Erratum: Of course I meant "solvent accessible", not "excluded".
On 05 Jan 2017, at 09:52, Thomas Holder wrote:
> Hi Vincent,
>
> Coloring the cartoon with a color ramp is not possible unfortunately.
> Incentive PyMOL since version 1.8 can color ribbon by ramp, if that helps.
>
> However, ele
Hi Vincent,
Coloring the cartoon with a color ramp is not possible unfortunately. Incentive
PyMOL since version 1.8 can color ribbon by ramp, if that helps.
However, electrostatic potential locally probed along the backbone will not be
very meaningful. Typically you would look at electrostatics
Vincent,
You could use data2bfactor.py and then "spectrum b" to color residues in
cartoon settings.
https://pymolwiki.org/index.php/Color
(data2bfactor from Robert Campbell's script repository:
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/
Jed
On 1/4/2017 11:05 AM, vincent Chaptal wrote
Hi everyone,
is there a way to color by electrostatic potential but display the
structure as cartoon?
a workaround could be :
color white, molecule
color red, resn asp+glu+thr+ser etc..
color blue, resn arg+lys
... but this seems rather flimsy.
Thank you and best wishes for the new year.
Vi
Dear all,
a colleague is interested in generating an electrostatic map of a protein
containing a citrulline. Does anybody have any experience with this and
could recommend any approach?
Cheers,
Andreas
--
Site24x7 APM In
an xplor file which seems to work but I have
> >> to adjust the position and scale to let it
> >> overlay the ion positions that I read from an xyz file.
> >>
> >> AFAICT xplor is about the only easy format that pymol takes
> >> but I was debating about trying to f
pped it.
>> The xplor approch seems to work well enough for now.
>>
>>
>> Is there an easier way?
>> Thanks.
>>
>>
>>
>>> Date: Wed, 27 Mar 2013 13:41:24 +0400
>>> From: jmsstarli...@gmail.c
rk well enough for now.
>
>
> Is there an easier way?
> Thanks.
>
>
>
>> Date: Wed, 27 Mar 2013 13:41:24 +0400
>> From: jmsstarli...@gmail.com
>> To: pymol-users@lists.sourceforge.net
>> Subject: [PyMOL] Electr
now.
Is there an easier way?
Thanks.
> Date: Wed, 27 Mar 2013 13:41:24 +0400
> From: jmsstarli...@gmail.com
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] Electrostatic potential surface
>
> Dear PyMol users!
>
>
&
Dear PyMol users!
I wounder to know about built-in PyMol option for electrostatic
potential visualisation.
For example I have pdb coordinates of my protein as well as its
electrostatic potential distribution (calculated by another software).
Using MolMol with both of that files I can visualize t
>
> Is it possible to generate electrostatic potential surfaces for small
> molecules (i.e. only for ligand, in the absence of a protein) with PyMol?
--
Everyone hates slow websites. So do we.
Make your web apps faster with
Hi Andrew.
I experienced something similar for the autodock_plugin.
http://www.pymolwiki.org/index.php/Autodock_plugin
During my trials, I notified two things for autodock.
It did not like "funny atom names" or "Alternative configuration"
Could this be a case for your protein / ligand?
I don't k
Hi Andrew,
The main limitation for problems like this is that you need to have
parameters for the ligand. Making sure that you have "good" parameters
is often an expert-level topic, and you're probably best served by the
APBS or PDB2PQR listservs as well as the literature ... but, you can
get a de
Hi all,
I would like to display the electrostatic potential of a small molecule which I
calculated with Gaussian in Pymol. I exported a cube-file of the ESP and loaded
it into Pymol. Afterwards, I generated an isosurface. The problem is that I
cannot manage to color that surface according to t
Could you please write the _exact_ steps you are doing? Also please
attach a the compressed cube file?
Best regards,
Marius
--
Département de Chimie Moléculaire
Université Joseph Fourier
301 Rue de la Chimie
BP 53, 38041 Grenoble Cedex 9, France
Tel: +33 (0) 4 76 63 44 03
GnuPG http://db.tt/rr7H
Hi all,
I would like to display the electrostatic potential of a small molecule which I
calculated with Gaussian in Pymol. I exported a cube-file of the ESP and loaded
it into Pymol. Afterwards, I generated an isosurface. The problem is that I
cannot manage to color that surface according to t
Andy,
Current PyMOL 1.2 beta builds ship with an APBS binary
($PYMOL_PATH/freemol/bin/apbs.exe).
Cheers,
Warren
-Original Message-
From: Andy Torelli [mailto:at...@cornell.edu]
Sent: Thu 2/12/2009 10:28 AM
To: PyMOL-users@lists.sourceforge.net
Subject: [PyMOL] Electrostatic
Hello everyone,
Is there a plugin similar to APBS that will work with Windows for the
purposes of electrostatic calculations?
Thanks,
-Andy
--
=
Andrew T. Torelli Ph.D.
Postdoctoral Associate
Department of Chemistry and Chemical Biology
Cornell Uni
ure how to continue.
http://www.pymolwiki.org/index.php/Color#Reassigning_B-Factors_and_Coloring
Regards,
-- Jason
On Tuesday 06 March 2007 09:03, pymol-users-requ...@lists.sourceforge.net
wrote:
> Message: 2
> Date: Tue, 6 Mar 2007 11:19:44 +0100
> From: "Gerebtzoff, Gregori
, 2007 11:40 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Electrostatic surface visualization
Dear all,
I'm new to this list and to the software.
I used PyMOL and APBS to calculate an electrostatic surface for a
small protein (I'm using the WindowsXP version) and everything
On 3/3/07, se...@uniroma2.it wrote:
Dear all,
I'm new to this list and to the software.
I used PyMOL and APBS to calculate an electrostatic surface for a
small protein (I'm using the WindowsXP version) and everything seems fine.
Now I would like to visualize this surface AND the secondary stru
Dear all,
I'm new to this list and to the software.
I used PyMOL and APBS to calculate an electrostatic surface for a
small protein (I'm using the WindowsXP version) and everything seems fine.
Now I would like to visualize this surface AND the secondary structure
of the protein, in order to unde
Am Mittwoch, 29. November 2006 15:31 schrieb shivesh kumar:
> Dear all,
> How can I get the electrostatic potential structure of my protein
> molecule.Thanx in advance. S
what do you mean by "electrostatic potential structure"? The potential can be
calculated with apbs (by hand or via plugin).
Dear all,
How can I get the electrostatic potential structure of my protein
molecule.Thanx in advance.
S
shivesh
-
Want to start your own business? Learn how on Yahoo! Small Business.
PyMOL takes care of this, thanks again Warren!
>
> Are you using the same platform for both Grasp and Pymol? I don't think
> that big-endian maps (written by an SGI computer) can be read by a
> little-endian platform, such as a x86 based PC.
===
Yu Chen
H
Are you using the same platform for both Grasp and Pymol? I don't think
that big-endian maps (written by an SGI computer) can be read by a
little-endian platform, such as a x86 based PC.
- Esben
> > The problem is getting the phi map in grasp. Can somebody
> explain me how to do it?
>
> This
> I have tried getting the electrostatic in pymol using the following commands:
> load molecule.pdb, mol-object
> load grasp-map.phi, map-object
> ramp_new ramp-name, map-object
> show surface, mol-object
> set surface_color, ramp-name, mol-object
> The problem is getting the phi map in grasp. Can
Hello everybody,
I have tried getting the electrostatic in pymol using the following commands:
load molecule.pdb, mol-object
load grasp-map.phi, map-object
ramp_new ramp-name, map-object
show surface, mol-object
set surface_color, ramp-name, mol-object
The problem is getting
Todd Geders said:
>Hello all,
>
>Here is a simple script that automates the electrostatic potential
>surface generation using Gromacs, MEAD, and Pymol for visualization.
>It's exclusively based off of the post by Esben Peter Friis:
>It requires you to massage your pdb file a bit, but it gets the
...@lists.sourceforge.net [mailto:pymol-users-
> > ad...@lists.sourceforge.net] On Behalf Of Sanishvili, Ruslan
> > Sent: Tuesday, December 16, 2003 8:29 AM
> > To: Warren L. DeLano; pymol-users@lists.sourceforge.net
> > Subject: [PyMOL] electrostatic surface
> >
> > Hi
Fax (650)-593-4020
> -Original Message-
> From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
> ad...@lists.sourceforge.net] On Behalf Of Sanishvili, Ruslan
> Sent: Tuesday, December 16, 2003 8:29 AM
> To: Warren L. DeLano; pymol-users@lists.sourceforge.n
Hi all,
Inexplicably, I haven't been following the PyMol news lately. Does it
now calculate and display the electrostatic fields/surfaces of proteins
(a la GRASP, or similar)? If it does, starting from which version?
Thanks,
Nukri
Ruslan Sanishvili (Nukri), Ph.D.
GM/CA-CAT, Bld. 436, D007
Biosci
m: Paulo Martel
To: EPF (Esben Peter Friis)
Sent: 14-09-03 20:28
Subject: Re: [PyMOL] Electrostatic potential maps in PyMOL
Dear Esben,
no matter how hard I try, I cannot make pymol read a phi map converted
from avs with your utility. The .fld file was generated with the
potential program in
If I understand the question correctly, the answer is
disable ramp-name
Cheers,
Warren
> Hello:
>
> Is there anyway to remove the colour ramp from an electrostatic
potential
> figure via a script (help hide doesn't list anything reasonable for
this
> and there is nothing that I can see in the s
Hello:
Is there anyway to remove the colour ramp from an electrostatic potential
figure via a script (help hide doesn't list anything reasonable for this
and there is nothing that I can see in the settings).
Cheers,
JTM
"We can be sure that if a detailed understanding of the molecular basis of
c
Dear Esben,
Gromacs can create pqr files, but does it in a very bad way - the radii
information comes from a very limited set of atoms, and not directly from
the forcefield parameters. A colleague of mine, Antonio Baptista, has
written an awk script that can generate a proper pqr file from a gro
Original Message-
From: Andreas Förster
To: EPF (Esben Peter Friis)
Cc: 'pymol-users@lists.sourceforge.net'
Sent: 10-07-03 21:25
Subject: Re: [PyMOL] Electrostatic potential maps in PyMOL
Hi Esben,
I tried to follow your instructions to create and display an
electrostatic surface potenti
Hi Esben,
I tried to follow your instructions to create and display an
electrostatic surface potential. I used 1UBQ.pdb as input. In Mead, I
encountered the following error when running
potential -epsin 2 -CoarseFieldOut 1UBQ 1UBQ
Starting potential for molecule named 1UBQ
with interior dielectri
: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
ad...@lists.sourceforge.net] On Behalf Of Warren L. DeLano
Sent: Wednesday, July 09, 2003 2:20 PM
To: 'EPF (Esben Peter Friis)'; 'Kaushik Raha '; 'Yu Chen '
Cc: pymol-users@lists.sourceforge.net
Subject: RE: [PyMOL] Ele
e (650)-346-1154
> Fax (650)-593-4020
>
> > -Original Message-
> > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
> > ad...@lists.sourceforge.net] On Behalf Of Warren L. DeLano
> > Sent: Wednesday, July 09, 2003 2:20 PM
> > To: 'EPF
Peter Friis)'; 'Kaushik Raha '; 'Yu Chen '
> Cc: pymol-users@lists.sourceforge.net
> Subject: RE: [PyMOL] Electrostatic potential maps in PyMOL
>
> Yes, you have identified the problem: PyMOL 0.90 currently only reads
> PHI files in one of the two endian formats
Yes, you have identified the problem: PyMOL 0.90 currently only reads
PHI files in one of the two endian formats (not sure if it is big or
little).
The problem is, how it PyMOL to determine which format the incoming map
is in? The file format is so darn implicit, I haven't yet come up with
any
Chen
Cc: pymol-users@lists.sourceforge.net
Sent: 09-07-03 22:42
Subject: Re: [PyMOL] Electrostatic potential maps in PyMOL
Yu Chen, I have attached the output from the load command (which loads
the phimap). I don't see the error that you describe. Does this output
mean that it is working fi
Yu Chen, I have attached the output from the load command (which loads
the phimap). I don't see the error that you describe. Does this output
mean that it is working fine? I can generate a surface and color it
with the electrostatic potential too. But I am not sure if I can trust
the result
Hello, Kaushik
Yeah, we do had problems with DelPhi to PyMoL. I don't know what your
mean by "modified version of Delphi..." We bought the latest Delphi from
their website, and used the data from all the example folders comes with
Delphi. The calculation all went well. When we tried to read the ph
There has been some talk on the list regarding failure of PyMOL in
reading Delphi generated potential maps that I missed. I have generated
phimap using a modified version of Delphi in the GRASP format that
PyMOL reads and displays without any problem. So I am not sure what the
problem is. C
Hi PyMOL users,
MEAD's potential maps can be used in PyMOL, but it requires a little more
than a bit of tweaking, as the maps are in the AVS .fld format, which can
not be read by PyMOL. (These maps can be read by Dino, as Paulo just
mentioned). Also, PyMOL reads (as far as I can see) only big-endi
Hi,
I know pymol can do surface. I want to know if the new release of pymol
0.83 can show electrostaic surface. Thanks.
Chun
> From: Eric C. Peterson [mailto:ecpe...@uark.edu]
> I am putting some figures together for an upcoming manuscript
> and am trying
> to figure out a few details. Some of the things I want to do may be
> possible, some not. Here are the questions I have:
>
> 1. How do you display electrostatic
First of all, I am quite impressed with this program, free or not. I also
saw Dr. Wells speak at the Keystone conference in Breckenridge in January
where he presented some graphics using Rigimol. Very nice.
I am putting some figures together for an upcoming manuscript and am trying
to figure out
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