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
> 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
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
-
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
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 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
Hello,
I am trying to carve a 2Fo-Fc map around a lipid molecule. The electron density
at 2 sigma is much smaller in PyMol than in Coot (the map at 1 sigma in PyMol
is similar to the 2 sigma level map in Coot). I used the "unset
normalize_ccp4_maps" command but that stops the carved map from be
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. However
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
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
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
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.
# mymap.
Dear all,
I have to show the electron density at two different positions in the
structure, wheree two residues are interacting.I have made the object.I load
the 2fofc.xplor.and given the isomesh m1,map1,1.0,(A...),carve=2.0.I can
select either the whole chainA or a particular residue,it sh
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
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 r
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-----
> >
Hi, I have been trying to visualize a DN6 electron density
map. Although it is read in apparently correctly nothing
shows on the screen. Are there any particular
parameters to be set? I can visualize it in
SwisspdbViewer but I was unable to produce surface
rendering. Can Pymol produce a surfac
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