VMD-L Mailing List

From: Jan Brezovsky (briza_at_chemi.muni.cz)
Date: Wed Nov 21 2012 - 08:54:18 CST

Hi Balaji,

there should be visualization scripts for Pymol and VMD in results
(out/pymol & out/vmd). However, it would depend on settings of your
calculation. Should all be well described in user guide (e.g. Quick
start section).
If you would have other questions, you should write to
caver_at_chemi.muni.cz <mailto:caver_at_chemi.muni.cz>

HTH,
Jan

On 11/21/2012 03:19 PM, Ban Arn wrote:
> Hi Jan
>
> Thanks for suggestion and its easy to run.
>
> I ran the program with 10 pdb structures and as a output I got 41
> possible tunnels.
>
> Its bit hard to guess the possible tunnels for the respective structures.
>
> I have tunnels_xx.pdb.obj 10 files in the tunnel folder
> (results->data->tunnel)
>
> I would like to know whether these files have respective tunnel for
> each structure and how to visualize these files.
>
> Kindly advice.
>
> Many Thanks
> Balaji
>
>
>
>
> On Wed, Nov 21, 2012 at 11:52 AM, Jan Brezovsky <briza_at_chemi.muni.cz
> <mailto:briza_at_chemi.muni.cz>> wrote:
>
> Hello all,
>
> just to add one more alternative program (Caver 3.0) which was
> designed for analysis of MD trajectories.
> http://caver.cz/
>
> Have a nice day,
> Jan
>
> --
> ***************************************
> Jan Brezovsky, Ph.D.
> Loschmidt Laboratories
> Department of Experimental Biology
> Faculty of Science, Masaryk University
> Kamenice 5/A13-2.19
> 625 00 Brno
> Czech Republic
> ***************************************
> tel.+420-54949-2616 <tel:%2B420-54949-2616>
> briza_at_chemi.muni.cz <mailto:briza_at_chemi.muni.cz>
> http://loschmidt.chemi.muni.cz/peg
> ***************************************
>
>
> On 11/21/2012 11:19 AM, Ban Arn wrote:
>> Hi all
>>
>> Thanks for the reply.
>>
>> John, I contacted Oliver through the above mail id, but didnt get
>> any reply from him.
>>
>> And Brain thanks for the alternative program, however the program
>> works for single pdb structure.
>>
>> I'm want to calculate the same for simulation trajectories.
>>
>> Kindly advice.
>>
>> Many Thanks
>> Balaji
>>
>>
>> On Tue, Nov 20, 2012 at 6:14 PM, Bennion, Brian
>> <Bennion1_at_llnl.gov <mailto:Bennion1_at_llnl.gov>> wrote:
>>
>> this program might work for your needs
>> http://mole.upol.cz/
>>
>>
>> ________________________________________
>> From: owner-vmd-l_at_ks.uiuc.edu
>> <mailto:owner-vmd-l_at_ks.uiuc.edu> [owner-vmd-l_at_ks.uiuc.edu
>> <mailto:owner-vmd-l_at_ks.uiuc.edu>] on behalf of John Stone
>> [johns_at_ks.uiuc.edu <mailto:johns_at_ks.uiuc.edu>]
>> Sent: Tuesday, November 20, 2012 8:54 AM
>> To: Ban Arn
>> Cc: vmd-l_at_ks.uiuc.edu <mailto:vmd-l_at_ks.uiuc.edu>
>> Subject: Re: vmd-l: Hole program for vmd hole tcl script
>>
>> Hi,
>> I recommend contacting Olver Smart, the author of HOLE
>> and ask him where to download it. The link on his page doesn't
>> work currently:
>> http://www.globalphasing.com/people/osmart/
>>
>> Cheers,
>> John Stone
>> vmd_at_ks.uiuc.edu <mailto:vmd_at_ks.uiuc.edu>
>>
>> On Tue, Nov 20, 2012 at 02:59:20PM +0000, Ban Arn wrote:
>> > Dear VMD users
>> > I am looking for download link for HOLE program.
>> > I came across the following thread in vmd
>> >
>> (http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/3461.html)
>> > Can anyone help me in this regard.
>> > Sorry for posting other threads that are not related to vmd.
>> > Many Thanks
>> > Balaji
>>
>> --
>> NIH Resource for Macromolecular Modeling and Bioinformatics
>> Beckman Institute for Advanced Science and Technology
>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>> http://www.ks.uiuc.edu/~johns/
>> <http://www.ks.uiuc.edu/%7Ejohns/> Phone:
>> 217-244-3349 <tel:217-244-3349>
>> http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078
>> <tel:217-244-6078>
>>
>>
>
> 

-- 
***************************************
  Jan Brezovsky, Ph.D.
  Loschmidt Laboratories
  Department of Experimental Biology
  Faculty of Science, Masaryk University
  Kamenice 5/A13-2.19
  625 00 Brno
  Czech Republic
***************************************
  tel. +420-54949-2616
  briza_at_chemi.muni.cz
  http://loschmidt.chemi.muni.cz/peg
***************************************