Hi Changdev -
Try the following command, which will save a ray-traced PNG image with
transparent background (which is what is represented by the checkerboard
pattern):
png myfigure.png, ray=1
Alternatively, you can adjust the ray background setting:
set ray_opaque_background, 1
Hello there,
When I do ray, it shows brown and white square in the background.
I want to capture image directly from screen but squares also get copied.
Is there any way to remove these squares and capture image directly from the
screen.
Regards,
Changdev
Dear Jared,I am using Open Source PyMOL 1.6.0.0. If you save the whole virus
structure as a single pdb file, and reload it into pymol and then show it as
cartoon, can you still display the whole structure? As for me, it can display
only one chain shown as cartoon_loop.Best regards.
Yeping Sun
发送时间：2014年7月10日(星期四) 21:20
收件人：pymol-users pymol-users@lists.sourceforge.net
主 题：Re: [PyMOL] what is the pymol representation in this figure?
It should be a solid surface with transparency on,
if I'm not getting it wrong.Dear Gianluca,Thank you for the response, but how
to set the side chain of
Dear Yeping,
you should check Jared's reponse to your message.
I think he gave you all the hints you need.
:)
Gian
On 7/11/14 8:27 AM, sunyeping wrote:
发送时间：2014年7月10日(星期四) 21:20
收件人：pymol-users pymol-users@lists.sourceforge.net
主 题：Re: [PyMOL] what is the pymol representation in this figure?
Hi Yeping -
It doesn’t look like Spectrumbar supports additional labeling, but you could
add labels at each end by using pseudoatoms at the positions where you want the
labels to appear (see the second example at
http://pymolwiki.org/index.php/Pseudoatom).
For the 2D gradient box, you can
Dear Jared,Thank you for the reply. But I still have a couple of questions:
As for the spectrumbar script, how could I assign a particular data value
to a particular color? By using the command:spectrumbar blue, white, redI can
get a spectrumbar. If the range of my data is -0.3~2.3, maybe
Hi Jason
It is exactly what I want !!!
Merci beaucoup
Cheers
Stephane
De : Jason Vertrees [jason.vertr...@schrodinger.com]
Date d'envoi : vendredi 10 mai 2013 20:25
À : ABEL Stephane 175950
Objet : Re: [PyMOL] Replicate a cubic unit cell in the x, y,
Hi Tsjerk,
Many thanks for your help, once again ;0 It works and it gives what i want.
cool !!
Stephane
De : Tsjerk Wassenaar [tsje...@gmail.com]
Date d'envoi : vendredi 1 mars 2013 13:56
À : ABEL Stephane 175950
Cc: pymol-users@lists.sourceforge.net
Thank you for your response, i will try your suggestion
A bientot
Stephane
De : Thomas Holder [ad...@thomas-holder.de] de la part de Thomas Holder
[spel...@users.sourceforge.net]
Date d'envoi : jeudi 22 septembre 2011 11:14
À : ABEL Stephane 175950
Cc :
Yes,I tried to install pymol_0.99 on fc4, and fc7 (my own is fc6) on different
machine .Only fc4 works .
Is there any simple way to fix it not changing the linux distribution.
Best
寄件人﹕ Warren DeLano war...@delsci.com
收件人 LIU Changdong dongyi2...@yahoo.com.hk;
Subject: [PyMOL] Superimpoition problem
Use first structure for reference and then align rest
of them to first one.
--- pymol-users-requ...@lists.sourceforge.net wrote:
Send PyMOL-users mailing list submissions to
pymol-users@lists.sourceforge.net
To subscribe or unsubscribe via
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net on behalf of Seth Harris
Sent: Tue 4/18/2006 2:45 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] RE: povray image mapping and default pigments
To answer my own question...instead of entirely taking out
Hi Michelle,
In case no one's mentioned it yet, Zac Panepucci has contributed a
grepset.py script which, after being run, allows you to type grepset x
to see all settings (and their values) associated with whatever x is.
It's not directly integrated into the pymol distribution but pretty
I probably didn't make myself clear in my last email.
What I meant is that there is an option in pymol APBS tool that allows one
to use pymol to generate pqr file from pdb file, instead of loading an pqr
file generated externally. I noticed that the electrostatic potential looks
quite different
Marilyn,
We saw this between unix and PC and one user figured out that
label_font_id's were different. Thus older versions didn't recognize as many
fonts as newer ones. I'm thinking this matches your description if the
binaries on the two machines are in fact different versions.
Try:
set
So,
I tried rendering using transparency_mode = 1 or 0 and got this result:
http://pwe.no-ip.org/other/Pymol2.png
Is there a way to get rid of the transparency that darkens some parts of
the surface where something lies behind?
I also tried povray to render the surface and it gives me a
Dear Warren,
this little thread points nicely to the major problem that I have quite
often with PyMol: it is a really powerful program, but the documentation
is somewhere scattered between various incomplete sources (manual,
reference list, wiki, bulletin board, user home pages, ...). This
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] RE: Angstrom-squared values for solvent/protein contact
surface per residue
--=_Part_19793_7876172.1144104983332
Content-Type: text/plain; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable
Content-Disposition: inline
Just
Hi Sun,
Warren (and others?) has posted some text before about this. A simple
template for it is as follows with the key being that mview interpolate
command at the end. This works, but I haven't been through it recently to
remind myself of the nuances of the animate=0 options and the view=0
Just to throw my 2 cents in following Warren's invitation, I think
Mark Gerstein's programs work well for this (calcsurf.exe or
something...they're on his web site)
ccp4's areaimol does something similar, though I can't recall whether
its output was atom by atom.
In either case, you may have to
Did you change anything on SourceForge? I lost CVS access
somehow. Is this due to the switch to SVN? Did you import
PyMol into SVN?
No. It's not just you -- SourceForge has been experiencing a major CVS outage
since early Thursday morning.
Thx Gilleain!
Cheers,
Alan
Message: 1
Date: Wed, 15 Mar 2006 09:37:55 +
From: gilleain torrance gilleain.torra...@gmail.com
To: Pymol pymol-users@lists.sourceforge.net
Subject: [PyMOL] Re: building peptides
Hi,
The wiki has a page on this:
http://www.pymolwiki.org/index.php
Hi,
The wiki has a page on this:
http://www.pymolwiki.org/index.php/Peptide_Sequence
except it doesn't mention the zwitterion details. There's a link to
Robert Campbell's scripts to do this sort of thing, so maybe the
answer is there.
As for for loops, this is best in a full python script (run
Isabel,
There is a PyMOL-Users mailing list for such questions at
http://lists.sourceforge.net/lists/listinfo/pymol-users
As for making stereo labels, the latest PyMOL release 0.99rc6
http://delsci.com/rel/099 has variable-size, stereo 3D labels that can be
positioning using the mouse (when
Dear All,
after reading the post below, for a new quad buffered stereo plugin
for OSIRIX,
I though I would try it out on my older apple G5 with GeForce
FX5200, just for a giggle, not expecting it to work
on this older graphics card. OSX 10.4.5
As far as I am aware, the only card apple
Jean,
I have been playing around with the Caver plugin to map concave areas on the
molecule. The program makes a mesh map of the tunnel that you can then
use as an object to select nearby atoms that tend to be on or near the
surface.
If anyone knows an easier way, please let us know.
Aaron New
Indraneel,
At present, wizards need to be located in the
$PYMOL_PATH/modules/pymol/wizard directory -- changing this would be
nontrivial, since all wizards are assumed to reside in the
pymol.wizard namespace.
FYI: module-name.__path__ has a different meaning than sys.path.
Cheers,
Warren
--
On Tue, Feb 28, 2006 at 10:38:40AM -0800, Warren DeLano wrote:
Indraneel,
At present, wizards need to be located in the
$PYMOL_PATH/modules/pymol/wizard directory -- changing this would be
nontrivial, since all wizards are assumed to reside in the
pymol.wizard namespace.
So this means the
Dear all,
I made a PQR file by PDB2PQR, and then in PyMOL, I run apbs.
I got an error. Help.
PyMOL(TM) Incentive Product - Copyright (C) 2006 DeLano Scientific LLC.
A current PyMOL Maintenance and/or Support Subscription may be required
for legal use of this Build beyond a finite
You can call the executable inside an application and it will work in the
normal unix way, eg
/Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL
You might want to make an alias or a function or a symbolic link like
alias pymol=/Applications/Xtal/MacPyMOL.app/Contents/MacOS/MacPyMOL
or
Yes. In fact I just added a description of how to do this in the PyMol
Wiki.
http://www.pymolwiki.org/index.php/APBS
The apbs plugin will work , but you should use pdb2pqr to generate the
nucleic acid pqr file externally, and then read it in.
Then it works the same as for proteins.
HTH,
Bill
I am having a hard time getting PymolX11Hybrid properly installed on
my G4 powerbook. My goal is to make molecular surfaces with
elctrostatic potentials. What am I doing wrong? I installed the
newest version of MacPymol, duplicated it, renamed it
PymolX11Hybrid. Then I downloaded the APBS
I too have had this problem. Even if you switch to 2-button selecting,
I can't seem to zoom, no matter what finger-twisting combinations I
try!
I do have a usb mouse, but I wonder if this is now vital, or merely
still convenient?
gilleain torrance
On 2/7/06, andr...@biochem.utah.edu
Hi Warren,
is this a stereo system? This would be very cheap, a quadro card costst
usually more.
Cheers,
Ulrich
- Original Message -
From: Warren DeLano war...@delsci.com
To: pymol-users@lists.sourceforge.net; CCL Subscribers
chemis...@ccl.net; CCP4BB ccp...@dl.ac.uk;
...@lists.sourceforge.net] On Behalf Of
Ulrich Baumann
Sent: Monday, February 06, 2006 12:27 AM
To: Warren DeLano; pymol-users@lists.sourceforge.net
Subject: [PyMOL] Re: [ccp4bb]: Mac Intel Benchmarks
Hi Warren,
is this a stereo system? This would be very cheap, a quadro
card costst
these displays for a rainy day. I've just given up on stereo and
switched
to using higher-end LCD displays. Less energy, less heat, and less
eye
fatigue for me.
Let me quote myself from a posting to o-info from September 1994:
Real men don't Use Stereo
A few hours later, Eleanor
Hi all -
While on the subject and after thanking Warren for providing the
excellent resource ...:
We have some nice 3D monitors and Nvidia cards in Linux PC's we do
stereo with.
Warren correctly points out that you need:
1280x960 @ 120 Hz requires H-sync of 123 kHz
Hi there,
Most modern monitors are very clever and tell the X server their
preferred sync rates (which never exceed 85 Hz). You can override
this functionality by adding
OptionUseEdidFreqs0
to the Device section of your Xorg (or XFree86) config file.
You will also need to specify
I believe that even the large Phillips (22) that you list is no longer
being made and that what is in stock at places is just old inventory (could
be wrong though). It is hard to believe, but these monitors just aren't
being made anymore. We literally have people in our modeling group hording
Irida,
I am looking for a free program
or script that can calculate all sulfur-sulfur distances in
pdb files from the Protein Data Bank.
This is the kind of problem you can solve in PyMOL with just a few lines
of Python code. For example:
from pymol import cmd
from glob import glob
for
how can i get 300 dpi image or picture of higher resolution from pymol
On 1/5/06, Robert Campbell r...@post.queensu.ca wrote:
Alexander,
* alexander.paut...@bc.boehringer-ingelheim.com wrote:
I would like to color my protein according to B-factor with a
self-defined
spectral palette
Alexander,
* alexander.paut...@bc.boehringer-ingelheim.com wrote:
I would like to color my protein according to B-factor with a self-defined
spectral palette (In this case I have put sequence conservation into the
Bfactor this column). I found that
spectrum b, blue_white_red,
This is more half an answer than the real deal, but when I had the same
issue I opted for the quick work around of setting the range from -100 to
100 for the blue-white-red palette which effectively made 0-100 correspond
to white to red only since there were no negative B factors/conservation
try this:
set cartoon_highlight_color=$COLOR
where $COLOR is the color of choice
Andrew Wollacott, PhD
University of Washington
On 12/11/05, pymol-users-requ...@lists.sourceforge.net
pymol-users-requ...@lists.sourceforge.net wrote:
Send PyMOL-users mailing list submissions to
John Alain,
I am not sure John really intended to cross-post that message, but now
that the damage is done, I'll take it one step further: I believe the
problem is our sacred open-source cow Linux, or rather that nasty
amalgamation of diverse hardware, operating systems, and drivers
Warren,
These commands (see below) go a long way toward solving the problem
of producing low resolution simple structures for my textbook
project. I have some questions:
The first command elicits an error:
PyMOLalter all,b=3D10
Alter-Error: Aborting on error. Assignment may be incomplete.
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
Sarina Bromberg
Sent: Thursday, December 01, 2005 9:45 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] RE: EMizing an xray structure (Warren
Stuart,
Stuart Endo-Streeter stuart.endostree...@duke.edu
Default view, white with black background (sticks):
Ray: total time: 15.68 sec. = 229.5 frames/hour. (15.68 sec. accum.)
Surface ray (white w/ black background):
Ray: total time: 32.67 sec. = 110.2 frames/hour. (48.35 sec. accum.)
Now this has got to be the funniest bounce I've received to date as
administrator of the PyMOL users list:
-Original Message-
From: pymol-users-ow...@lists.sourceforge.net
[mailto:pymol-users-ow...@lists.sourceforge.net] On Behalf Of
Of course within minutes of posting my question about transpose_selection, I
have found the answer for myself. There are a couple of new flags added to the
command, which is now:
def transform_selection(selection,matrix,state=0,log=0,homogenous=0,transpose=0)
When I call it with the flag
HI Mac users,
Brian Goodfellow wrote:
has anyone noticed an annoying flickering appearing when rotating a =20
molecule in PymolX11 and MacPyMOL under 10.4.3 that wasn't present =20
under 10.4.2? The problem appears on both my iBookG4 and iMacG5. If =20
the window is moved then the flickering
Hi Warren,
Tested 99beta21 and 99beta25 on a dual 2.5 with ATI 9800 XT (256 MB)
with 10.4.2 and it works fine. After upgrading to 10.4.3 on that
machine, everything is still fine.
Also tried 99beta25 on my machine (ATI 9600 Pro - 64MB) and that
still has a problem. I then booted into
On Nov 4, 2005, at 12:38, Martin Montgomery wrote:
Tested 99beta21 and 99beta25 on a dual 2.5 with ATI 9800 XT (256
MB) with 10.4.2 and it works fine. After upgrading to 10.4.3 on
that machine, everything is still fine.
Also tried 99beta25 on my machine (ATI 9600 Pro - 64MB) and that
I've just tested a G5 imac with a GeForce FX5200 with 64MB RAM and
macpymol 99beta21/25 and it works fine with 10.4.3. It seems the
problem is limited to ATI graphics cards with less than 256 RAM.
nVidea cards are not affected. Will try an ATI card with 128MB RAM
if I can find one here.
Flicker problem here on a PowerBook 1.5 G4 w/ 64 MB ATI card under
10.4.3 however, if I launch X11 and run PyMol under that - (version
0.97), then there's no problem
Chris
On Nov 4, 2005, at 7:26 AM, Martin Montgomery wrote:
I've just tested a G5 imac with a GeForce FX5200 with 64MB RAM
Hi Mac users,
MGM wrote:
Having just read Jesper's email regarding getting drivers at ATI's
website, I had a look and there are no mac drivers available as far
as I can see. Only the ATI Displays software. After installing this
on my machine, nothing has changed. The molecule loads
. Daniel Moriarty
Siena College
Chemistry and Biochemistry Dept.
515 Loudon Road
Loudonville, NY 12211
(518) 783-2472
fax: (518) 276-4887
From: Martin Montgomery m...@mrc-dunn.cam.ac.uk
Date: Fri, 4 Nov 2005 13:05:10 +
To: pymol-users pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL
Hi,
Using the callbacks on the newest macpymol on tiger doesn't work:
run /Applications/MacPyMOL.app/pymol/examples/devel/gl01.py
Traceback (most recent call last):
File /Users/delwarl/MacPyMOL/build/MacPyMOL.app/pymol/modules/
pymol/parser.py, line 273, in parse
File
I just fired up pymol installed via fink using Python compiled
against a Framework build of Python that in turn is build against the
TCL TK framework.
your either get interaction with the GLUT GUI, or the Tcl/Tk user
interface, but not both : (.
I can't reproduce the problem, i.e., both
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
William Scott
Sent: Thursday, October 20, 2005 4:28 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Re: Apple's tk and pymol
I just fired up
Hi Warren:
The display window is actually X so I assume it must be fink/X11 glut.
Sorry I omitted that.
Bill
Are you using Framework GLUT or Fink/Xll GLUT? The latter might work
Oliver,
I know it'll sound crazy but -- get. :-)
For example,
get two_sided_lighting
or
get bg_rgb
I think this is covered on the Wiki somewhere, too.
(http://www.pymolwiki.org/)
HTH,
-- Jason
On Wed, 2005-10-19 at 20:24 -0700,
pymol-users-requ...@lists.sourceforge.net wrote:
Message: 3
On Tuesday 18 October 2005 16:36, pymol-users-requ...@lists.sourceforge.net
wrote:
Hi Warren
It's been a long time since my last post. Anyway I tried the polar contacts
identifier as written below
dist name, sel1, sel2, mode=3D2
and I get the following error
Traceback (most recent call last):
Kostas,
This command:
dist name, sel1, sel2, mode=3D2
doesn't work because the move value should be a whole number ie. 1,2,3 etc.
Also unless you have some objects actually called sel1 and sel2 you
won't get anything meaningful back.
something like this:
dist name, resn lys, resn glu,
Michael Morbious wrote:
Dear All,
I am a new pymol user. Does anyone know if it is
possible to merge four units (all units are same) of a
tetrameric assembly by using pymol? Each unit has the
same Id and when I load each of them, they overlap.
If you please help me, I will be really
Hi Warren:
For cutting-edge Mac users, there is a new MacPyMOL for Tiger that
integrates into a single window and links to the system Python instead
of bringing its own copy (in part this is necessary preparation for
Intel...).
http://delsci.com/beta
Works great here, too. My only request
...@delsci.com
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
Kevin Gardner
Sent: Saturday, October 15, 2005 5:01 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Re: Need testers for new
check this link!
http://www.csb.yale.edu/userguides/graphics/pymol/electro.html
Hope it wud help.
best sn
--- pymol-users-requ...@lists.sourceforge.net wrote:
Send PyMOL-users mailing list submissions to
pymol-users@lists.sourceforge.net
To subscribe or unsubscribe via the World Wide
On Tue, 13 Sep 2005, surendra negi wrote:
check this link!
http://www.csb.yale.edu/userguides/graphics/pymol/electro.html
That page is actually quite out of date. I emailed them about it a few
months ago, but didn't get a response.
You don't need to go through any of that hassle to use
: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
wenming hu
Sent: Wednesday, August 24, 2005 6:29 PM
To: Warren DeLano; pymol-users@lists.sourceforge.net
Subject: [PyMOL] Re： RE: [PyMOL] question about _cmd.pyd
I see. thank you for your
I see. thank you for your answer. and i'm wondering, how do u develop python
modules like _cmd.pyd? only via setup.py, and type python setup.py build to
compile it? how do u debug it on the procudure of development? for me, it's not
easy to develop _cmd.pyd only via setup.py script, i think,
On [2005-Aug-19] Christopher Colbert co...@chop.swmed.edu wrote:
Hi Pymol'rs,
I have search the Wiki and Mail-list archive to find a protocul for using
the CMYK color space, but have only found color-safe definitions.
My Question(s):
When do you define the color space during the creation
On Mon, August 22, 2005 2:55 pm, Warren DeLano said:
Hold on -- from the end-user's standpoint, the only thing that matters
is: does the image I see on the screen match what comes out of the
printer. Who cares about the printer's point of view?!
The printer (a person running the press) does;
*** ABOUT RivaTuner (suggested by Wang Chern Hoe): ***
I'll keep that trick for my personal record and use, but we don't want
to use any dual boot solution in the lab (at least not yet). For a
whole lab solution I will agree with Cameron (cm...@ucsd.edu) who
suggests to opt for a real
Sreekala,
You want to 'split_states'. Load the biological unit into Pymol then
run 'split_states'.
Check out the PyMolWiki: http://www.pymolwiki.org/index.php/Split_States
where it's described more fully.
-- Jason
On Mon, 2005-08-01 at 20:22 -0700,
pymol-users-requ...@lists.sourceforge.net
On Fri, Jul 15, 2005 at 01:15:13PM -0700, Cameron Mura wrote:
there may be many O and PyMOL users who use stereo with a monitor
connected through a KVM switch?
3) would be nice if the KVM, linux boxes, and USB mouse were all
interoperable. Reason i point this out is that the logitech USB
Hi Philippe,
If you are using the Windows platform, I suggest you get a Geforce 6800Ultra,
and use rivatuner from http://downloads.guru3d.com/download.php?det=163 to
modify the driver to Quadro FX 4400 under Windows XP. Thereafter, substitute O
with NOC from http://noc.ibp.ac.cn/ and you
Yes. You can do this with pymol easily.First open both
PDB files in PYMOL. Now go to mounse menu option and
click on 3 Button editing mode. Next step double click
on any atom of the PDB file which you want to rotate
or translate wrt first. Press shift and use left mouse
button to rotate or press
Hi,
I can't comment about how the NVidia stereo works with other packages
but there are a few facts about the NVidia drivers that apply equally
to all of us:
- Unlike classic graphics workstations like SGI and Sun, with NVidia
you can have _either_ stereo, or you can have multisample
Try, LAPACK packages. Available for most GNU/Linux
distributions
--
Message: 4
Date: Tue, 19 Jul 2005 14:53:47 +0200
From: tanri...@stud.uni-frankfurt.de
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Implementing PCA
Hi everybody,
I want to write a PCA
I try to play with apbs and finally it is working. But
some time it is still giving me following message
ObjectMapLoadDXFile-Error: Unable to open file!
because it is not generating the dx file.
thanks and regards
sn
--- pymol-users-requ...@lists.sourceforge.net wrote:
Send PyMOL-users
Hi Marty,
Sorry if this misses your point, but it is possible to translate molecules
independantly in pymol:
http://sourceforge.net/mailarchive/message.php?msg_id=11658301
However, that won¹t help if you want to show overlap. To do this, you would
have to repeatedly call translate and
Thanks a lot for all your prompt replies.
Correct usage: set stick_transparency, 0.7, ligand (hmmm)
Sona
On 5/17/05, Sona Vasudevan sona.vasude...@gmail.com wrote:
Hi!
I am getting the following error when I try to set stick transparency of
my object ligand
PyMOLset
PyMOL Users:
There have been several reports of crashes when launching PyMOL show (PSW)
files (ie. PSE files renamed PSW to trigger the full-screen mode). The
common factor behind in these crashes seems to have been Intel Extreme
Graphics chips and Windows XP Service Pack 2.
We managed to
Hi Nicolas,
I have the same SGI computer, Indigo 2 Impact 1
running IRIX 6.5.22m (BTW upgrade to this release is free from
supportfolio at SGI, might have to install patch 5086 first)
I have stereo graphics emitter and glasses,
and stereo works fine,
i just double click a link on my
Dear All,
Thanks for public and private replies alike.
The set max_threads, n construct works a treat, giving a 3.6x speedup
going from 1 to 4 cpu's.
A quad opteron is now an extremely fast rendering machine indeed!
Best regards,
Neil.
I have stumbled across the parameter causing the difference.
In all of the examples distributed with APBS, the pdie (solute dielectric)
value is set to 2.0 whereas ABPS-tools.py defaults this to 20.0. I find
that if I use 2.0 instead of 20.0 for pdie, the resulting electrostatic
potential map
Hi Jack,
In all of the examples distributed with APBS, the pdie (solute dielectric)
The pdie must be the protein dielectric constant though the comment for
pdie in the pymol generated .in-file reads # Solute dielectric ...
that is probably a mistake. The APBS-plugin says Protein Dielectric.
The
Richard,
Actually I don't have a copy of Delphi available (hence the use
of APBS). I did notice that I see more positive surface area on a
molecule with a -13 net charge when the run is done with pdie of 2.0
compared to 20.0 even in the presence of 0.150 mM NaCl ions. I also
noticed an oddity
is it possible to use the pdb loader in a *.pml style script?
With the shipped plugin it may be hard. I wrote the original, but have
since written a new/improved one that does not tough the filesystem and
adds a remote command that will fetch and load pdbs as well. You can
see the code for
Hello,
The setting menu doesn't seem to save the changes we do in it.
So, I seek for the file where default color is coded, e.g. for cartoon, to
save my changes.
I use PyMOL 0.97 on Linux OS.
Thanks
I found a way to resolve it in the old e-mails of the mailing list.
Create a $HOME/.pymolrc
Hi,
I get these as a digest so sorry if someone's already
spoken to this.
Laurence Pearl wrote some code to interpolate between
scenes as you describe. Kristian Rother wrote a very nice
set of framework commands (and more) to make movies. I
wrote an extension of Laurence's commands so
Hi Dustin,
I have used a combination of perl and bash scripts to accomplish something
similar to what you're doing. The one small difference is that I was loading
several PDB files (not SDFs). You'll have to figure out how to do this part
if it's significantly different from the loading
Dear Andreas,
I have a similar problem, cause there is no description of the internal
surface format, and there is no way to save or load created surfaces in
that format. (all you can do is create surfaces (with your own program
like MSMS ore something else) , convert and load it as a cgo-
Hello,
I apologize for being late, but... how about a section about nucleic
acids? As in any other related program, they always end up being the
poor siblings of proteins (I can't believe PyMOL's cartoon command
still does not recognise the most common 5' and 3' nucleotides!), and
I'm
Dear Torin,
Thanks for your reply. However my question was not about automatic
alignment of two protein structures. I want to move one of the structures
while keeping the other one fixed, so that I can consider alternate
alignments etc ..
So is there a way to do that with PyMOL.
thanks
...@delsci.com
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
Luca Jovine
Sent: Thursday, February 17, 2005 8:12 AM
To: Mailing List PyMol Users
Cc: javer...@utmb.edu
Subject: [PyMOL] Re: PyMolWiki
: Re: [PyMOL] Re: align proteins in pymol
If you set the mouse mode to 3-button editing mode, you'll
see that Shift-Left and Shift-Middle are RotF and MovF, respectively.
So with nothing selected, if you do Shift-Left, grab an atom
of a molecule and move it, the whole molecule will rotate
.
Sri Krishna Subramanian kris...@sdsc.edu
Sent by: pymol-users-ad...@lists.sourceforge.net
02/17/2005 11:35 AM
To
cc
PyMOL-users@lists.sourceforge.net
Subject
[PyMOL] Re: align proteins in pymol
Dear Torin,
Thanks for your reply. However my question was not about
automatic
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