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 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
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 generated in your IT infrastructure
contains a definitive record of c
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
I am having trouble to generate an electron density map (2FoFc) around some
selected residues and metal ion ligand. I have data as MTZfile which I use
to generate my map using FFT in ccp4i then further add a .ccp4 extension
for pymol to read. Then I give the map double command select the 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
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
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
Hi everybody,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 the density isn't so thick. If anyone has any advice,
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
...@lists.sourceforge.net on behalf of Akanksha Nagpal
Sent: Mon 04/07/2005 13:27
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Electron density around selected residues
Dear PyMol Users:
I found a lot of e-mails in the archives discussing drawing electron density
around selected residue or ligand. The
Dear PyMol Users:
I found a lot of e-mails in the archives discussing drawing electron density
around selected residue or ligand. The carve command works fine but I also see
density for other residues, which are adjacent to selected redidue. Is there
any way to just exclusively draw density around
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
I am using pymol 0.97 version, I tried to contour the
electron density around the object I selected like,
load d1.pdb, d1
isomesh mesh1, map1, 1.0, (d1), carve=4.0
I can able to display the map, but i could not display
around the object.
any help might be useful
thanks
vk
=
Kabaleeswaran V
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
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.
Thanks
funne...@hotmail.com
_
Express yourself instantly with MS
Hi PyMOL users,
I am wondering there is any way to draw electron density only around
inhibitor/substrate/cofactor?
If possible, let me know.
Thanks.
Tommy Matsui
_
楽しい絵文字でココロ伝わるメッセンジャー
http://www.special-msn.com/messenger/defa
To: 'Warren L. DeLano'
> Cc: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] electron density settings
>
> Hi there,
>
> 1. How can I reduce the density-map line thickness in the ray-traced
> image?
> 2. Is there a way to just display the density around a ligand
>
&
Hi there,
1. How can I reduce the density-map line thickness in the ray-traced
image?
2. Is there a way to just display the density around a ligand
many thanks
robert
Robert Schwarzenbacher, PhD
The Joint Center for Structural Genomics
phone: 858 822 3637
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
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 these variables
sen [mailto:clas...@uclink.berkeley.edu]
> Sent: Friday, September 20, 2002 3:11 PM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] electron density maps
>
>
> Hello fellow PyMOL users,
> I am trying to display a ccp4 map over just a ligand. I have
> successfully read in th
Hello fellow PyMOL users,
I am trying to display a ccp4 map over just a ligand. I have
successfully read in the map and displayed it around the ligand with:
isomesh msh1, map1, 1.5, myobject
but the map has bits and peices of the surrounding sidechains.
Is there a way to only display the map
Hi,
I would like to do the following: define a plane, e.g. the center of the
clipping volume/slab (which probably is already defined somewhere), and
colour it according to electron density, if possible transparent.
So one would have to make an intersection of the clipping plane with the
electron
I would like to display an electron density as a surface instead of a mesh.
Is this somehow possible with PyMOL?
Thanks in advance for any help
Manfredbegin:vcard
n:Baumstark;Manfred
tel;fax:+49 761 270 7470
tel;work:+49 761 270 7496
x-mozilla-html:TRUE
org:University Hospital Freiburg;Rehabilit
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