pymol-users

[PyMOL] Hiding individual dash/distance objects within a merged-dash object

[Harry J. <hj...@ca...>]

Hi Everyone,

I'd like to ask for some help with dash/distance objects. I have PyMOL session files  which show inter-molecular interactions using PyMOL distance objects. These were created using a script which colours each distance object and merges them according to type of interaction. The problem I'm having is that I would prefer to visualise the interactions on a per-residue basis, i.e. showing all the interactions for one or more residues but not the others, but as the dashes are merged by interaction type I can only hide by that category. Extensive Googling has not led me to a solution to select and hide individual dashes that are merged into one UI object, so I'd like to ask if it is possible to do this? I'm unfortunately no longer able to run the script again (I am at the end of a time limited project and am preparing figures) and I would prefer not to replace each dash manually.

I hope this is clear, the crux of what I am asking is if it is possible to select and/or hide individual distance objects in a pymol session after they have been merged into one object. Un-merging them would also be an attractive solution.

Thanks,

Harry

Re: [PyMOL] Hiding individual dash/distance objects within a merged-dash object

[Michael L. <mgl...@gm...>]

Hi Harry,

If they've been combined using the group command, you can ungroup them:

fetch 1rx1
# make some distance objects
dist measure01, 19/C, 20/C
dist measure02, 20/C, 21/C
dist measure03, 158/C, 159/C
dist measure04, 157/C, 159/C
# group them
group g1, measure01 or measure02
group g2, measure03 or measure04
#ungroup all of them (this leaves empty groups, which you can delete if
you'd like)
ungroup measure*

Hope that helps,

-Michael

On Tue, Apr 26, 2011 at 5:47 AM, Harry Jubb <hj...@ca...> wrote:

> Hi Everyone,
>
> I'd like to ask for some help with dash/distance objects. I have PyMOL
> session files  which show inter-molecular interactions using PyMOL distance
> objects. These were created using a script which colours each distance
> object and merges them according to type of interaction. The problem I'm
> having is that I would prefer to visualise the interactions on a per-residue
> basis, i.e. showing all the interactions for one or more residues but not
> the others, but as the dashes are merged by interaction type I can only hide
> by that category. Extensive Googling has not led me to a solution to select
> and hide individual dashes that are merged into one UI object, so I'd like
> to ask if it is possible to do this? I'm unfortunately no longer able to run
> the script again (I am at the end of a time limited project and am preparing
> figures) and I would prefer not to replace each dash manually.
>
> I hope this is clear, the crux of what I am asking is if it is possible to
> select and/or hide individual distance objects in a pymol session after they
> have been merged into one object. Un-merging them would also be an
> attractive solution.
>
> Thanks,
>
> Harry
>
> ------------------------------------------------------------------------------
> WhatsUp Gold - Download Free Network Management Software
> The most intuitive, comprehensive, and cost-effective network
> management toolset available today.  Delivers lowest initial
> acquisition cost and overall TCO of any competing solution.
> http://p.sf.net/sfu/whatsupgold-sd
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909, MSC 9314
Rockville, MD 20852 (UPS/FedEx/Reality)
Bethesda MD 20892-9314 (USPS)

Re: [PyMOL] Hiding individual dash/distance objects within a merged-dash object

[Harry J. <hj...@ca...>]

Hi Michael,

Thank you for your response. The problem is that for types of inter-molecular interaction all of the visual distances are merged into one object in the sidebar (as if created using the measurement wizard with the "merge with previous" option on), for which unfortunately the ungroup command doesn't seem to work for. Left-clicking on the interaction type in the GUI sidebar toggles show/hide for every distance of that interaction type, and there are no further disclosure squares which indicates that the distances are grouped rather than merged. Ideally I'd like to be able to un-merge these objects to make each dash an object that I can hide or show individually so I can switch off the ones not connected to a residue of interest. Even better (if possible) would be to only show dashes connected to a residue of choice.

I hope that makes sense. Thank you for your help,

Harry


On 26 Apr 2011, at 13:59, Michael Lerner wrote:

> Hi Harry,
> 
> If they've been combined using the group command, you can ungroup them:
> 
> fetch 1rx1
> # make some distance objects
> dist measure01, 19/C, 20/C
> dist measure02, 20/C, 21/C
> dist measure03, 158/C, 159/C
> dist measure04, 157/C, 159/C
> # group them
> group g1, measure01 or measure02
> group g2, measure03 or measure04
> #ungroup all of them (this leaves empty groups, which you can delete if you'd like)
> ungroup measure*
> 
> Hope that helps,
> 
> -Michael
> 
> On Tue, Apr 26, 2011 at 5:47 AM, Harry Jubb <hj...@ca...> wrote:
> Hi Everyone,
> 
> I'd like to ask for some help with dash/distance objects. I have PyMOL session files  which show inter-molecular interactions using PyMOL distance objects. These were created using a script which colours each distance object and merges them according to type of interaction. The problem I'm having is that I would prefer to visualise the interactions on a per-residue basis, i.e. showing all the interactions for one or more residues but not the others, but as the dashes are merged by interaction type I can only hide by that category. Extensive Googling has not led me to a solution to select and hide individual dashes that are merged into one UI object, so I'd like to ask if it is possible to do this? I'm unfortunately no longer able to run the script again (I am at the end of a time limited project and am preparing figures) and I would prefer not to replace each dash manually.
> 
> I hope this is clear, the crux of what I am asking is if it is possible to select and/or hide individual distance objects in a pymol session after they have been merged into one object. Un-merging them would also be an attractive solution.
> 
> Thanks,
> 
> Harry
> ------------------------------------------------------------------------------
> WhatsUp Gold - Download Free Network Management Software
> The most intuitive, comprehensive, and cost-effective network
> management toolset available today.  Delivers lowest initial
> acquisition cost and overall TCO of any competing solution.
> http://p.sf.net/sfu/whatsupgold-sd
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
> 
> 
> 
> -- 
> Michael Lerner, Ph.D.
> IRTA Postdoctoral Fellow
> Laboratory of Computational Biology NIH/NHLBI
> 5635 Fishers Lane, Room T909, MSC 9314
> Rockville, MD 20852 (UPS/FedEx/Reality)
> Bethesda MD 20892-9314 (USPS)

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

Harry Jubb
Part II Biochemistry
Homerton College

UTN: 131 2726
M: 0790 813 4735

Re: [PyMOL] Hiding individual dash/distance objects within a merged-dash object

[Michael L. <mgl...@gm...>]

Hi Harry,

As far as I know, this is not currently possible in PyMOL, but perhaps
someone will correct me on this.

-Michael

On Tue, Apr 26, 2011 at 9:27 AM, Harry Jubb <hj...@ca...> wrote:

> Hi Michael,
>
> Thank you for your response. The problem is that for types of
> inter-molecular interaction all of the visual distances are merged into one
> object in the sidebar (as if created using the measurement wizard with the
> "merge with previous" option on), for which unfortunately the ungroup
> command doesn't seem to work for. Left-clicking on the interaction type in
> the GUI sidebar toggles show/hide for every distance of that interaction
> type, and there are no further disclosure squares which indicates that the
> distances are grouped rather than merged. Ideally I'd like to be able to
> un-merge these objects to make each dash an object that I can hide or show
> individually so I can switch off the ones not connected to a residue of
> interest. Even better (if possible) would be to only show dashes connected
> to a residue of choice.
>
> I hope that makes sense. Thank you for your help,
>
> Harry
>
>
> On 26 Apr 2011, at 13:59, Michael Lerner wrote:
>
> Hi Harry,
>
> If they've been combined using the group command, you can ungroup them:
>
> fetch 1rx1
> # make some distance objects
> dist measure01, 19/C, 20/C
> dist measure02, 20/C, 21/C
> dist measure03, 158/C, 159/C
> dist measure04, 157/C, 159/C
> # group them
> group g1, measure01 or measure02
> group g2, measure03 or measure04
> #ungroup all of them (this leaves empty groups, which you can delete if
> you'd like)
> ungroup measure*
>
> Hope that helps,
>
> -Michael
>
> On Tue, Apr 26, 2011 at 5:47 AM, Harry Jubb <hj...@ca...> wrote:
>
>> Hi Everyone,
>>
>> I'd like to ask for some help with dash/distance objects. I have PyMOL
>> session files  which show inter-molecular interactions using PyMOL distance
>> objects. These were created using a script which colours each distance
>> object and merges them according to type of interaction. The problem I'm
>> having is that I would prefer to visualise the interactions on a per-residue
>> basis, i.e. showing all the interactions for one or more residues but not
>> the others, but as the dashes are merged by interaction type I can only hide
>> by that category. Extensive Googling has not led me to a solution to select
>> and hide individual dashes that are merged into one UI object, so I'd like
>> to ask if it is possible to do this? I'm unfortunately no longer able to run
>> the script again (I am at the end of a time limited project and am preparing
>> figures) and I would prefer not to replace each dash manually.
>>
>> I hope this is clear, the crux of what I am asking is if it is possible to
>> select and/or hide individual distance objects in a pymol session after they
>> have been merged into one object. Un-merging them would also be an
>> attractive solution.
>>
>> Thanks,
>>
>> Harry
>>
>> ------------------------------------------------------------------------------
>> WhatsUp Gold - Download Free Network Management Software
>> The most intuitive, comprehensive, and cost-effective network
>> management toolset available today.  Delivers lowest initial
>> acquisition cost and overall TCO of any competing solution.
>> http://p.sf.net/sfu/whatsupgold-sd
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>
>
>
> --
> Michael Lerner, Ph.D.
> IRTA Postdoctoral Fellow
> Laboratory of Computational Biology NIH/NHLBI
> 5635 Fishers Lane, Room T909, MSC 9314
> Rockville, MD 20852 (UPS/FedEx/Reality)
> Bethesda MD 20892-9314 (USPS)
>
>
>   -----------------------------------
>
> Harry Jubb
> Part II Biochemistry
> Homerton College
>
> UTN: 131 2726
> M: 0790 813 4735
>
>


-- 
Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909, MSC 9314
Rockville, MD 20852 (UPS/FedEx/Reality)
Bethesda MD 20892-9314 (USPS)

Re: [PyMOL] Hiding individual dash/distance objects within a merged-dash object

[Hongbo Z. <hon...@bi...>]

Hi, Harry,

I am curious. How do you merge objects resulting from >>distance<< ? Do 
you mean to "group" them? If so, you can use ungroup command to, well, 
ungroup them. But if the merged object is generated using a CGO, I doubt 
you can unmerge the CGO object. But I don't know dash CGOs, either. 
(Unless you make dashes using small line fragments :)

So do you have dashes or solid lines? Do you see a plus sign before the 
object in PyMOL?

hongbo

On 04/26/2011 11:47 AM, Harry Jubb wrote:
> Hi Everyone,
>
> I'd like to ask for some help with dash/distance objects. I have PyMOL session files  which show inter-molecular interactions using PyMOL distance objects. These were created using a script which colours each distance object and merges them according to type of interaction. The problem I'm having is that I would prefer to visualise the interactions on a per-residue basis, i.e. showing all the interactions for one or more residues but not the others, but as the dashes are merged by interaction type I can only hide by that category. Extensive Googling has not led me to a solution to select and hide individual dashes that are merged into one UI object, so I'd like to ask if it is possible to do this? I'm unfortunately no longer able to run the script again (I am at the end of a time limited project and am preparing figures) and I would prefer not to replace each dash manually.
>
> I hope this is clear, the crux of what I am asking is if it is possible to select and/or hide individual distance objects in a pymol session after they have been merged into one object. Un-merging them would also be an attractive solution.
>
> Thanks,
>
> Harry
> ------------------------------------------------------------------------------
> WhatsUp Gold - Download Free Network Management Software
> The most intuitive, comprehensive, and cost-effective network
> management toolset available today.  Delivers lowest initial
> acquisition cost and overall TCO of any competing solution.
> http://p.sf.net/sfu/whatsupgold-sd
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

Re: [PyMOL] Hiding individual dash/distance objects within a merged-dash object

[Jason V. <jas...@sc...>]

Hi Harry,

For "measures" (distances, angles, dihedrals), PyMOL can color down to
the level of an object (eg. color blue, measure01).  So, once you add
another measure into an extant object, PyMOL cannot separate those two
colors.  My suggestion is that you measure into new objects if you
need new coloring.  If you have lots of measurements as a result, then
you can group them and color by wildcard.

Cheers,

-- Jason

On Tue, Apr 26, 2011 at 5:47 AM, Harry Jubb <hj...@ca...> wrote:
> Hi Everyone,
>
> I'd like to ask for some help with dash/distance objects. I have PyMOL session files  which show inter-molecular interactions using PyMOL distance objects. These were created using a script which colours each distance object and merges them according to type of interaction. The problem I'm having is that I would prefer to visualise the interactions on a per-residue basis, i.e. showing all the interactions for one or more residues but not the others, but as the dashes are merged by interaction type I can only hide by that category. Extensive Googling has not led me to a solution to select and hide individual dashes that are merged into one UI object, so I'd like to ask if it is possible to do this? I'm unfortunately no longer able to run the script again (I am at the end of a time limited project and am preparing figures) and I would prefer not to replace each dash manually.
>
> I hope this is clear, the crux of what I am asking is if it is possible to select and/or hide individual distance objects in a pymol session after they have been merged into one object. Un-merging them would also be an attractive solution.
>
> Thanks,
>
> Harry
> ------------------------------------------------------------------------------
> WhatsUp Gold - Download Free Network Management Software
> The most intuitive, comprehensive, and cost-effective network
> management toolset available today.  Delivers lowest initial
> acquisition cost and overall TCO of any competing solution.
> http://p.sf.net/sfu/whatsupgold-sd
> _______________________________________________
> 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
PyMOL Product Manager
Schrodinger, LLC

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

Re: [PyMOL] Hiding individual dash/distance objects within a merged-dash object

[Harry J. <hj...@ca...>]

Hi Jason,

Thanks for your response. The colouring is all correct as there is an object for each interaction type, the problem now is splitting the measures back into single objects, which Dr Lerner has mentioned is not currently possible. If this is the case I will try to refine my figures another way, the main objective was to selectively hide all the dashes except for those connected to a residue of interest purely for clarity of presentation.

Thanks once more,

Harry

On 26 Apr 2011, at 15:50, Jason Vertrees wrote:

> Hi Harry,
> 
> For "measures" (distances, angles, dihedrals), PyMOL can color down to
> the level of an object (eg. color blue, measure01).  So, once you add
> another measure into an extant object, PyMOL cannot separate those two
> colors.  My suggestion is that you measure into new objects if you
> need new coloring.  If you have lots of measurements as a result, then
> you can group them and color by wildcard.
> 
> Cheers,
> 
> -- Jason
> 
> On Tue, Apr 26, 2011 at 5:47 AM, Harry Jubb <hj...@ca...> wrote:
>> Hi Everyone,
>> 
>> I'd like to ask for some help with dash/distance objects. I have PyMOL session files  which show inter-molecular interactions using PyMOL distance objects. These were created using a script which colours each distance object and merges them according to type of interaction. The problem I'm having is that I would prefer to visualise the interactions on a per-residue basis, i.e. showing all the interactions for one or more residues but not the others, but as the dashes are merged by interaction type I can only hide by that category. Extensive Googling has not led me to a solution to select and hide individual dashes that are merged into one UI object, so I'd like to ask if it is possible to do this? I'm unfortunately no longer able to run the script again (I am at the end of a time limited project and am preparing figures) and I would prefer not to replace each dash manually.
>> 
>> I hope this is clear, the crux of what I am asking is if it is possible to select and/or hide individual distance objects in a pymol session after they have been merged into one object. Un-merging them would also be an attractive solution.
>> 
>> Thanks,
>> 
>> Harry
>> ------------------------------------------------------------------------------
>> WhatsUp Gold - Download Free Network Management Software
>> The most intuitive, comprehensive, and cost-effective network
>> management toolset available today.  Delivers lowest initial
>> acquisition cost and overall TCO of any competing solution.
>> http://p.sf.net/sfu/whatsupgold-sd
>> _______________________________________________
>> 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
> PyMOL Product Manager
> Schrodinger, LLC
> 
> (e) Jas...@sc...
> (o) +1 (603) 374-7120

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

Harry Jubb
Part II Biochemistry
Homerton College

UTN: 131 2726
M: 0790 813 4735