VMD-L Mailing List

From: Amit Jaiswal (amitjai20_at_gmail.com)
Date: Sun Mar 24 2013 - 02:26:04 CDT

Dear VMD Users,
                       I am new to VMD and currently trying to find
out the hydrogen bonds formed between two protein. The
protein complex is given by HADDOCK server. So please
let me know how to visualize the hydrogen bonds?

On Fri, Mar 22, 2013 at 3:16 AM, vmd-l digest
<owner-vmd-l-digest_at_ks.uiuc.edu> wrote:
>
> vmd-l digest Thursday, March 21 2013 Volume 01 : Number 2344
>
>
>
> In this issue:
>
> Re: vmd-l: phantom omni linux install: Phantom OMNI HOWTO
> Re: vmd-l: Slow display with nVidia GeForce 9400GT and 3xx drivers on Linux
> Re: vmd-l: phantom omni linux install
> Re: vmd-l: phantom omni linux install: Phantom OMNI HOWTO
> Re: vmd-l: VMD 1.9.1 for 64-bit Windows
> vmd-l: protein secondary structure
>
> ----------------------------------------------------------------------
>
> Date: Wed, 20 Mar 2013 12:52:17 -0500
> From: "Thomas C. Bishop" <bishop_at_latech.edu>
> Subject: Re: vmd-l: phantom omni linux install: Phantom OMNI HOWTO
>
> Here's info on how to get the PHANTOM omni devidce setup under linux.
> Thought I'd post it while I have it
>
> Haven't gotten to point of it w/ VMD yet but the PHantom Demos work.
>
> The Sensable manual I downnloaded is a bit out of date
> as the linux kernel does not have raw1394 modules.
> OpenHapticsAE_Linux_v3_0
> OpenHaptics_3.1_Academic_Edition
>
> The trick is to spoof raw1394 module s.t. the sensable drivers think
> they are loaded. Here's a work around from
>
> http://ubuntuforums.org/archive/index.php/t-1750274.html
>
> If there are better solutions I'd love to know.
> Thanks
> TOm
>
> ****************************************
> quoting... http://ubuntuforums.org/archive/index.php/t-1750274.html
>
> It is a rather ugly fix, but as I cannot modify "Open"Haptics it will
> have to do in my case. I've looked quite a lot around the web as well,
> and I can't find any other solution.
>
> After installing "Open"Haptics and the device drivers which SensAble
> provides (using dpkg) you will have to work your way around the
> dependency of raw1394. I am not really sure which steps ultimately made
> it work for me, but the following steps are necessary.
>
> 1. Spoof the /dev/raw1394 device
> 2. Create a dummy kernel node
>
> 1. To spoof the /dev/raw1394 device, simply use ln and hard link the
> /dev/fw0 (or some other fwX) by typing the following commands:
>
> sudo ln /dev/fw0 /dev/raw1394
> sudo chmod 0777 /dev/raw1394
>
> 2. As I believe "Open"Haptics checks if the raw1394 module is present
> during launch (using lsmod or similar), I created a kernel module that
> doesn't do anything at all called raw1394. This can be done by making
> two files: Makefile and raw1394.c
> These should be stored in the same folder and compiled using "make".
> When this is done, you will have a file called raw1394.ko which can be
> loaded using insmod.
>
> Makefile
>
>
> obj-m += raw1394.o
> all:
> make -C /lib/modules/$(shell uname -r)/build M=$(PWD) modules
> clean:
> make -C /lib/modules/$(shell uname -r)/build M=$(PWD) clean
>
> raw1394.c
>
>
> #include <linux/module.h>
> #include <linux/kernel.h>
>
> int init_module(void)
> {
> printk(KERN_INFO "Loaded dummy raw1394 module\n");
> return 0;
> }
>
>
> Commands to compile and load module:
>
>
> make
> sudo insmod raw1394.ko
>
>
>
>
>
> On 03/19/2013 11:28 AM, Thomas C. Bishop wrote:
>> Dear VMD and Will Ray,
>>
>> are there any updates/developments w/r/to VMD and a Phantom Omni?
>>
>> Instead of having an actual dedicated windows machine does anyone have
>> experience with a Windows machine w/in VirtualBox inside the same server?
>>
>> I'm using Opensuse 12.4
>>
>> TOm
>>
>>
>> From: John Stone (johns_at_ks.uiuc.edu)
>> Date: Sat Dec 01 2012 - 23:20:06 CST
>>
>> Next message: John Stone: "Re: cant open .car file"
>> Previous message: John Stone: "Re: unable to load cartoon
>> represention of my peptide"
>> In reply to: Ray, William: "Setting up a Phantom Omni for use with
>> VMD on CentOS 6"
>> Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [
>> attachment ]
>>
>> Hi,
>> We've never had the firewire drivers working well enough
>> under Linux to run the Phantom devices natively on a Linux
>> machine. Up to now, we have always run the Phantom devices
>> off of a Windows machine. We would then setup a VRPN server on
>> the Windows machine, and connect to it over the network from
>> our Linux/Windows/MacOS machines as needed. This wastes a windows
>> laptop on running the phantom, but it was very expedient and trouble
>> free for the most part. I don't have any particular advice about
>> getting the Phantom drivers working on Linux, from your description
>> it sounds like the Sensable people aren't working very hard on the
>> Linux support, so you might be better off just using a Windows machine,
>> unless the Sensable people know for sure that there's some particular
>> version of Linux that their current drivers have been tested on recently.
>>
>> Cheers,
>> John Stone
>> vmd_at_ks.uiuc.edu
>>
>> On Thu, Nov 29, 2012 at 06:22:23PM +0000, Ray, William wrote:
>> > Hello,
>> >
>> > We are working on setting up a Phantom Omni to use with VMD on a
>> CentOS 6 machine. We have confirmed that the Phantom Omni itself works
>> on Windows 7. We are still early in the set up process for CentOS, and
>> were wondering if anyone has any tips on setting it up?
>> >
>> > So far we have the PDD installed, and when we run
>> PHANToMConfiguration, the device's serial number is found. When we run
>> PHANToMTest, however, the application comes up, but we are not able to
>> do anything. Since the support at Sensable is fairly minimal for CentOS,
>> we have decided to move on to installing cmake and trying to set up
>> VRPN. Does anyone have any tips on anything to watch out for with the
>> VRPN set up, or on whether we should pursue getting PHANToMTest to
>> actually work?
>> >
>> > Thanks for any thoughts anyone might have on this!
>> > Will Ray
>
> ------------------------------
>
> Date: Thu, 21 Mar 2013 10:43:25 -0500
> From: John Stone <johns_at_ks.uiuc.edu>
> Subject: Re: vmd-l: Slow display with nVidia GeForce 9400GT and 3xx drivers on Linux
>
> Bogdan,
> Sorry for the slow reply, I'm out of town at a conference and I haven't
> been email accessible for a few days. There was a bug in my code (somehow
> a half-finished change got into CVS rather than the right one) which
> I will fix when I return home. The next build should work correctly.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Mon, Mar 18, 2013 at 01:19:09PM +0100, Bogdan Costescu wrote:
>> Hi John!
>>
>> The 1.9.2a20 version seems to have cured the performance issue, but
>> not with the default setting. I have to set VMDMAXAASAMPLES to 4 to
>> get about to about the same speed as the 2xx drivers.
>>
>> The VMD startup text doesn't change, still reporting:
>>
>> Info) [0] GeForce 9400 GT 4 SM_1.1 @ 1.38 GHz, 511MB RAM, KTO, OIO, ZCP
>> Info) OpenGL renderer: GeForce 9400 GT/PCIe/SSE2
>> Info) Features: STENCIL MSAA(16) MDE CVA MTX NPOT PP PS GLSL(OVFG)
>> Info) Full GLSL rendering mode is available.
>> Info) Textures: 2-D (8192x8192), 3-D (2048x2048x2048), Multitexture (4)
>>
>> i.e. the MSAA(16) is still present. When I set VMDMAXAASAMPLES, I see
>> printed 5 times:
>>
>> Info) User-requested OpenGL AA sample depth: 4
>>
>> but all that follows is again the same (including MSAA(16)). I don't
>> know if this is only cosmetic...
>>
>> But... the above results hold for driver 310.32; if using 313.09, I
>> get the slow speed independent of the VMDMAXAASAMPLES setting - but
>> this being a beta version might not mean much.
>>
>> Let me know if you'd like me to test some more.
>>
>> Cheers,
>> Bogdan
>>
>> On Fri, Mar 15, 2013 at 3:25 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>> > Bogdan,
>> > I posted a new test build of VMD, give it a try and let me know
>> > if it cures the performance issue you'd observed previously.
>> >
>> > Cheers,
>> > John Stone
>> > vmd_at_ks.uiuc.edu
>
> - --
> NIH Center 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/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/
>
> ------------------------------
>
> Date: Thu, 21 Mar 2013 10:57:58 -0500
> From: John Stone <johns_at_ks.uiuc.edu>
> Subject: Re: vmd-l: phantom omni linux install
>
> Tom,
> I'm out of town at a conference and haven't been able to check
> email for a few days.
>
> All you really need to do to get VMD working with a Phantom is
> get the Phantom working itself, and then compile a VRPN server
> for it. If you can get VRPN working, then from there it is easy
> to get VMD talking to VRPN. It is just the first two steps that
> are historically tricky, and in my experience it's whether your
> linux kernel has working firewire drivers etc. I see you wrote
> another subsequent email so I'll check that one next...
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
>
> On Tue, Mar 19, 2013 at 11:28:14AM -0500, Thomas C. Bishop wrote:
>> Dear VMD and Will Ray,
>>
>> are there any updates/developments w/r/to VMD and a Phantom Omni?
>>
>> Instead of having an actual dedicated windows machine does anyone have
>> experience with a Windows machine w/in VirtualBox inside the same server?
>>
>> I'm using Opensuse 12.4
>>
>> TOm
>>
>>
>> From: John Stone (johns_at_ks.uiuc.edu)
>> Date: Sat Dec 01 2012 - 23:20:06 CST
>>
>> Next message: John Stone: "Re: cant open .car file"
>> Previous message: John Stone: "Re: unable to load cartoon
>> represention of my peptide"
>> In reply to: Ray, William: "Setting up a Phantom Omni for use with
>> VMD on CentOS 6"
>> Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [
>> attachment ]
>>
>> Hi,
>> We've never had the firewire drivers working well enough
>> under Linux to run the Phantom devices natively on a Linux
>> machine. Up to now, we have always run the Phantom devices
>> off of a Windows machine. We would then setup a VRPN server on
>> the Windows machine, and connect to it over the network from
>> our Linux/Windows/MacOS machines as needed. This wastes a windows
>> laptop on running the phantom, but it was very expedient and trouble
>> free for the most part. I don't have any particular advice about
>> getting the Phantom drivers working on Linux, from your description
>> it sounds like the Sensable people aren't working very hard on the
>> Linux support, so you might be better off just using a Windows machine,
>> unless the Sensable people know for sure that there's some particular
>> version of Linux that their current drivers have been tested on recently.
>>
>> Cheers,
>> John Stone
>> vmd_at_ks.uiuc.edu
>>
>> On Thu, Nov 29, 2012 at 06:22:23PM +0000, Ray, William wrote:
>> > Hello,
>> >
>> > We are working on setting up a Phantom Omni to use with VMD on a
>> CentOS 6 machine. We have confirmed that the Phantom Omni itself works
>> on Windows 7. We are still early in the set up process for CentOS, and
>> were wondering if anyone has any tips on setting it up?
>> >
>> > So far we have the PDD installed, and when we run
>> PHANToMConfiguration, the device's serial number is found. When we run
>> PHANToMTest, however, the application comes up, but we are not able to
>> do anything. Since the support at Sensable is fairly minimal for CentOS,
>> we have decided to move on to installing cmake and trying to set up
>> VRPN. Does anyone have any tips on anything to watch out for with the
>> VRPN set up, or on whether we should pursue getting PHANToMTest to
>> actually work?
>> >
>> > Thanks for any thoughts anyone might have on this!
>> > Will Ray
>> --
>> *******************************
>> Thomas C. Bishop
>> Tel: 318-257-5209
>> Fax: 318-257-3823
>> www.latech.edu/~bishop
>> ********************************
>
> - --
> NIH Center 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/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/
>
> ------------------------------
>
> Date: Thu, 21 Mar 2013 11:00:46 -0500
> From: John Stone <johns_at_ks.uiuc.edu>
> Subject: Re: vmd-l: phantom omni linux install: Phantom OMNI HOWTO
>
> Tom,
> If you have it working well enough for the Phantom demos,
> then you may be very close to being able to get VMD to work.
>
> The next step is to compile VRPN against your Phantom drivers,
> and then compile VMD against VRPN, and you're in business.
>
> If you can get the VRPN server running with your phantom with any
> of its test codes, then I can do a VMD build for you with the same
> version of VRPN, and it should then work. I am out of town until
> Monday but I can work on this with you after I get back. Let me
> know if you can get VRPN compiled on your machine.
>
> Cheers,
> John Stone
> johns_at_ks.uiuc.edu
>
> On Wed, Mar 20, 2013 at 12:52:17PM -0500, Thomas C. Bishop wrote:
>> Here's info on how to get the PHANTOM omni devidce setup under linux.
>> Thought I'd post it while I have it
>>
>> Haven't gotten to point of it w/ VMD yet but the PHantom Demos work.
>>
>> The Sensable manual I downnloaded is a bit out of date
>> as the linux kernel does not have raw1394 modules.
>> OpenHapticsAE_Linux_v3_0
>> OpenHaptics_3.1_Academic_Edition
>>
>> The trick is to spoof raw1394 module s.t. the sensable drivers think
>> they are loaded. Here's a work around from
>>
>> http://ubuntuforums.org/archive/index.php/t-1750274.html
>>
>> If there are better solutions I'd love to know.
>> Thanks
>> TOm
>>
>> ****************************************
>> quoting... http://ubuntuforums.org/archive/index.php/t-1750274.html
>>
>> It is a rather ugly fix, but as I cannot modify "Open"Haptics it will
>> have to do in my case. I've looked quite a lot around the web as well,
>> and I can't find any other solution.
>>
>> After installing "Open"Haptics and the device drivers which SensAble
>> provides (using dpkg) you will have to work your way around the
>> dependency of raw1394. I am not really sure which steps ultimately made
>> it work for me, but the following steps are necessary.
>>
>> 1. Spoof the /dev/raw1394 device
>> 2. Create a dummy kernel node
>>
>> 1. To spoof the /dev/raw1394 device, simply use ln and hard link the
>> /dev/fw0 (or some other fwX) by typing the following commands:
>>
>> sudo ln /dev/fw0 /dev/raw1394
>> sudo chmod 0777 /dev/raw1394
>>
>> 2. As I believe "Open"Haptics checks if the raw1394 module is present
>> during launch (using lsmod or similar), I created a kernel module that
>> doesn't do anything at all called raw1394. This can be done by making
>> two files: Makefile and raw1394.c
>> These should be stored in the same folder and compiled using "make".
>> When this is done, you will have a file called raw1394.ko which can be
>> loaded using insmod.
>>
>> Makefile
>>
>>
>> obj-m += raw1394.o
>> all:
>> make -C /lib/modules/$(shell uname -r)/build M=$(PWD) modules
>> clean:
>> make -C /lib/modules/$(shell uname -r)/build M=$(PWD) clean
>>
>> raw1394.c
>>
>>
>> #include <linux/module.h>
>> #include <linux/kernel.h>
>>
>> int init_module(void)
>> {
>> printk(KERN_INFO "Loaded dummy raw1394 module\n");
>> return 0;
>> }
>>
>>
>> Commands to compile and load module:
>>
>>
>> make
>> sudo insmod raw1394.ko
>>
>>
>>
>>
>>
>> On 03/19/2013 11:28 AM, Thomas C. Bishop wrote:
>> >Dear VMD and Will Ray,
>> >
>> >are there any updates/developments w/r/to VMD and a Phantom Omni?
>> >
>> >Instead of having an actual dedicated windows machine does anyone have
>> >experience with a Windows machine w/in VirtualBox inside the same server?
>> >
>> >I'm using Opensuse 12.4
>> >
>> >TOm
>> >
>> >
>> >From: John Stone (johns_at_ks.uiuc.edu)
>> >Date: Sat Dec 01 2012 - 23:20:06 CST
>> >
>> > Next message: John Stone: "Re: cant open .car file"
>> > Previous message: John Stone: "Re: unable to load cartoon
>> >represention of my peptide"
>> > In reply to: Ray, William: "Setting up a Phantom Omni for use with
>> >VMD on CentOS 6"
>> > Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [
>> >attachment ]
>> >
>> >Hi,
>> > We've never had the firewire drivers working well enough
>> >under Linux to run the Phantom devices natively on a Linux
>> >machine. Up to now, we have always run the Phantom devices
>> >off of a Windows machine. We would then setup a VRPN server on
>> >the Windows machine, and connect to it over the network from
>> >our Linux/Windows/MacOS machines as needed. This wastes a windows
>> >laptop on running the phantom, but it was very expedient and trouble
>> >free for the most part. I don't have any particular advice about
>> >getting the Phantom drivers working on Linux, from your description
>> >it sounds like the Sensable people aren't working very hard on the
>> >Linux support, so you might be better off just using a Windows machine,
>> >unless the Sensable people know for sure that there's some particular
>> >version of Linux that their current drivers have been tested on recently.
>> >
>> >Cheers,
>> > John Stone
>> > vmd_at_ks.uiuc.edu
>> >
>> >On Thu, Nov 29, 2012 at 06:22:23PM +0000, Ray, William wrote:
>> > > Hello,
>> > >
>> > > We are working on setting up a Phantom Omni to use with VMD on a
>> >CentOS 6 machine. We have confirmed that the Phantom Omni itself works
>> >on Windows 7. We are still early in the set up process for CentOS, and
>> >were wondering if anyone has any tips on setting it up?
>> > >
>> > > So far we have the PDD installed, and when we run
>> >PHANToMConfiguration, the device's serial number is found. When we run
>> >PHANToMTest, however, the application comes up, but we are not able to
>> >do anything. Since the support at Sensable is fairly minimal for CentOS,
>> >we have decided to move on to installing cmake and trying to set up
>> >VRPN. Does anyone have any tips on anything to watch out for with the
>> >VRPN set up, or on whether we should pursue getting PHANToMTest to
>> >actually work?
>> > >
>> > > Thanks for any thoughts anyone might have on this!
>> > > Will Ray
>
> - --
> NIH Center 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/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/
>
> ------------------------------
>
> Date: Thu, 21 Mar 2013 11:12:02 -0500
> From: John Stone <johns_at_ks.uiuc.edu>
> Subject: Re: vmd-l: VMD 1.9.1 for 64-bit Windows
>
> Hi guys,
> The long standing issue with 64-bit builds of VMD on windows has
> to do with the libraries that are needed. I would do the compilation
> with the MS compilers rather than minGW or cygwin as they historically
> had issues with OpenGL, but you can certainly give it a try if that's
> what you have to work with. The major issue has always been getting
> a correctly functioning Tcl/TK+FLTK, once that is sorted, the rest
> is mostly easy. The other issues on 64-bit Windows will be that
> the drivers for the Spacenavigator that we have been using aren't
> supported for 64-bit mode, and similar issues for other (optional)
> libraries. The only things you _must_ have working to get VMD up
> and running on Windows are Tcl/TK and FLTK, the rest could be dealt
> with later. I'm out of town at the GPU Tech. conference until next
> week, but I am happy to work with you guys on this when I return.
> In particular, I would suggest trying Tcl/Tk 8.6.0 and see if you
> can get that build on 64-bit Windows and we can go from there.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
>
> On Wed, Mar 20, 2013 at 02:12:34PM +0100, Ajasja Ljubeti?? wrote:
>> Hi Jernej!
>>
>> Have you searched the mailing list? It's a popular request, that went
>> unheeded up to now:)
>> You can try compiling with minGW, it should not be that bad, but the devil
>> is in the details. I have not managed yet, as I did not have a strong
>> enough incentive. We can also try to work something out together next
>> week.
>>
>> Regards,
>> Ajasja
>>
>> On 20 March 2013 03:18, Jernej Zidar <jernej.zidar_at_gmail.com> wrote:
>>
>> Hi.
>> Are there plans for a 64-bit version of VMD?
>>
>> At work we have a workstation used only for visualizations but it
>> unfortunately runs Windows 7 Ultimate and on several occasions I had
>> VMD crashing on me when I tried to visualize a large trajectory. I can
>> visualize the same trajectory in 64-bit VMD under Linux tho.
>>
>> I also understand compiling code under Windows must be a real pain...
>>
>> Thanks for any information,
>> Jernej
>
> - --
> NIH Center 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/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/
>
> ------------------------------
>
> Date: Thu, 21 Mar 2013 17:42:25 -0400
> From: Juan Antonio Raygoza Garay <raygozag_at_psu.edu>
> Subject: vmd-l: protein secondary structure
>
> Hi, i'm using VMD 1.9.1 on mac os and whenever I load any pdb with protein in it, it won't show the secondary structure of the protein in new cartoon, it only shows the proteins as coils, i already installed stride and restarted vmd but keeps showing me the same result.
>
> thanks
>
> ------------------------------
>
> End of vmd-l digest V1 #2344
> ****************************
> 

-- 
Yours Sincerely,
~~~~~~~~~~~~~~~~~~~~~~~~
Amit Jaiswal,
Department of Bioinformatics,
School of Life Sciences,
Pondicherry Central University,
Kalapet, Pondicherry,
Puducherry - 605 014.
~~~~~~~~~~~~~~~~~~~~~~~~~