Thanks monica for the reply. I know modvectors in pymol can be used but the
problem is how to integrate the PCA analysis result into the mod vectors code.
Can i generate PDB files which show motion only along the first eigen vector ??
Soma
>
>
> HI
>
> Porcupine plots can be generated by pymol also.
>
> On 2013-09-20 11:28, Soma Ghosh wrote:
>
>> Dear AMBER Users,
>>
>> I am trying to study domain motions in my protein using PCA analysis of the
>> ptraj module. I have successfully performed PCA and have got the projection
>> files.
>>
>> The next problem is to visualize the motions and generate porcupine plots. For
>> this, I installed ied-2.02 as a plugin in VMD 1.8.6. The plugin seems to work
>> fine with gromacs examples but fails to work with AMBER format files. I
>> checked
>> online and it says that ied can only use formats generated using ptraj8. Is
>> this
>> true?? Also i am not able to draw the arrows using this plugin , which seems
>> to
>> be a bug with vmd 1.8.6.
>>
>> I can use PCASuite, however my CRD files are in the .gz format and PCASuite is
>> not able to read the gunzipped files. Also, I have a set of 20 CRD files and I
>> want PCASuite to read all the CRD files one after another, how can this be
>> done???? Is there a way of scripting PCASuite, wherein one can use trajin
>> command and PCAsuite in combination ??
>>
>> Finally, can some one take me through the process of generating poocupine
>> plots
>> from the PCA analysis done using ptraj of AMBER 9. Also, is there a way of
>> quantifying domain motions. Is it ok if i calculate the angles between two set
>> of residues from the centre of the domains ???
>>
>> Thanks,
>> Soma
>
>
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Received on Fri Sep 20 2013 - 00:00:02 PDT
