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Re: [PyMOL] electron density map

From: Troels Emtekær Linnet <tlinnet@gm...> - 2011-08-24 20:58

Have you tried this:

load run02-Protein-ANP-BA_ligands_omitmap.map.ccp4, fofc-map
isomesh +fofc_all, fofc-map, 3 , within_Ba , carve=1.5
isomesh -fofc_all, fofc-map, -3 , within_Ba , carve=1.5
color green, +fofc_all
color red, -fofc_all
set mesh_width=0.75, +fofc_all
set mesh_width=0.75, -fofc_all


2011/8/24 Jason Vertrees <jason.vertrees@...>

> Hi Claudia,
>
> We can't yet copy/extend maps. For the time being, you need to use
> symmetry expansion on your molecule to get them into the density. See,
>
> * -- http://www.pymolwiki.org/index.php/Symexp
> * -- http://www.pymolwiki.org/index.php/Supercell
>
> Cheers,
>
> -- Jason
>
> On Wed, Aug 24, 2011 at 3:57 PM, DelCampo, Claudia
> <Claudia.DelCampo@...> wrote:
> >
> > Hello,
> >
> > I am trying to display a ccp4 map together with my protein model in
> Pymol. I followed the directions given in Pymol-wiki: "display ccp4 maps"
> and I get to see the map but it is not superimposed with the protein
> structure. How can i get the map to be positioned correctly?
> >
> > Thanks for your help!
> >
> > Post-doc
> > Lambright Lab
> > Program in Molecular Medicine
> > Biotech Two - UMMS
> > Phone:508-856-1087
> >
> >
> ------------------------------------------------------------------------------
> > EMC VNX: the world's simplest storage, starting under $10K
> > The only unified storage solution that offers unified management
> > Up to 160% more powerful than alternatives and 25% more efficient.
> > Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev
> > _______________________________________________
> > PyMOL-users mailing list (PyMOL-users@...)
> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > Archives: http://www.mail-archive.com/pymol-users@...>
> >
>
>
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
>
> (e) Jason.Vertrees@...
> (o) +1 (603) 374-7120
>
>
> ------------------------------------------------------------------------------
> EMC VNX: the world's simplest storage, starting under $10K
> The only unified storage solution that offers unified management
> Up to 160% more powerful than alternatives and 25% more efficient.
> Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev
> _______________________________________________
> PyMOL-users mailing list (PyMOL-users@...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@...>
>

Thread View

Thread	Author	Date
[PyMOL] electron density map	shivesh kumar <shivesh_sls@ya...>

[PyMOL] electron density map

From: DelCampo, Claudia <Claudia.DelCampo@um...> - 2011-08-24 19:57

Hello,

I am trying to display a ccp4 map together with my protein model in Pymol. I followed the directions given in Pymol-wiki: "display ccp4 maps" and I get to see the map but it is not superimposed with the protein structure. How can i get the map to be positioned correctly?

Thanks for your help!

Post-doc
Lambright Lab
Program in Molecular Medicine
Biotech Two - UMMS
Phone:508-856-1087

Re: [PyMOL] electron density map

From: Jason Vertrees <jason.vertrees@sc...> - 2011-08-24 20:03

Hi Claudia,

We can't yet copy/extend maps. For the time being, you need to use
symmetry expansion on your molecule to get them into the density. See,

* -- http://www.pymolwiki.org/index.php/Symexp
* -- http://www.pymolwiki.org/index.php/Supercell

Cheers,

-- Jason

On Wed, Aug 24, 2011 at 3:57 PM, DelCampo, Claudia
<Claudia.DelCampo@...> wrote:
>
> Hello,
>
> I am trying to display a ccp4 map together with my protein model in Pymol. I followed the directions given in Pymol-wiki: "display ccp4 maps" and I get to see the map but it is not superimposed with the protein structure. How can i get the map to be positioned correctly?
>
> Thanks for your help!
>
> Post-doc
> Lambright Lab
> Program in Molecular Medicine
> Biotech Two - UMMS
> Phone:508-856-1087
>
> ------------------------------------------------------------------------------
> EMC VNX: the world's simplest storage, starting under $10K
> The only unified storage solution that offers unified management
> Up to 160% more powerful than alternatives and 25% more efficient.
> Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev
> _______________________________________________
> PyMOL-users mailing list (PyMOL-users@...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@...>
>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jason.Vertrees@...
(o) +1 (603) 374-7120

Re: [PyMOL] electron density map

From: Troels Emtekær Linnet <tlinnet@gm...> - 2011-08-24 20:58

Attachments: Message as HTML

Have you tried this:

load run02-Protein-ANP-BA_ligands_omitmap.map.ccp4, fofc-map
isomesh +fofc_all, fofc-map, 3 , within_Ba , carve=1.5
isomesh -fofc_all, fofc-map, -3 , within_Ba , carve=1.5
color green, +fofc_all
color red, -fofc_all
set mesh_width=0.75, +fofc_all
set mesh_width=0.75, -fofc_all


2011/8/24 Jason Vertrees <jason.vertrees@...>

> Hi Claudia,
>
> We can't yet copy/extend maps. For the time being, you need to use
> symmetry expansion on your molecule to get them into the density. See,
>
> * -- http://www.pymolwiki.org/index.php/Symexp
> * -- http://www.pymolwiki.org/index.php/Supercell
>
> Cheers,
>
> -- Jason
>
> On Wed, Aug 24, 2011 at 3:57 PM, DelCampo, Claudia
> <Claudia.DelCampo@...> wrote:
> >
> > Hello,
> >
> > I am trying to display a ccp4 map together with my protein model in
> Pymol. I followed the directions given in Pymol-wiki: "display ccp4 maps"
> and I get to see the map but it is not superimposed with the protein
> structure. How can i get the map to be positioned correctly?
> >
> > Thanks for your help!
> >
> > Post-doc
> > Lambright Lab
> > Program in Molecular Medicine
> > Biotech Two - UMMS
> > Phone:508-856-1087
> >
> >
> ------------------------------------------------------------------------------
> > EMC VNX: the world's simplest storage, starting under $10K
> > The only unified storage solution that offers unified management
> > Up to 160% more powerful than alternatives and 25% more efficient.
> > Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev
> > _______________________________________________
> > PyMOL-users mailing list (PyMOL-users@...)
> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > Archives: http://www.mail-archive.com/pymol-users@...>
> >
>
>
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
>
> (e) Jason.Vertrees@...
> (o) +1 (603) 374-7120
>
>
> ------------------------------------------------------------------------------
> EMC VNX: the world's simplest storage, starting under $10K
> The only unified storage solution that offers unified management
> Up to 160% more powerful than alternatives and 25% more efficient.
> Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev
> _______________________________________________
> PyMOL-users mailing list (PyMOL-users@...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@...>
>

Re: [PyMOL] electron density map

From: Jason Vertrees <jason.vertrees@sc...> - 2011-08-24 22:17

Hi Troels,

Thanks--I did forget about carving!

PyMOL still needs easier map extending, though.

Cheers,

-- Jason

2011/8/24 Troels Emtekær Linnet <tlinnet@...>:
> Have you tried this:
>
> load run02-Protein-ANP-BA_ligands_omitmap.map.ccp4, fofc-map
> isomesh +fofc_all, fofc-map, 3 , within_Ba , carve=1.5
> isomesh -fofc_all, fofc-map, -3 , within_Ba , carve=1.5
> color green, +fofc_all
> color red, -fofc_all
> set mesh_width=0.75, +fofc_all
> set mesh_width=0.75, -fofc_all
>
>
> 2011/8/24 Jason Vertrees <jason.vertrees@...>
>>
>> Hi Claudia,
>>
>> We can't yet copy/extend maps. For the time being, you need to use
>> symmetry expansion on your molecule to get them into the density. See,
>>
>> * -- http://www.pymolwiki.org/index.php/Symexp
>> * -- http://www.pymolwiki.org/index.php/Supercell
>>
>> Cheers,
>>
>> -- Jason
>>
>> On Wed, Aug 24, 2011 at 3:57 PM, DelCampo, Claudia
>> <Claudia.DelCampo@...> wrote:
>> >
>> > Hello,
>> >
>> > I am trying to display a ccp4 map together with my protein model in
>> > Pymol. I followed the directions given in Pymol-wiki: "display ccp4 maps"
>> > and I get to see the map but it is not superimposed with the protein
>> > structure. How can i get the map to be positioned correctly?
>> >
>> > Thanks for your help!
>> >
>> > Post-doc
>> > Lambright Lab
>> > Program in Molecular Medicine
>> > Biotech Two - UMMS
>> > Phone:508-856-1087
>> >
>> >
>> > ------------------------------------------------------------------------------
>> > EMC VNX: the world's simplest storage, starting under $10K
>> > The only unified storage solution that offers unified management
>> > Up to 160% more powerful than alternatives and 25% more efficient.
>> > Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev
>> > _______________________________________________
>> > PyMOL-users mailing list (PyMOL-users@...)
>> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> > Archives: http://www.mail-archive.com/pymol-users@...>
>> >
>>
>>
>>
>> --
>> Jason Vertrees, PhD
>> PyMOL Product Manager
>> Schrodinger, LLC
>>
>> (e) Jason.Vertrees@...
>> (o) +1 (603) 374-7120
>>
>>
>> ------------------------------------------------------------------------------
>> EMC VNX: the world's simplest storage, starting under $10K
>> The only unified storage solution that offers unified management
>> Up to 160% more powerful than alternatives and 25% more efficient.
>> Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev
>> _______________________________________________
>> PyMOL-users mailing list (PyMOL-users@...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pymol-users@...>
>
>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jason.Vertrees@...
(o) +1 (603) 374-7120

Re: [PyMOL] electron density map

From: Francis E Reyes <Francis.Reyes@Co...> - 2011-08-24 22:21

And support to parse mtz's and calculate map coefficients on the fly. :)


On Aug 24, 2011, at 3:11 PM, Jason Vertrees wrote:

> PyMOL still needs easier map extending, though.



---------------------------------------------
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder

Re: [PyMOL] electron density map

From: Jason Vertrees <jason.vertrees@sc...> - 2011-08-24 23:32

Hi Francis,

> And support to parse mtz's and calculate map coefficients on the fly. :)

Incentive PyMOL already reads MTZ maps--we added that a few months
ago. It'll also auto-open MTZ files and synthesize the map based on
common defaults. Instructions and demo videos for supporting PyMOL
users can be found here,
http://pymol.org/dsc/dokuwiki/doku.php?id=media:edmaps.

Cheers,

-- Jason

-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jason.Vertrees@...
(o) +1 (603) 374-7120

[PyMOL] electron density map

From: Mehdi Talebzadeh Farooji <mahditzf@ya...> - 2012-11-01 17:07

Attachments: Message as HTML

Dear All,

I am trying to create a electron density map for the pdb file which is not deposited in RCSB bank, however I do not find any option on http://eds.bmc.uu.se/eds/. Is there any way to get density map for the pdb files which are not deposited in pdb data bank?

All the best,

Mehdi

Re: [PyMOL] electron density map

From: Troels Emtekær Linnet <tlinnet@gm...> - 2012-11-01 18:10

Attachments: Message as HTML

Hi mehdi.

Look for inspiration here.
http://www.pymolwiki.org/index.php/Dynamic_mesh

fetch 1HWK, async=1
fetch 1HWK, 1hwk_map, type=2fofc, async=1

Best
Den 01/11/2012 18.09 skrev "Mehdi Talebzadeh Farooji" <mahditzf@...>:

> Dear All,
>
> I am trying to create a electron density map for the pdb file which is not
> deposited in RCSB bank, however I do not find any option on
> http://eds.bmc.uu.se/eds/. Is there any way to get density map for the
> pdb files which are not deposited in pdb data bank?
>
> All the best,
>
> Mehdi
>
>
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_sfd2d_oct
> _______________________________________________
> PyMOL-users mailing list (PyMOL-users@...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@...>
>

Re: [PyMOL] electron density map

From: Edward A. Berry <BerryE@up...> - 2012-11-01 18:26

The electron density we usually display with an atomic model is based on
experimental diffraction data (usually x-ray). The purpose of the density map
is usually to validate the model, i.e. show it is consistent with the map
calculated using experimental data. Even for many structures that are at
the PDB (deposited before 2009?) the data is not available, so you cannot
make an experimental density map. Likewise for NMR structures,
but they have experimental data of a different kind.

If you got the pdb file from a colleague who solved the structure, you can ask
him for the data or for a map. If the structure is a theoretical model that
you built, then the usual reason for showing a density map (to validate the structure)
doesn't exist.

You can calculate a purely theoretical electron density map from any
pdb file using for example CCP4's SFALL  and FFT programs (actually sfall by itself
run in mapout mode, I think). But before you do this you should think about what
you want the map for, and if a theoretical map serves your purpose.
And if you display the model with theoretical electron density, you should
make it very clear that the map is calculated from the model, otherwise
most people will take it as evidence tat you have solved the structure by
crystallography.

HTH,
eab

Mehdi Talebzadeh Farooji wrote:
> Dear All,
>
> I am trying to create a electron density map for the pdb file which is not deposited in RCSB bank, however I do
> not find any option on http://eds.bmc.uu.se/eds/. Is there any way to get density map for the pdb files which are
> not deposited in pdb data bank?
>
> All the best,
>
> Mehdi
>
>
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_sfd2d_oct
>
>
>
> _______________________________________________
> PyMOL-users mailing list (PyMOL-users@...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@...>

[PyMOL] electron density map

From: amna khan <amnakhan369@gm...> - 2012-11-11 09:24

Attachments: Message as HTML

hi,

i want to calculate the electeon density maps for my docked protein from
autodock4.2, when i load. fld.maps file genrated by autodocked and my
docked protein at smae tme , no maps are generated.

please help

regards

Re: [PyMOL] electron density map

From: Folmer Fredslund <folmerf@gm...> - 2012-11-11 12:22

Attachments: Message as HTML

Dear Amna (?),


2012/11/11 amna khan <amnakhan369@...>

> hi,
>
> i want to calculate the electron density maps for my docked protein from
> autodock4.2, when i load. fld.maps file generated by autodock and my docked
> protein at same time , no maps are generated.
>


1. electron density maps are calculated from experimental data and model
phases. No computer program will ever give you any (real) electron density.
I think you are confusing the terms here.

2. Are you trying to dock a ligand, or dock two proteins together?  There
is a very nice plugin (http://www.pymolwiki.org/index.php/Autodock_plugin)
by Daniel Seeliger. I would use that.

Hope this helps

Folmer Fredslund







>
> please help
>
> regards
>
>
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_nov
> _______________________________________________
> PyMOL-users mailing list (PyMOL-users@...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@...>
>



-- 
Folmer Fredslund

Re: [PyMOL] electron density map

From: Folmer Fredslund <folmerf@gm...> - 2012-11-12 10:54

Attachments: Message as HTML

Dear Amna (?),


2012/11/12 amna khan <amnakhan369@...>

> i have docked ligand with protein and final docked protein containing
> ligand conformation have been generated into one file. Now for this
> docked ligand-protein structure i want to calculate the electron dennsity
> map by pymol.
>
>

If I understand correctly, what you are doing does not make any sense (I am
a protein crystallographer...)

To the best of my knowledge, what you are trying to do is not possible.

With best intentions,

Folmer



>
>
> On Sun, Nov 11, 2012 at 5:22 PM, Folmer Fredslund <folmerf@...:
>
>> Dear Amna (?),
>>
>>
>> 2012/11/11 amna khan <amnakhan369@...>
>>
>>> hi,
>>>
>>> i want to calculate the electron density maps for my docked protein from
>>> autodock4.2, when i load. fld.maps file generated by autodock and my docked
>>> protein at same time , no maps are generated.
>>>
>>
>>
>> 1. electron density maps are calculated from experimental data and model
>> phases. No computer program will ever give you any (real) electron density.
>> I think you are confusing the terms here.
>>
>> 2. Are you trying to dock a ligand, or dock two proteins together?  There
>> is a very nice plugin (http://www.pymolwiki.org/index.php/Autodock_plugin)
>> by Daniel Seeliger. I would use that.
>>
>> Hope this helps
>>
>> Folmer Fredslund
>>
>>
>>
>>
>>
>>
>>
>>>
>>> please help
>>>
>>> regards
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Everyone hates slow websites. So do we.
>>> Make your web apps faster with AppDynamics
>>> Download AppDynamics Lite for free today:
>>> http://p.sf.net/sfu/appdyn_d2d_nov
>>> _______________________________________________
>>> PyMOL-users mailing list (PyMOL-users@...)
>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>> Archives: http://www.mail-archive.com/pymol-users@...>
>>>
>>
>>
>>
>> --
>> Folmer Fredslund
>>
>>
>


-- 
Folmer Fredslund