From: CPMAS Chen (cpmasmit_at_gmail.com)
Date: Mon Jan 22 2018 - 15:58:44 CST

I did.

I tried it on VMD-1.9.2, the same result. My colleague had VMD-1.9.3, the
same result. Do not have a clue why.

Thanks!

On Sun, Jan 21, 2018 at 10:43 PM, Murpholino Peligro <murpholinox_at_gmail.com>
wrote:

> Have you tried with a stable version of VMD?
>
> 2018-01-21 9:04 GMT-06:00 CPMAS Chen <cpmasmit_at_gmail.com>:
>
>> Hi, Phenix users,
>>
>> This may be a little off-topic. I have posted this in VMD users mail
>> list. I want to try here too to see if anyone experienced similar issue.
>>
>> VMD and pymol gave different presentation on the secondary structure of a
>> protein.
>>
>> During phenix.refinement, I added secondary structure restraints and
>> correctly labelled all helices and sheets. However, VMD does not correctly
>> present the secondary structure in cartoon/new-cartoon presentation.
>>
>> A little more detail.
>>
>> In VMD-1.9.4a12, after I loaded the pdb, I chose new cartoon to present
>> the secondary structure. All chains are presented as random coil, the same
>> as tube representation. However, pymol correctly shows the secondary
>> structure of the same pdb file in cartoon representation.
>>
>> Has anyone encountered similar situation? what would be the fix?
>>
>>
>> Thanks!
>>
>>
>> Best Regards,
>>
>> Charles
>>
>> --
>>
>> ***************************************************
>>
>> Charles Chen
>>
>> Research Instructor
>>
>> University of Pittsburgh School of Medicine
>>
>> Department of Anesthesiology
>>
>> ******************************************************
>>
>>
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>>
>
>

-- 
***************************************************
Charles Chen
Research Instructor
University of Pittsburgh School of Medicine
Department of Anesthesiology
******************************************************