VMD-L Mailing List

From: Nuno Sousa Cerqueira (nscerque_at_fc.up.pt)
Date: Thu Dec 10 2009 - 07:13:07 CST

Begin forwarded message:

> From: Nuno Sousa Cerqueira <nscerque_at_fc.up.pt>
> Date: December 10, 2009 1:12:57 PM GMT+00:00
> To: MUHAMMAD IMTIA SHAFIQ <imtiazshafiq_at_gmail.com>
> Subject: Re: vmd-l: Calculation the Surface Area/Volume of a Protein
> Cavity
>
> Hello,
>
> We are actually finishing a plugin for VMD to do such type of
> calculations. When it is finished ( in the end of the year) I will
> contact you.
>
> But for sasa it is easy. You can use the command: measure sasa 1.4
> $sel
>
> Regards,
>
> Nuno S Cerqueira
>
>
> On Dec 10, 2009, at 11:24 AM, MUHAMMAD IMTIA SHAFIQ wrote:
>
>> Dear All,
>>
>> Have a nice day. Is there any way I can calculate the Surface Area/
>> Volume of a protein cavity in VMD.
>>
>> I have tried Caver in pyMol and it is a good tool for
>> visualisation, but I am unable to quantify the cavity volume or
>> surface area.
>>
>> Anybody have experience in this area please suggest me something
>>
>> Regards
>> Imtiaz
>>
>>
>>
>> On 10 Dec 2009, at 10:43, Carsten Olbrich wrote:
>>
>>> Dear Dawn,
>>> a colleague of mine has just sent me his latest version of a VMD
>>> script
>>> to visualize conformational changes similar to the Porcupine plots
>>> of
>>> Dynamite. As he has also mentioned to me, he would be happy to get
>>> any
>>> response, if you can think of any further improvements or have any
>>> questions.
>>> In general, this script should not require further changes in the
>>> code
>>> as long as there are no bugs. :)
>>> The output should be a collection of arrows pointing from one
>>> state of
>>> the selected atoms to the other, including the deviation color-
>>> coded and
>>> indicated by the length. Hence, you can simply load the PCA
>>> trajectory
>>> of the eigenvector and use the script to visualize the
>>> conformational
>>> changes.
>>>
>>> If you would be interested in really using this tool, he would be
>>> open
>>> to sent you any new version, if any changes are required or
>>> wanted...
>>>
>>> Best regards,
>>>
>>> Carsten
>>>
>>>
>>>
>>> On Mon, Dec 7, 2009 at 1:49 PM, Joshua Adelman <jla65_at_pitt.edu>
>>> wrote:
>>>> Hi Dawn,
>>>> You can convert a dcd file to a trr file using catdcd which you
>>>> can get off
>>>> of the VMD/NAMD website. Then using trajconv which is a tool
>>>> distributed
>>>> with Gromacs, you can convert from a .trr to a .xtc file. There
>>>> may be other
>>>> tools that can go directly from .dcd to .xtc, but this is
>>>> generally what I
>>>> do.
>>>> Josh
>>>>
>>>> On Dec 7, 2009, at 3:43 AM, Dawn wrote:
>>>>
>>>> Thank you for your response. I will try and hope it works.
>>>> I know Dynamite can do it, but needing xtc file instead of Charmm
>>>> dcd file.
>>>> I'll appreciate if you know the transition of dcd to xtc.
>>>> Thank you!
>>>>
>>>> On Sun, Dec 6, 2009 at 11:22 PM, Joshua Adelman <jla65_at_pitt.edu>
>>>> wrote:
>>>>>
>>>>> Hi Dawn,
>>>>>
>>>>> There is probably a fancy way to do it, but a quick and dirty
>>>>> method that
>>>>> I've used is the following. If you have a series of
>>>>> conformations along the
>>>>> mode, you can have VMD display all frames simultaneously in the
>>>>> 'Trajectory'
>>>>> tab of the Representations GUI. I select the CA atoms and draw
>>>>> them in the
>>>>> VdW representation. Play around with the size of the spheres so
>>>>> that they
>>>>> overlap such that they look like a line or bar along the mode.
>>>>> You can color
>>>>> them by the frame index for clarity. Create another selection
>>>>> where you show
>>>>> the reference structure in whatever representation that you want.
>>>>>
>>>>> Josh
>>>>>
>>>>>
>>>>> On Dec 6, 2009, at 2:29 PM, Dawn wrote:
>>>>>
>>>>>> Hi,
>>>>>> I want to have porcupine plots for the first principal component
>>>>>> PC1(derived from PCA). Would you please tell me if VMD have
>>>>>> such function
>>>>>> and how to do it?
>>>>>>
>>>>>> Thanks a lot!
>>>>>> Dawn
>>>>>
>>>>>
>>>>
>>> <PorcupinePlot.tcl>
>>
>> IMTIAZ SHAFIQ
>> imtiazshafiq_at_gmail.com
>>
>>
>>
>>
>