pymol-users Mailing List for PyMOL Molecular Graphics System

Hi Jason and Takanori,
This was exactly what I was looking for. Thanks for your help.
Chris

> On 29/10/2013, at 18.48, Jason Vertrees <jas...@sc...> wrote:
>
> Hi Chris,
>
> if objName in cmd.get_names(enabled_only=1):
> print "objName is enabled"
>
> Cheers,
>
> -- Jason
>
>> On Tue, Oct 29, 2013 at 5:50 AM, Christoffer Norn <ch...@gm...> wrote:
>> Hi All,
>> How can I, from the command line, get information on whether a object is enabled or disabled? I need this to flip through thousands of designed proteins — and with this many proteins, mouse-clicking to enable/disable them becomes a bit cumbersome.
>> Thanks,
>> Chris
>> ------------------------------------------------------------------------------
>> Android is increasing in popularity, but the open development platform that
>> developers love is also attractive to malware creators. Download this white
>> paper to learn more about secure code signing practices that can help keep
>> Android apps secure.
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>> _______________________________________________
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>
>
>
> --
> Jason Vertrees, PhD
> Director of Core Modeling Products
> Schrödinger, Inc.
>
> (e) Jas...@sc...
> (o) +1 (603) 374-7120

Hello List,

So far I use PyMOL to visualize polygonal chain through an expurged PDB data file when the chain is not ring.
Now I would like to visualize chain rings: what is the best way to make PyMOL understand that the two end points coincide ?

Thanks in advance,
Jerome

Hi Chris,

if objName in cmd.get_names(enabled_only=1):
  print "objName is enabled"

Cheers,

-- Jason

On Tue, Oct 29, 2013 at 5:50 AM, Christoffer Norn <ch...@gm...> wrote:
> Hi All,
> How can I, from the command line, get information on whether a object is enabled or disabled? I need this to flip through thousands of designed proteins — and with this many proteins, mouse-clicking to enable/disable them becomes a bit cumbersome.
> Thanks,
> Chris
> ------------------------------------------------------------------------------
> Android is increasing in popularity, but the open development platform that
> developers love is also attractive to malware creators. Download this white
> paper to learn more about secure code signing practices that can help keep
> Android apps secure.
> http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/4140/ostg.clktrk
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...



-- 
Jason Vertrees, PhD
Director of Core Modeling Products
Schrödinger, Inc.

(e) Jas...@sc...
(o) +1 (603) 374-7120

Hi All,
How can I, from the command line, get information on whether a object is enabled or disabled? I need this to flip through thousands of designed proteins — and with this many proteins, mouse-clicking to enable/disable them becomes a bit cumbersome. 
Thanks,
Chris

Dear PyMOL connoisseurs,

I’m writing a small package for visualizing hundreds of designed proteins. In this quest I need a function which for-objects-in-a-selection asks the user for comments and then save the object name together with the comment in a textfile. I would like to use the same interface for user interaction as the one the rename function uses. I tried reading the wizard for rename, but to no use. Hope you can help.

An additional question: When double-clicking to open a pdb file, I need pymol to run .pymolrc before it uses the cmd.load to load the double-clicked pdb file. Is there any way to do this? 

Thanks,
Chris

Hi Nick,

unfortunately such a zooming feature is still missing on the movie panel. I absolutely agree that it would be a much appreciated addition.

Cheers,
  Thomas

On Oct 23, 2013, at 11:14 PM, "Noinaj, Nicholas (NIH/NIDDK) [E]" <no...@ni...> wrote:

> Hi,
> 
> I am wondering if it is possible to zoom onto a region of the movie panel in order to visualize and edit the individual keyframes easier?  Similar to what you would find in other keyframing software like Adobe After Effects or Flash?  While it is ok for movies with few frames, the more frames you have, the more difficult it becomes.  For example, say i have 5000 frames, if i want to fine tune the motions of a ligand as it enters the binding pocket, it becomes quite tedious (and annoying) since the more frames you have in your movie, the smaller the key frames become and therefore the more difficult to work with the keyframes directly.  It would be really nice to have the option of zooming within the movie panel and then have a horizontal scroll bar to scroll as needed.  
> 
> Thanks in advance for any feedback!
> 
> Cheers,
> Nick
> 
> --------------------------------
> 
> [ Nicholas Noinaj ]
> the Buchanan Lab
> Laboratory of Molecular Biology
> LMB-NIDDK, NIH
> 50 South Drive, Room 4505
> Bethesda, MD  20892-8030
> 1-301-594-9230 (lab)
> 1-859-893-4789 (cell)
> no...@ni...
> 
> [ the Buchanan Lab ]
> http://www-mslmb.niddk.nih.gov/buchanan/

Hi,

I am wondering if it is possible to zoom onto a region of the movie panel in order to visualize and edit the individual keyframes easier?  Similar to what you would find in other keyframing software like Adobe After Effects or Flash?  While it is ok for movies with few frames, the more frames you have, the more difficult it becomes.  For example, say i have 5000 frames, if i want to fine tune the motions of a ligand as it enters the binding pocket, it becomes quite tedious (and annoying) since the more frames you have in your movie, the smaller the key frames become and therefore the more difficult to work with the keyframes directly.  It would be really nice to have the option of zooming within the movie panel and then have a horizontal scroll bar to scroll as needed.  

Thanks in advance for any feedback!








Cheers,
Nick





--------------------------------

[ Nicholas Noinaj ]
the Buchanan Lab
Laboratory of Molecular Biology
LMB-NIDDK, NIH
50 South Drive, Room 4505
Bethesda, MD  20892-8030
1-301-594-9230 (lab)
1-859-893-4789 (cell)
no...@ni...

[ the Buchanan Lab ]
http://www-mslmb.niddk.nih.gov/buchanan/



 

Hi Thomas.


I think that I this might be an issue of display adapter driver. I'll check
this first and give you an update.


On Tue, Oct 22, 2013 at 2:28 PM, Thomas Holder <
sp...@us...> wrote:

> Hi Yotam,
>
> you are welcome to send me your file, then I'll have a look.
>
> Cheers,
>   Thomas
>
> On Oct 22, 2013, at 5:52 AM, Yotam Avital <yo...@gm...> wrote:
>
> > Hi Thomas.
> >
> > Thanks for the quick replay. I installed the svn version of pymol with
> the same result. I know that 6000 atoms isn't much for this task and this
> baffle me. Is there a way for me to de-bug this? Perhaps my input file is
> faulty.
> >
> >
> > On Tue, Oct 22, 2013 at 1:32 AM, Thomas Holder <
> sp...@us...> wrote:
> > Hi Yotam,
> >
> > 6000 atoms should be absolutely no problem, even with much less memory.
> There were few known memory leaks that have been fixed since 1.4, so could
> you try to compile the latest code from SVN?
> >
> > http://pymolwiki.org/index.php/Linux_Install
> >
> > Cheers,
> >   Thomas
> >
> > On Oct 21, 2013, at 4:58 PM, Yotam Avital <yo...@gm...> wrote:
> > > Hi.
> > >
> > > I have python (1.4) on a xubuntu 12.04 machine (fresh install). The
> machine has 6GB ram and an intel i3 processor (I don't remember the exact
> model). On a previous install of Ubuntu (13.04) I had no trouble viewing
> files of that size, but now I can't. I get the "standard" EEK! pymol just
> run out of memory etc.
> > >
> > > To my knowledge, 6GB of ram should be sufficient for such task, isn't
> that so?
> > >
> > > How can I view these files?
>



-- 
My other email account has a "professional" signature.

Hi Yotam,

you are welcome to send me your file, then I'll have a look.

Cheers,
  Thomas

On Oct 22, 2013, at 5:52 AM, Yotam Avital <yo...@gm...> wrote:

> Hi Thomas. 
> 
> Thanks for the quick replay. I installed the svn version of pymol with the same result. I know that 6000 atoms isn't much for this task and this baffle me. Is there a way for me to de-bug this? Perhaps my input file is faulty. 
> 
> 
> On Tue, Oct 22, 2013 at 1:32 AM, Thomas Holder <sp...@us...> wrote:
> Hi Yotam,
> 
> 6000 atoms should be absolutely no problem, even with much less memory. There were few known memory leaks that have been fixed since 1.4, so could you try to compile the latest code from SVN?
> 
> http://pymolwiki.org/index.php/Linux_Install
> 
> Cheers,
>   Thomas
> 
> On Oct 21, 2013, at 4:58 PM, Yotam Avital <yo...@gm...> wrote:
> > Hi.
> >
> > I have python (1.4) on a xubuntu 12.04 machine (fresh install). The machine has 6GB ram and an intel i3 processor (I don't remember the exact model). On a previous install of Ubuntu (13.04) I had no trouble viewing files of that size, but now I can't. I get the "standard" EEK! pymol just run out of memory etc.
> >
> > To my knowledge, 6GB of ram should be sufficient for such task, isn't that so?
> >
> > How can I view these files?

Hi Thomas.

Thanks for the quick replay. I installed the svn version of pymol with the
same result. I know that 6000 atoms isn't much for this task and this
baffle me. Is there a way for me to de-bug this? Perhaps my input file is
faulty.


On Tue, Oct 22, 2013 at 1:32 AM, Thomas Holder <
sp...@us...> wrote:

> Hi Yotam,
>
> 6000 atoms should be absolutely no problem, even with much less memory.
> There were few known memory leaks that have been fixed since 1.4, so could
> you try to compile the latest code from SVN?
>
> http://pymolwiki.org/index.php/Linux_Install
>
> Cheers,
>   Thomas
>
> On Oct 21, 2013, at 4:58 PM, Yotam Avital <yo...@gm...> wrote:
> > Hi.
> >
> > I have python (1.4) on a xubuntu 12.04 machine (fresh install). The
> machine has 6GB ram and an intel i3 processor (I don't remember the exact
> model). On a previous install of Ubuntu (13.04) I had no trouble viewing
> files of that size, but now I can't. I get the "standard" EEK! pymol just
> run out of memory etc.
> >
> > To my knowledge, 6GB of ram should be sufficient for such task, isn't
> that so?
> >
> > How can I view these files?
>



-- 
My other email account has a "professional" signature.

Hi Yotam,

6000 atoms should be absolutely no problem, even with much less memory. There were few known memory leaks that have been fixed since 1.4, so could you try to compile the latest code from SVN?

http://pymolwiki.org/index.php/Linux_Install

Cheers,
  Thomas

On Oct 21, 2013, at 4:58 PM, Yotam Avital <yo...@gm...> wrote:
> Hi. 
> 
> I have python (1.4) on a xubuntu 12.04 machine (fresh install). The machine has 6GB ram and an intel i3 processor (I don't remember the exact model). On a previous install of Ubuntu (13.04) I had no trouble viewing files of that size, but now I can't. I get the "standard" EEK! pymol just run out of memory etc. 
> 
> To my knowledge, 6GB of ram should be sufficient for such task, isn't that so? 
> 
> How can I view these files?

Hi.

I have python (1.4) on a xubuntu 12.04 machine (fresh install). The machine
has 6GB ram and an intel i3 processor (I don't remember the exact model).
On a previous install of Ubuntu (13.04) I had no trouble viewing files of
that size, but now I can't. I get the "standard" EEK! pymol just run out of
memory etc.

To my knowledge, 6GB of ram should be sufficient for such task, isn't that
so?

How can I view these files?


-- 
My other email account has a "professional" signature.

Wow that would be so great if you could buy these from Lego. I passed it on.

On Oct 18, 2013, at 1:47 PM, "Hurt, Darrell (NIH/NIAID) [E]" <dar...@ni...> wrote:

> Hi Tsjerk,
> 
> If you have the POV-Ray file, that would be a great first step to creating a 3D-printable file. In fact, we're building a database of scientifically-relevant 3D print files for use in classrooms and labs. These core pieces would be a great addition to our public library. Maybe you could share the POV-Ray files with me and then I can "solidify" and scale them appropriately for the connecting LEGO pieces. What do you think?
> 
> http://www.hhs.gov/open/initiatives/ignite/3d-printing-exchange.html
> 
> Cheers,
> Darrell
> 
> --
> Darrell Hurt, Ph.D.
> Section Head, Computational Biology
> Bioinformatics and Computational Biosciences Branch (BCBB)
> OCICB/OSMO/OD/NIAID/NIH
> 
> 31 Center Drive, Room 3B62B, MSC 2135
> Bethesda, MD 20892-2135
> Office: 301-402-0095
> Mobile: 301-758-3559
> Web: BCBB Home Page<" rel="nofollow">http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.aspx#niaid_inlineNav_Anchor>
> Twitter: @niaidbioit<" rel="nofollow">https://twitter.com/niaidbioit>
> 
> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.
> 
> From: Tsjerk Wassenaar <ts...@gm...<mailto:ts...@gm...>>
> Date: Friday, October 18, 2013 2:39 PM
> To: Darrell Hurt <dar...@ni...<mailto:dar...@ni...>>
> Cc: pymol-users <pym...@li...<mailto:pym...@li...>>
> Subject: Re: [PyMOL] Molecular models with LEGO
> 
> Hi Darrell,
> 
> I made these in POV-Ray. For a 3D print, I would really need to have the exact measurements of the LEGO connector piece. That would be awesome though! I was thinking of building a nucleotide in POV-Ray using these, and then go for a piece of DNA. But having a photo of a 3D printed prototype would be even better.
> 
> Cheers,
> 
> Tsjerk
> 
> 
> On Fri, Oct 18, 2013 at 8:24 PM, Hurt, Darrell (NIH/NIAID) [E] <dar...@ni...<mailto:dar...@ni...>> wrote:
> Wow! Do you have the CAD drawings for these? A 3D printer might work to build some prototypes…
> 
> 
> --
> Darrell Hurt, Ph.D.
> Section Head, Computational Biology
> Bioinformatics and Computational Biosciences Branch (BCBB)
> OCICB/OSMO/OD/NIAID/NIH
> 
> 31 Center Drive, Room 3B62B, MSC 2135
> Bethesda, MD 20892-2135
> Office: 301-402-0095<tel:301-402-0095>
> Mobile: 301-758-3559<tel:301-758-3559>
> Web: BCBB Home Page<" rel="nofollow">http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.aspx#niaid_inlineNav_Anchor>
> Twitter: @niaidbioit<" rel="nofollow">https://twitter.com/niaidbioit>
> 
> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.
> 
> From: Tsjerk Wassenaar <ts...@gm...<mailto:ts...@gm...><mailto:ts...@gm...<mailto:ts...@gm...>>>
> Date: Friday, October 18, 2013 2:05 PM
> To: pymol-users <pym...@li...<mailto:pym...@li...><mailto:pym...@li...<mailto:pym...@li...>>>
> Subject: [PyMOL] Molecular models with LEGO
> 
> 
> Hey :)
> 
> What if you could hold the molecules you view in your hands? Ever thought of using LEGO to build molecular models? It may happen if we raise 10 000 votes for my LEGO chemistry project at http://lego.cuusoo.com/ideas/view/51273
> 
> Please consider forwarding this mail to anyone you think would be interested.
> 
> Groetjes,
> 
> Tsjerk
> 
> --
> Tsjerk A. Wassenaar, Ph.D.
> 
> 
> 
> 
> --
> Tsjerk A. Wassenaar, Ph.D.
> 
> 
> ------------------------------------------------------------------------------
> October Webinars: Code for Performance
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> Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from 
> the latest Intel processors and coprocessors. See abstracts and register >
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> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366

Hi Tsjerk,

If you have the POV-Ray file, that would be a great first step to creating a 3D-printable file. In fact, we're building a database of scientifically-relevant 3D print files for use in classrooms and labs. These core pieces would be a great addition to our public library. Maybe you could share the POV-Ray files with me and then I can "solidify" and scale them appropriately for the connecting LEGO pieces. What do you think?

http://www.hhs.gov/open/initiatives/ignite/3d-printing-exchange.html

Cheers,
Darrell

--
Darrell Hurt, Ph.D.
Section Head, Computational Biology
Bioinformatics and Computational Biosciences Branch (BCBB)
OCICB/OSMO/OD/NIAID/NIH

31 Center Drive, Room 3B62B, MSC 2135
Bethesda, MD 20892-2135
Office: 301-402-0095
Mobile: 301-758-3559
Web: BCBB Home Page<" rel="nofollow">http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.aspx#niaid_inlineNav_Anchor>
Twitter: @niaidbioit<" rel="nofollow">https://twitter.com/niaidbioit>

Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

From: Tsjerk Wassenaar <ts...@gm...<mailto:ts...@gm...>>
Date: Friday, October 18, 2013 2:39 PM
To: Darrell Hurt <dar...@ni...<mailto:dar...@ni...>>
Cc: pymol-users <pym...@li...<mailto:pym...@li...>>
Subject: Re: [PyMOL] Molecular models with LEGO

Hi Darrell,

I made these in POV-Ray. For a 3D print, I would really need to have the exact measurements of the LEGO connector piece. That would be awesome though! I was thinking of building a nucleotide in POV-Ray using these, and then go for a piece of DNA. But having a photo of a 3D printed prototype would be even better.

Cheers,

Tsjerk


On Fri, Oct 18, 2013 at 8:24 PM, Hurt, Darrell (NIH/NIAID) [E] <dar...@ni...<mailto:dar...@ni...>> wrote:
Wow! Do you have the CAD drawings for these? A 3D printer might work to build some prototypes…


--
Darrell Hurt, Ph.D.
Section Head, Computational Biology
Bioinformatics and Computational Biosciences Branch (BCBB)
OCICB/OSMO/OD/NIAID/NIH

31 Center Drive, Room 3B62B, MSC 2135
Bethesda, MD 20892-2135
Office: 301-402-0095<tel:301-402-0095>
Mobile: 301-758-3559<tel:301-758-3559>
Web: BCBB Home Page<" rel="nofollow">http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.aspx#niaid_inlineNav_Anchor>
Twitter: @niaidbioit<" rel="nofollow">https://twitter.com/niaidbioit>

Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

From: Tsjerk Wassenaar <ts...@gm...<mailto:ts...@gm...><mailto:ts...@gm...<mailto:ts...@gm...>>>
Date: Friday, October 18, 2013 2:05 PM
To: pymol-users <pym...@li...<mailto:pym...@li...><mailto:pym...@li...<mailto:pym...@li...>>>
Subject: [PyMOL] Molecular models with LEGO


Hey :)

What if you could hold the molecules you view in your hands? Ever thought of using LEGO to build molecular models? It may happen if we raise 10 000 votes for my LEGO chemistry project at http://lego.cuusoo.com/ideas/view/51273

Please consider forwarding this mail to anyone you think would be interested.

Groetjes,

Tsjerk

--
Tsjerk A. Wassenaar, Ph.D.




--
Tsjerk A. Wassenaar, Ph.D.

Hi Darrell,

I made these in POV-Ray. For a 3D print, I would really need to have the
exact measurements of the LEGO connector piece. That would be awesome
though! I was thinking of building a nucleotide in POV-Ray using these, and
then go for a piece of DNA. But having a photo of a 3D printed prototype
would be even better.

Cheers,

Tsjerk


On Fri, Oct 18, 2013 at 8:24 PM, Hurt, Darrell (NIH/NIAID) [E] <
dar...@ni...> wrote:

> Wow! Do you have the CAD drawings for these? A 3D printer might work to
> build some prototypes…
>
>
> --
> Darrell Hurt, Ph.D.
> Section Head, Computational Biology
> Bioinformatics and Computational Biosciences Branch (BCBB)
> OCICB/OSMO/OD/NIAID/NIH
>
> 31 Center Drive, Room 3B62B, MSC 2135
> Bethesda, MD 20892-2135
> Office: 301-402-0095
> Mobile: 301-758-3559
> Web: BCBB Home Page<
> http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.aspx#niaid_inlineNav_Anchor
> >
> Twitter: @niaidbioit<" rel="nofollow">https://twitter.com/niaidbioit>
>
> Disclaimer: The information in this e-mail and any of its attachments is
> confidential and may contain sensitive information. It should not be used
> by anyone who is not the original intended recipient. If you have received
> this e-mail in error please inform the sender and delete it from your
> mailbox or any other storage devices. National Institute of Allergy and
> Infectious Diseases shall not accept liability for any statements made that
> are sender's own and not expressly made on behalf of the NIAID by one of
> its representatives.
>
> From: Tsjerk Wassenaar <ts...@gm...<mailto:ts...@gm...>>
> Date: Friday, October 18, 2013 2:05 PM
> To: pymol-users <pym...@li...<mailto:
> pym...@li...>>
> Subject: [PyMOL] Molecular models with LEGO
>
>
> Hey :)
>
> What if you could hold the molecules you view in your hands? Ever thought
> of using LEGO to build molecular models? It may happen if we raise 10 000
> votes for my LEGO chemistry project at
> http://lego.cuusoo.com/ideas/view/51273
>
> Please consider forwarding this mail to anyone you think would be
> interested.
>
> Groetjes,
>
> Tsjerk
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
>


-- 
Tsjerk A. Wassenaar, Ph.D.

Wow! Do you have the CAD drawings for these? A 3D printer might work to build some prototypes…


--
Darrell Hurt, Ph.D.
Section Head, Computational Biology
Bioinformatics and Computational Biosciences Branch (BCBB)
OCICB/OSMO/OD/NIAID/NIH

31 Center Drive, Room 3B62B, MSC 2135
Bethesda, MD 20892-2135
Office: 301-402-0095
Mobile: 301-758-3559
Web: BCBB Home Page<" rel="nofollow">http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.aspx#niaid_inlineNav_Anchor>
Twitter: @niaidbioit<" rel="nofollow">https://twitter.com/niaidbioit>

Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

From: Tsjerk Wassenaar <ts...@gm...<mailto:ts...@gm...>>
Date: Friday, October 18, 2013 2:05 PM
To: pymol-users <pym...@li...<mailto:pym...@li...>>
Subject: [PyMOL] Molecular models with LEGO


Hey :)

What if you could hold the molecules you view in your hands? Ever thought of using LEGO to build molecular models? It may happen if we raise 10 000 votes for my LEGO chemistry project at http://lego.cuusoo.com/ideas/view/51273

Please consider forwarding this mail to anyone you think would be interested.

Groetjes,

Tsjerk

--
Tsjerk A. Wassenaar, Ph.D.

Hey :)

What if you could hold the molecules you view in your hands? Ever thought
of using LEGO to build molecular models? It may happen if we raise 10 000
votes for my LEGO chemistry project at
http://lego.cuusoo.com/ideas/view/51273

Please consider forwarding this mail to anyone you think would be
interested.

Groetjes,

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.

Hi Mengbin,

it's all about the "mview" command. It can associate states, camera positions and object positions with movie frames.

# store state 5 with frame 100
mview store, 100, state=5
# store camera position with current frame
mview store
# store all object positions with current frame
mview store, object=*

What you want might look like this:

mset 1-30 30x50
mview store, 1
mview store, 30
set_view ... (zoomed in view)
mview store, 80

Cheers,
  Thomas

On Oct 10, 2013, at 3:52 PM, Mengbin Chen <men...@sa...> wrote:

> Dear Pymol Users,
> 
> While I am trying to make a movie that contains morph, a gradual zoom-in view of active site, and rotation, I don't know how to put all these things together as a movie. The morph part is an object with multiple states, and the zoom-in view follows the last state of morph object immediately. Anyone has any idea of how to do this?
> 
> Thanks in advance,
> Mengbin

Hi Chris,

put something like this in your ~/.pymolrc.py script:

from pymol import cmd
def customload(*args, **kwargs):
    print "do stuff"
cmd.load = customload
cmd.extend('load', cmd.load)

Make sure your customload function doesn't call cmd.load itself, but rather pymol.importing.load if you need to.

Cheers,
  Thomas

On Oct 16, 2013, at 2:56 AM, Christoffer Norn <ch...@gm...> wrote:

> Hi all,
> I've written a script to load pdbs with extra information. Now I would like this script to used instead of the standard load command when I double-click pdb files. How would I go about doing this?
> Thanks,
> Chris

Hi all,
I've written a script to load pdbs with extra information. Now I would like this script to used instead of the standard load command when I double-click pdb files. How would I go about doing this?
Thanks,
Chris

Hi Tsjerk & Aiqun,

very good find, puzzled me as well. There is a setting "pdb_unbond_cations" which seems to be implemented a bit buggy, I think it should only prevent distance-based connectivity of cations, and not interfere with explicit CONECT records.

Cheers,
  Thomas

On Oct 15, 2013, at 5:45 AM, Tsjerk Wassenaar wrote:
> Hi Aiqun Huang,
> 
> It puzzled me for a while. I found that renaming all 'K' atoms to 'C' the bonds are drawn correctly. That still puzzles me, but at least it offers a way to get the desired view.
> 
> Are you actually running simulations with this model? And are you interested in converting the CG model back to atomistic? 
> 
> Cheers,
> Tsjerk
> 
> On Mon, Oct 14, 2013 at 2:32 AM, Aiqun Huang <all...@gm...> wrote:
> Hi dear PyMol users,
> 
> I am new to PyMol. I have a pdb file(see attached cg_dna.pdb) for a coarse-grained model of DNA, 
> 
> this file includes the "CONECT" section which specifying the connectivity of the coarse-grained beads.
> 
> I have tried the following commands:
> 
> load cg_dna.pdb, cg
> set connect_mode, 1
> show spheres
> show sticks
> 
> 
> But still I can not see the bonds showing in the image.  I searched a lot but still have no clue how to show the bonds between the coarse-grained beads.
> 
> Can anyone help me? Thanks!!

Hi Aiqun Huang,

It puzzled me for a while. I found that renaming all 'K' atoms to 'C' the
bonds are drawn correctly. That still puzzles me, but at least it offers a
way to get the desired view.

Are you actually running simulations with this model? And are you
interested in converting the CG model back to atomistic?

Cheers,

Tsjerk



On Mon, Oct 14, 2013 at 2:32 AM, Aiqun Huang <all...@gm...> wrote:

> Hi dear PyMol users,
>
> I am new to PyMol. I have a pdb file(see attached cg_dna.pdb) for a
> coarse-grained model of DNA,
>
> this file includes the "CONECT" section which specifying the connectivity
> of the coarse-grained beads.
>
> I have tried the following commands:
>
> load cg_dna.pdb, cg
> set connect_mode, 1
> show spheres
> show sticks
>
>
> But still I can not see the bonds showing in the image.  I searched a lot
> but still have no clue how to show the bonds between the coarse-grained
> beads.
>
> Can anyone help me? Thanks!!
>
>
> ------------------------------------------------------------------------------
> October Webinars: Code for Performance
> Free Intel webinars can help you accelerate application performance.
> Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most
> from
> the latest Intel processors and coprocessors. See abstracts and register >
> http://pubads.g.doubleclick.net/gampad/clk?id=60134071&iu=/4140/ostg.clktrk
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Tsjerk A. Wassenaar, Ph.D.

With the help of NVIDIA support (very good), I was able to solve the
problem I was having displaying 3D using my NVIDIA 3d vision and NVIDIA
K600 video card.  It was actually simple, and I should have worked it out
myself.  I  just had to set the scan rate from 60 to  120Hz.

Dick

In my first e-mail I made a mistake a protonated His is a charged His.

Thanks to the guidance of Jason I found that the more convenient way to
solve my problem was modifying the file
"/usr/lib/python2.7/dist-packages/pymol/editor.py", inside that file there
is dictionary, relating the names of the pkl fragments (located in the
"/usr/share/chempy/fragments" folder) with a One letter code. I use
lowercase for the neutral Asp, Glu, Lys and Arg and also lowercase for the
protonated His (the default His in PyMOL is the neutral NE2 tautomer).


_aa_codes =  {
    'A' : 'ala',
    'B' : 'ace',
    'C' : 'cys',
    'D' : 'asp',
    'd' : 'asph',
    'E' : 'glu',
    'e' : 'gluh',
    'F' : 'phe',
    'G' : 'gly',
    'H' : 'his',
    'h' : 'hip',
    'I' : 'ile',
    'K' : 'lys',
    'k' : 'lysn',
    'L' : 'leu',
    'M' : 'met',
    'N' : 'asn',
    'P' : 'pro',
    'Q' : 'gln',
    'R' : 'arg',
    'r' : 'argn',
    'S' : 'ser',
    'T' : 'thr',
    'V' : 'val',
    'W' : 'trp',
    'Y' : 'tyr',
    'Z' : 'nme',
    }


Cheers,

Osvaldo


On Fri, Oct 11, 2013 at 3:25 PM, Osvaldo Martin <alo...@gm...>wrote:

> Thanks for the tip!
>
>
>
> On Fri, Oct 11, 2013 at 8:53 AM, Jason Vertrees <
> jas...@sc...> wrote:
>
>> Osvaldo,
>>
>> To make PyMOL pick fragments from another location just edit the path
>> at the top of pymol/modules/chempy/fragments/__init__.py.
>>
>> The fab command is in pymol/modules/pymol/editor.py.
>>
>> Cheers,
>>
>> -- Jason
>>
>>
>>
>> On Thu, Oct 10, 2013 at 11:38 PM, Osvaldo Martin <alo...@gm...>
>> wrote:
>> > BTW, there is an easy option to make cmd.fab() to pick the fragments
>> from an
>> > alternative location? (just to avoid modifying the original fragments
>> files)
>> >
>> > thanks,
>> >
>> > Osvaldo.
>> >
>> > On Fri, Oct 11, 2013 at 12:32 AM, Osvaldo Martin <alo...@gm...
>> >
>> > wrote:
>> >>
>> >> Ok, I will try editing those files.
>> >>
>> >> Cheers,
>> >>
>> >> Osvaldo.
>> >>
>> >>
>> >>
>> >> On Fri, Oct 11, 2013 at 12:12 AM, Jason Vertrees
>> >> <jas...@sc...> wrote:
>> >>>
>> >>> Hi Osvaldo,
>> >>>
>> >>> This isn't built in yet. But, if you need to do that, you can edit the
>> >>> Python picked files found here:
>> >>>
>> >>> pymol/data/chempy/fragments
>> >>>
>> >>> Cheers
>> >>>
>> >>> -- Jason
>> >>>
>> >>> On Thu, Oct 10, 2013 at 2:41 PM, Osvaldo Martin <
>> alo...@gm...>
>> >>> wrote:
>> >>> >
>> >>> > I am using the comand cmd.fab() to create small peptides. There is
>> an
>> >>> > easy
>> >>> > option to add neutral aminoacids? The default behaviour is to add
>> >>> > charged
>> >>> > amino acids with the charge of the free amino acid in solution at
>> pH =
>> >>> > 7
>> >>> > i.e. Lys and Arg protonated and Glu, Asp and His unprotonated.
>> >>> >
>> >>> > Thanks in advance.
>> >>> >
>> >>> >
>> >>> >
>> ------------------------------------------------------------------------------
>> >>> > October Webinars: Code for Performance
>> >>> > Free Intel webinars can help you accelerate application performance.
>> >>> > Explore tips for MPI, OpenMP, advanced profiling, and more. Get the
>> >>> > most
>> >>> > from
>> >>> > the latest Intel processors and coprocessors. See abstracts and
>> >>> > register >
>> >>> >
>> >>> >
>> http://pubads.g.doubleclick.net/gampad/clk?id=60134071&iu=/4140/ostg.clktrk
>> >>> > _______________________________________________
>> >>> > PyMOL-users mailing list (PyM...@li...)
>> >>> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> >>> > Archives:
>> http://www.mail-archive.com/pym...@li...
>> >>>
>> >>>
>> >>>
>> >>> --
>> >>> Jason Vertrees, PhD
>> >>> Director of Core Modeling Products
>> >>> Schrödinger, Inc.
>> >>>
>> >>> (e) Jas...@sc...
>> >>> (o) +1 (603) 374-7120
>> >>
>> >>
>> >
>>
>>
>>
>> --
>> Jason Vertrees, PhD
>> Director of Core Modeling Products
>> Schrödinger, Inc.
>>
>> (e) Jas...@sc...
>> (o) +1 (603) 374-7120
>>
>
>

Hi Claus,

going from the example on the PyMOLWiki, which uses also one structure with ligand and one without:

fetch 1akeA 4akeA, async=0
align 1akeA, 4akeA
morph mout, 1akeA, 4akeA
extract ligand, 1akeA and organic
hide everything
show cartoon, mout
show sticks, ligand

The ligand can't be part of the morphed multi-state object (mout), because there are no target coordinates for it. But if you just extract it to a separate object (with one state), it still can be part of a movie and even move around independently. Try this:

mset 1-30
unset movie_auto_store
mview store, 1, object=ligand
translate [10,0,0], object=ligand
mview store, 30, object=ligand

(this might move in a silly direction, but you get the idea...)

Cheers,
  Thomas

On Oct 11, 2013, at 9:59 AM, "Kuhn, Claus-Dieter" <ku...@cs...> wrote:
> Hi everyone,
> 
> I am trying to use the new morph command with incentive Pymol 1.6. The 2 states I am morphing between show an enzyme, which closes its active site over an incoming small molecule, meaning, the small molecule is only present in the second structure.
> How can I get Pymol to display the small molecule during morphing? 
> I always receive an error message where Pymol tells me that it couldnt recognize the small molecule. Is there a way I can load a library into Pymol as can be easily done in Coot?
> 
> Thanks for any advice,
> 
> Claus
> 
> Cold Spring Harbor Laboratory
> Cold Spring Harbor, NY, USA