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,
Hello,
I've been trying to color my Fo-Fc electron density maps in pymol with the
positive Fo-Fc maps showing as green and negative Fo-Fc maps showing as red
and having no luck with it. They either show up as red or green.
I generate my maps by converting .mtz from phenix to .ccp4 files on ccp4.
Dear Amna (?),
2012/11/12 amna khan amnakhan...@gmail.com
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
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
Dear Amna (?),
2012/11/11 amna khan amnakhan...@gmail.com
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
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
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 mahdi...@yahoo.com:
Dear All,
I am trying to create a electron density map for the pdb
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
Hi Troels,
Thanks--I did forget about carving!
PyMOL still needs easier map extending, though.
Cheers,
-- Jason
2011/8/24 Troels Emtekær Linnet tlin...@gmail.com:
Have you tried this:
load run02-Protein-ANP-BA_ligands_omitmap.map.ccp4, fofc-map
isomesh +fofc_all, fofc-map, 3 , within_Ba ,
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 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
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
Dear All,
Is there any limits in Pymol that it can not display electron density map of
a structure beyond a certain X-Ray resolution ?
I can see Electron Density Map of few structures with an X-Ray Resolution of
2.90 or 3.00 in coot and wincoot but I am unable to visualize these in
Pymol.
Hello all pymol users
I am trying to make a density map image in pymol. but, some very good
density which i can see in coot. Although i have used the same map, which i
am not able to see in pymol. Inspite of changing the selection and
Buffer parameters, it is not appearing in pymol. what could be
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 .xplor file through mapman.
#
2008/9/26 Jhon Thomas jhon1.tho...@gmail.com:
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
2008/9/26 Jhon Thomas jhon1.tho...@gmail.com:
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
Subject: [PyMOL] Electron density map in pymol
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
Dear all
How can the dot representation of electron density map is made as in the
figure in attachment,I know the mess representation through isomesh
command.Please suggest.Thanx in advance.
Shivesh kumar
shivesh
-
Be a better Heartthrob. Get better
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
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
slice_new slice1,map1
I get the message:
Syntax Error: invalid syntax
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