VMD-L Mailing List

From: Eric H. Lee (ericlee_at_ks.uiuc.edu)
Date: Tue Dec 15 2009 - 20:54:17 CST

Labels on the VMD screen do not always show up where you want at the size and position you would ideally want to place them (without manually writing a script to place them anyways). If you are preparing a figure for publication, why not render just the protein, then do some postprocessing afterwards with a program like Illustrator - add labels, distances, lines, etc...

Eric

On Dec 15, 2009, at 8:39 PM, YangMingjun wrote:

> Hi Eric,
> Thanks for your response. I checked vecdist, but it doesn't seem to be able to label the distance in the structure model. Is it? I am going to prepare a figure for our manualscript. So the distance should be labeled onto the figures, not only calculate the distance between two atoms. Then how should I do it?
>
> Many thanks.
>
>
> Mingjun
> 2009-12-16
> --------
> Dalian Institute of Chemical Physics (DICP),
> Chinese Academy of Sciences (CAS).
> Zhongshan Road457, Dalian City, 116023, China.
>
>
> ------------ At 2009-12-16 10:30:52 you wrote: -------------
> From: Eric H. Lee
> Sent: 2009-12-16 10:30:52
> To: YangMingjun
> CC: vmd-l
> Subject: Re: vmd-l: how to label the distances using tk console mode
>
> You can make the regular atom selection (atomselect), calculate their geometric center of mass (google or search VMD-L for script examples), and then use a vector math tool (such as vecdist) to calculate the actual distance between those two points.
>
> Eric H. Lee
> Medical Scholars Program
> Theoretical and Computational Biophysics Group, UIUC
> ericlee_at_ks.uiuc.edu
>
> On Dec 15, 2009, at 7:24 PM, YangMingjun wrote:
>
>> Dear all,
>>
>> I am going to label distances between each of two sets of atoms. Any one who can tell me how to do it under the tk console mode?
>>
>> Many thanks.
>>
>> Best Regards.
>> Mingjun
>>
>>
>>
>> -----------------------------------------------
>> Dalian Institute of Chemical Physics(DICP),
>> the Chinese Academy of Sciences(CAS),
>>
>> Zhongshan Road457, Dalian City,
>> Liaoning Province 116023,P. R. China
>>
>>
>> E-mail:
>> mjyang_at_dicp.ac.cn
>> Office Phone:
>> +86+411+84379352
>>
>
>
>
> ------------------------------------------------------
>