>>> residueScores)"
>>>
>>> And then a bunch of stuff I do not understand. There is no QH score when
>>> highlighting the modified structure and another structure.
>>>
>>> The three aquaporins will align properly like they should but none of
>>> them will align with 3d9s proper resulting in the error message "Structures
>>> not aligned. Writing structure files could not be performed."
>>>
>>> I'm not sure where to go from here and am not sure if it is a problem
>>> with the structures or the system.
>>>
>>> Thanks for the help.
>>>
>>
>>
>