Hi Vatsal,
This is how you show positive and negative contour:
fetch 1ubq, diffmap, type=fofc, async=0
isomesh diffmesh, diffmap, 3.0
color green, diffmesh
set mesh_negative_color, red
set mesh_negative_visible
Example copied from:
https://pymolwiki.org/index.php/mesh_negative_visible
Cheers,
Dear Amna (?),
2012/11/12 amna khan
> 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 corr
Dear Amna (?),
2012/11/11 amna khan
> 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 e
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
t
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" :
> Dear All,
>
> I am trying to create a electron density map for the pdb file which is
Hi Manas Sule,
this is a bit more complicated:
For PyMOL, you usually calculate an electron density map covering your
molecule. As far as I understand PyMOL, the sigma is taken directly from
your input map.
For Coot, this is completely different. Coot tries to reconstruct from
your input ma
Hi Manas,
have you tried turning the normalize_* setting off?
set normalize_ccp4_maps, off
set normalize_o_maps, off
set normalize_grd_maps, off
http://pymolwiki.org/index.php/Normalize_ccp4_maps
http://pymolwiki.org/index.php/Display_CCP4_Maps#User_Notes
Cheers,
Thomas
On 12/06/2011 03:12
Is there a difference in the sigma values assigned by pymol and coot
I am able to see the density at 8 sigma in coot for the Fo-Fc map but can
go to maximum at 4.5 sigma in pymol after which it disappears
On Mon, Dec 5, 2011 at 11:33 PM, Roger Rowlett wrote:
> I think the isomesh comman
I think the isomesh command will let you set
whatever contour level you wish, e.g.:
isomesh map, mymap.map, X.X, maparea
Where map is the name of the mesh object, mymap.map is the map
file name, X.X is the desired contour level, and maparea, is the
Hi Manas,
You have two options: use volumes
(http://www.youtube.com/watch?v=tuAo_8-_HIc; http://pymol.org/volume)
or
isomesh myMesh, theMap, level=6
To change the isomesh level to 7.5 just do,
isolevel myMesh, 7.5
Cheers,
-- Jason
On Mon, Dec 5, 2011 at 12:49 PM, Manas Sule wrote:
> I have
isomesh [mesh name], [map name], 6.0
Manas Sule wrote:
> Is there some way to show electron density at 6 sigma and above in pymol
> especially for metal ions like in Coot?
>
> Manas
>
--
All the data continuously
I have tried that...but i can see the density in coot at even 8 sigma..
however the maximum i can go to in pymol is 4.5 simga on a F0-Fc map
Can u suggest any method to see the same density at 6 sigma
Manas
On Mon, Dec 5, 2011 at 11:14 PM, Pete Meyer wrote:
> isomesh [mesh name], [map name], 6
Hi Sree,
After your map is loaded click: Wizard > Density. The map will
replicate according to the symmetry operators.
Cheers,
-- Jason
On Thu, Dec 1, 2011 at 12:53 PM, SREEJESH SHANKER wrote:
> Hi
>
> I am having trouble to generate an electron density map (2FoFc) around some
> selected resid
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 ca
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
--
Hi Troels,
Thanks--I did forget about carving!
PyMOL still needs easier map extending, though.
Cheers,
-- Jason
2011/8/24 Troels Emtekær Linnet :
> 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
> i
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
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 P
Hi Saif,
I checked the same file in PyMOL and Coot. You're right, there are
some differences at the boundaries, but they still look insignificant.
Maybe you can point out a residue with a large deviation. For this
map, Coot shows large blocks of red/green mesh indicating differences
in the obse
Hi Saif,
Can you please show us the commands you used in PyMOL to load the data
and generate the map? (Also, can you send me a copy of the map and
structure?) Has anyone else seen this problem?
I've looked over a few CCP4 maps in PyMOL, Maestro, and Coot
side-by-side, and at various contours, t
On Thu, Dec 17, 2009 at 10:54 AM, Jason C Porta wrote:
> I have been trying to modify the grid spacing on 2Fo-Fc map that was loaded
> into PyMol directly from phenix.refine. The mesh object is generated from
> the isomesh command. Basically, I would like there to be fewer grid points
> so that t
Jhon,
all the newer builds of PyMol are able to read ccp4 maps, no need to convert to
xplor format.
As far as your commands are concerned, you are almost there.
Try this:
load mymap.ccp4, format=ccp4, mymap
isomesh map, mymap, 2.0, site, carve=1.6
were map is the name of the map graphical obje
2008/9/26 Jhon Thomas :
> hello Mr. Fredslund
>
> I tried the way you have written but it is not working--
>
> map file name - test_map.xplor
> load test_map.xplor
>
> isomeah map, test_map.xplor, 2.0, site, carve=1.6
>
> Is this is the correct of writing the command
Dear Mr. Thomas
Ok, some basi
2008/9/26 Jhon Thomas :
> Hello all pymol users
>
> I am new to pymol and trying to open a .xplor map file in pymol to get the
> electron density map of publication grade.
> The command i write for pymol to open the file and show electron density
> map is -
>
> 1) I convert ccp4 .map file into the
You can do this with the isodot command.
Are you using the PyMOL-APBS plugin to generate or view electron
density maps? If so, would you like me to add dot representations to
the plugin in the next release?
Thanks,
-michael
--
Biophysics Graduate Student
Carlson Lab, University of Michigan
htt
Akanksha,
The carve option to isomesh and isosurface uses a distance-based cutoff for
display around the selected atoms. To accomplish what you seek, you should be
able to simply reduce that cutoff.
Cheers,
Warren
From: pymol-users-ad...@lists.sourceforge
Behalf Of
> dieter blaas
> Sent: Friday, January 28, 2005 1:19 AM
> To: pymol-users@lists.sourceforge.net
> Cc: Warren DeLano
> Subject: RE: [PyMOL] electron density map manipulation
>
> Thanx Warren, perfect! But when entering:
>
> "> load map1.dsn6
> > slic
Scientific LLC
> . 400 Oyster Point Blvd., Suite 213
> . South San Francisco, CA 94080
> . Biz:(650)-872-0942 Tech:(650)-872-0834
> . Fax:(650)-872-0273 Cell:(650)-346-1154
> . mailto:war...@delsci.com
>
>
> > -----Original Message-
> >
On Sun, 08 Aug 2004 17:57:00 -0400, christopher faehnle
wrote:
I am a new pymol user and am trying to load an electron density map
(ccp4 format). When I do this nothing happens. Any suggestions, tips,
etc would be appreciated.
The map probably loads just fine (there should be a new obj
Robert,
If you're using version 0.93 or greater, set mesh_width, value
will adjust the mesh thickness in units of pixels. Something in the
range of 1.5-2.5 usually works best.
set mesh_width,2.0
ray
If you're using an older version, you'll need to set mesh_radius
instead, which is in an
t; Cc: pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] electron density settings
>
> mwilke :
> > Does anyone know how to alter the isomesh settings? I'm trying to
> prepare
> > a figure with pretty electron density and would like to be able to
> decrease
&g
mwilke :
> Does anyone know how to alter the isomesh settings? I'm trying to prepare
> a figure with pretty electron density and would like to be able to decrease
> the gap size of the mesh. I found the variables that seem to make sense
> like "mesh_quality" and "min_mesh_spacing", but changing
Scott,
isomesh msh1, map1, 1.5, myobject, carve=2.1
The postfix "carve=2.1" will trim density which is more than 2.1 A from
myobject.
You may want to play around with the exact cutoff...
Cheers,
Warren
> -Original Message-
> From: Scott Classen [mailto:clas...@uclink.berkeley.edu
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