rtrees [mailto:jason.vertr...@schrodinger.com]
> Sent: Friday, June 17, 2011 11:57 AM
> To: Schubert, Carsten [PRDUS]
> Cc: pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] Retention of ANISO Records was How to merge
> molecules in Pymol?
>
> Hi Carsten,
>
> PyMOL doesn&#x
sday, June 16, 2011 6:14 PM
> To: Schubert, Carsten [PRDUS]
> Cc: pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] How to merge molecules in Pymol?
>
> Hi Carsten,
>
> > Is there an (un)documented way of merging multiple molecular objects
> in
> > Pymol
Hi,
Is there an (un)documented way of merging multiple molecular objects in
Pymol into one molecule, which then can be written in a nicely formatted
PDB file? I cobbled something cludgy together with 'multisave' and a
couple read-sort-save cycles, but this is ugly and probably quite
fragile. An AP
Hi Jason,
thanks for the follow-up. Let us know when the issue is fixed.
Cheers,
Carsten
> -Original Message-
> From: Jason Vertrees [mailto:jason.vertr...@schrodinger.com]
> Sent: Thursday, May 19, 2011 12:11 PM
> To: Schubert, Carsten [PRDUS]
>
Has the length of the object name entry in the right hand menu been
restricted to 16 characters in v1.4.x? Prior to 1.4.x there seemed to
have been no limit on the length of the entry. For instance
cmd.load("reallylongmapnamehere",
format="ccp4",object="reallylongmapnamehere") would truncate the di
.vertr...@schrodinger.com]
> Sent: Wednesday, May 11, 2011 6:37 PM
> To: Schubert, Carsten [PRDUS]
> Cc: pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] Pymol 1.4.1 does not load PDBs from command line
> anymore
>
> Hi Carsten,
>
> That's pretty odd. Can
hat mechanism
worked.
Cheers,
Carsten
> -Original Message-
> From: Alvin Oga [mailto:pymol.l...@mail.linux-1u.net]
> Sent: Wednesday, May 11, 2011 5:49 PM
> To: Schubert, Carsten [PRDUS]
> Cc: pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] Pymol 1.4.1
Hi,
The latest PyMol (1.4.1, 32bit Linux version) does not load PDB files
from the command line anymore. Does anybody have the same problem? What
am I missing?
Cheers,
Carsten
--
Achieve unprecedented app perf
Kasper, not sure if this will help you, but I think the GLEW stuff was
added recently in V1.4.x and it seems to be still somewhat experimental.
May be to get you started you could switch to v1.3r1 from the repository
and try to embedd that version. V1.3.x should not contain the new GL
stuff.
Go
Nadine,
Probably the command line is your best friend here. Look into the 'clip
near,x' and 'clip far,x' command, which allows to move the front and
back clipping planes in x increments. Positive values move towards you,
negative values of x away from you.
If that does not provide enough fine grai
Joachim,
I'm running into the same issue on a SuSe SLED10 box. The 32bit binary
(on the 64bit OS) displays the same behavior, i.e. only the MESA libs
were used. The 64bit version actually core dumps during startup. I
opened up a bug report with Schrodinger and they were already working on
it (I su
Maia,
as far as I know a .pse is just a dump of the internal data structure of
Pymol. You can save the molecules contained in the session, but the
graphical representation and any modifications would need to be
recreated.
Hopefully Jason proves me wrong ...
Cheers,
Carsten
> -Original Mess
Not sure if this is possible but it would be a nice feature to have. Since it
mimics the way helices are drawn, when cartoon_highlight_color is set.
Cheers,
Carsten
> -Original Message-
> From: Keitaro Yamashita [mailto:yamash...@castor.sci.hokudai.ac.jp]
> Sent: Sunday, March
Roberto,
partial answer to point 3. Adding a "_" before an object name hides it
from the panel.
For points 1 or 2. Could you please expand on your question? Is this for
interactive
or scripted mode?
For scripted mode you could modify the coordinates of the pseudoatom to
be closer to the target
To: Michael Lerner
> Cc: Schubert, Carsten [PRDUS]; pymol-users@lists.sourceforge.net
> Subject: [PyMOL] Color scale changed in APBS?
>
> Thank you very much for the suggestions.
> I have been mapping the potential on the solvent accessible surface
> and displaying the molecular
Hi Wataru,
in addition to what Jason mentioned: Have you tried to look at the
potential mapped on the solvent accessible surface and display the
molecular surface? If you display the potential like this the colors
will be much more muted, on the other hand this is the setting you will
find most o
Aiko,
I can't directly comment on your problem, but I had good experience with
the eMovie plugin. May be give that a try.
http://www.weizmann.ac.il/ISPC/eMovie.html
HTH
Carsten
> -Original Message-
> From: Aiko Matsumoto [mailto:aikomatsumoto1...@googlemail.com]
> Sent: Friday,
Sean,
Just a thought, but the translate command looks like as if it should be
possible to selectively modify the viewmatrix on a per object basis:
"translate" translates the atomic coordinates of atoms in a
selection. Alternatively, is modifies the matrix associated with
a particular
AM, Schubert, Carsten [PRDUS]
wrote:
I am just getting a blank page when I try to access the Pymol Wiki. Do
other people see the same problem?
Working fine for me (using Safari on a Mac).
-Nat
--
Special Offer
I am just getting a blank page when I try to access the Pymol Wiki. Do
other people see the same problem?
Carsten
--
Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
Finally, a world-class log manageme
Hi Madhavi,
with regards to your first question:
I usually add text after rendering the stereo figures. That gives much
better control and has the advantage that label come out cleaner. Look
into Canvas, Photoshop or GIMP to do this. As an additional tip you can
control the depth of the labels thi
Hello List:
Has anyone been able to put together a workable system where they can
run PyMOL from a 3D HDTV using a regular workstation (Linux or Windoze)
and the NVIDIA 3D Kit for presentation purposes? I did some preliminary
research and while there is a wide range of 3D TVs out there I am not
su
burn
> the background but doesn't any longer. I just set my background to
> white and tested all ray_trace_mode settings (with fog on) and the
> background is pure white. Can you please provide a snippet of code
> that produces the effect?
>
> Cheers,
>
> -- Jas
Hi Pymolers,
I just noticed that Pymol produces an off-whitish background when ray
tracing a figure with fog enabled. The RGB values are (252,253,254) with
my standard settings and are devilishly hard to spot on a monitor, but
show up on some printers as a grayish background. Is there a setting or
Hi Martin,
not directly applicable to your question, but may be it directs your
thinking into a different direction. If I remember correctly Warren
pointed out a couple of year ago the p1m file format was supposed to
support downloading of structural information from the web with some
limited scri
Chris,
I don't know much about MACs, but on Linux you can have a look at
/var/log/xorg.?.log or some similar log file. Take a look at the
equivalent log file. May be there is some clue as to why the emitter
won't work. Looks to me like a driver issue.
Good luck,
Carsten
> -Original
Sebastian,
individual clipping planes for objects has been a long standing request and I
am not sure how far it is the queue. Jason may have some more in-depth insight.
If you really want individual clipping planes for object you need to use PovRay
and play around with bounding boxes. That appr
import sys
print sys.version
> -Original Message-
> From: Vivek Ranjan [mailto:vran...@gmail.com]
> Sent: Monday, July 12, 2010 10:37 AM
> To: Pymol
> Subject: [PyMOL] python
>
> Hello,
>
> How can I find out what version of python my current installation of
> pymol is using ?
>
> --
>
Vivek,
you need to put the script in the directory from where you launched
pymol. I.e if you launched pymol from your home directory with pymol,
you need to place the script there.
Pymol knows some basic shell like commands, like cd, ls, and may be some
more. Using these should get you were you
Hi Nat,
"group" works for me in 1r1 or later. Not sure about earlier version of
the 1.0 vintage.
HTH
Carsten
From: Nat Echols [mailto:nathaniel.ech...@gmail.com]
Sent: Thursday, June 17, 2010 12:58 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] what versi
Seemingly simple, but I can't figure it out:
I modeled a loop in 2 alternate conformations and want to display both
of the conformations in a ribbon or cartoon. The selection "show ribbon,
prot and alt B" does not do the trick. The selection syntax must be
correct since "color red, prot and alt B;
Steve,
you need to use PDB2PQR to generate your pqr file, with choice of pH and
then run APBS on that file. I pulled reasonable defaults for APBS from
the APBS plugin tool. PDB2PQR is accessible through the APBS website.
HTH
Carsten
From: Soisson, Stephen M [m
Norbert,
Try something like this for a side-by-side stereo image:
turn y,3
draw
png left_image.png
turn y, -6
draw
png right_image.png
turn y,3
Caveat is that potential shadows may not be rendered correctly in stereo.
That's why the angle option was implemented in ray.
HTH
Carsten
Not much of a help, but WingIDE Professional Edition has a very good
indentation manager, which takes care of the mixed/space tab issues. If you are
working in python frequently it is a worthwhile investment.
Cheers,
Carsten
> -Original Message-
> From: Jason Vertrees [mailto:
Jason,
here are my feature requests, only slightly biased by the fact that some
of them would be useful for my paper now (-:
1) arbitrary clipping planes bound to an object with an intelligent gui
to place them. Something akin to be found in Maestro or semi-transparent
CGO objects which can be ma
Hi,
I am trying to make a movie form a set of morphed pdb files. Currently
the individual files are loaded into the same object with increasing
states, all pdb files contain the SHEET and HELIX record created by
dssp. The object is then displayed as a cartoon. When I loop over the
states I notice
you are looking for?
> http://www.mail-archive.com/pymol-
> us...@lists.sourceforge.net/msg05888.html
>
> Best regards,
> Folmer Fredslund
>
> 2009/9/24 Schubert, Carsten [PRDUS] :
> > Hi,
> >
> > Does anyone know how to get a hold of the viewport dimensio
Hi,
Does anyone know how to get a hold of the viewport dimensions from
within a script? I vaguely remember some posts about this subject, but
could not find anything in my archive.
Thanks
Carsten
--
Come build w
Peter,
here are some general considerations for stereo images
A. The images should be ~63mm apart with respect to a point which you
consider to be neutral, i.e. neither lies in front or in the back of the
"zero-plane"
B. The distance of the images also put restrictions on thei
Dirk,
you could try playing around with different transparency settings in
subsequent scenes to emulate the effect.
HTH
Carsten
From: Dirk Kostrewa [mailto:kostr...@genzentrum.lmu.de]
Sent: Tuesday, September 01, 2009 8:57 AM
To: PyMOLBB
Subject: [PyMOL] Smooth fading of surface
mooth transparency fading-in from 0 to 1 and that I could use in my
pymol-scripts? Unfortunately, I'm not familiar with python, yet ...
Best regards,
Dirk.
Am 01.09.2009 um 15:39 schrieb Schubert, Carsten [PRDUS]:
Dirk,
you could try playing around with different transparency s
pping
planes. If we can achieve this in PyMol then the rest is fairly easy.
Cheers,
Carsten
> -Original Message-
> From: Warren DeLano [mailto:war...@delsci.com]
> Sent: Friday, May 01, 2009 8:53 PM
> To: Schubert, Carsten [PRDUS]; pymol-users@lists.sourceforge.net
>
Hi Warren,
I would be interested to see the OpenGL version implemented, despite the
lack of raytracing support. In a pinch the draw command could just be
sufficient to produce a good picture.
As for the implementation in a raytracer context I second Tsjerk's and
Harry's thoughts on the subject. P
Christian,
as far as I know, PyMol is only able to draw bonds between atoms within the
same object. The easiest way would be to combine the pdb files, probably a good
idea to give the symm-mate a different chain or segid and then issue the bond
command to draw the bond.
HTH
Carsten
--
Wulf,
suppose you have this scenario:
Protein in chain A
Ligand in chain I
Then
create b-site, byres chain A within 5 of chain I
show sticks, chain I
show surface, b-site
should get you close.
HTH
Carsten
BTW If you replace the "create" command with "select" your surface will be
"s
Hi,
how would I go about adding a package to the $PYMOL_PATH/ext/.../site-packages
w/o screwing up the install?
For most packages the mechanism is "python setup.py install". Would this work
to run this from within pymol?
Thanks
Carsten
Nunzio,
make sure that either the DNA is present with ATOM records instead of HETATM
records or set "surface_mode" to 1.
HTH
Carsten
-Original Message-
From: Nunzio Iraci [mailto:nunzio.ir...@gmail.com]
Sent: Saturday, February 28, 2009 7:28 AM
To: pymol-users@lists.sourceforge.
Scott,
the MSEs are probably HETATM records instead of ATOM records. You can either
replace the HETATM records to ATOM records or set surface_mode to 1 which
allows rendering of surfaces with HETATM records (I think, am a bit fuzzy on
that)
HTH
Carsten
-Original Message-
From
Michael, play around with the hash_max value, which seem to partially control
how much memory is used during rendering. You can also reduce the quality of
the rendering Display->Quality, that should reduce memory requirements too. I
know you don't want that, but do you really need max quality? F
Jan,
viewport x,y should do what you want
Cheers
Carsten
-Original Message-
From: Jan Kosinski [mailto:k...@genesilico.pl]
Sent: Wednesday, January 14, 2009 10:11 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] setting window size from the script
Is there a (python an
Buz your image size will automatically be limited by the separation of two
equal points in the respective images, which should be ~62 mm apart. Let me
know if you need more details.
Carsten
-Original Message-
From: Buz Barstow [mailto:b...@mac.com]
Sent: Monday, November 24, 2008 3:01 P
Tom,
you need to hide the 'nonbonded' representation of your ion, which shows up as
a little coordinate system i.e.
hide nonbonded, chain I#if your ion is in chain I
show spheres, chain I
set sphere_transparency=0.5, chain I
Cheers,
Carsten
-Original Message-
From: Thomas
Jhon,
all the newer builds of PyMol are able to read ccp4 maps, no need to convert to
xplor format.
As far as your commands are concerned, you are almost there.
Try this:
load mymap.ccp4, format=ccp4, mymap
isomesh map, mymap, 2.0, site, carve=1.6
were map is the name of the map graphical obje
phenix.reduce is an option
-Original Message-
From: pymol-users-boun...@lists.sourceforge.net
[mailto:pymol-users-boun...@lists.sourceforge.net]on Behalf Of David A. Horita
Sent: Thursday, August 21, 2008 3:32 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] hydrogen naming
Hi,
I believe "show valence=on,your_selection" will do the trick. Where
your_selection is the ligand or whatever you want to display.
Good luck
Carsten
-Original Message-
From: pymol-users-boun...@lists.sourceforge.net
[mailto:pymol-users-boun...@lists.sourceforge.net]on Behalf Of P
Joris,
you should be able to apply different transparency settings if your proteins
are part of different objects i.e.
set transparency=0.8, sel1
set transparency=0.5, sel2
HTH
Carsten
-Original Message-
From: pymol-users-boun...@lists.sourceforge.net
[mailto:pymol-users-boun
Just to add onto what Tsjerk had to say about running python snippets in a .pml
script. You can also encapsulate the python code in blocks like this:
python
python end
This works with all newer version of pymol (>1.0) and enhances readability of
the code quite a bit.
HTH
Carsten
>
to:del...@delsci.info]
> Sent: Friday, April 25, 2008 3:28 PM
> To: Schubert, Carsten [PRDUS]; pymol-users@lists.sourceforge.net
> Subject: RE: [PyMOL] Embeding commands in PyMol session?
>
>
> Hi Carsten,
>
> The best way to share PyMOL content with novice users is via
> pre-def
Hi,
is it possible to embed commands or scripts into a pymol session? I am
routinely creating PyMol sessions for users who for the most part have no clue
how to use PyMol. So I'd like to include a dialog or message, which gets
displayed after the session has loaded and clues the user in how to
Mark,
you need to set
set stick_transparency=0.9, M223Dser
> -Original Message-
> From: Dr. Mark Mayer [mailto:may...@mail.nih.gov]
> Sent: Thursday, March 20, 2008 5:22 PM
> To: Schubert, Carsten [PRDUS]
> Cc: pymol-users@lists.sourceforge.net
> Subject: RE: [PyMO
Joris,
this is a well known problem with the NVIDIA cards. It gets better with the
newer highend cards but does not go away completely. You may want to invest in
such a card and play around with different drivers.
Carsten
> -Original Message-
> From: pymol-users-boun...@lists.sourcefor
JunJun
there are a couple of settings which relate to dashes. Go to Setting->Edit
All... and filter by dash. You need to play around with these settings to get
the desired effect. Be aware, some of these changes only become visible after
raytracing.
Cheers
Carsten
> -Original Me
Warren,
this thread gave me an idea about an enhancement request I had for some time.
Would it be possible to extend the molecular object module in a way that 2 or
more general properties per atoms would be available in PyMol in addition to b
and q. For instance in Grasp 2 properties (Prop1, Pr
Hi
I am trying to define 2 scenes, in one the protein is represented in "cartoon
automatic" mode in the other with "cartoon putty". Pymol (1.0 on Linux or 1.1b
on Windows) both only draw the recalled scenes in putty mode. Is that expected
behaviour? I would have thought that the cartoon mode is
Satinder,
make sure you have the correct CRYST record in your file, then load it and
in the graphics GUI under S(how) select the Cell menu item. That should do
the trick.
Cheers
Carsten
-Original Message-
From: pymol-users-boun...@lists.sourceforge.net
[mailto:pymol-users-boun.
Hi,
does anyone know a trick to force pymol to wait from within a python script
to complete resizing and drawing the canvas?
I used cmd.refresh and cmd.rebuild in various places in the script, but the
raytracing still only shows part of the images. I suspect that the
cmd.viewport command is the
Joris,
just an idea. Check if the /dev entry for your video card has the right
permissions. For the nvidia board I observed that sometimes the entries
(/dev/nvidia0 and/or /dev/nvidiactl) are crw-- instead of crw-rw-rw.
Check if changing the permissions on these entries or changing the owner
m
Bill,
the Linux NVidia driver does not (yet) seem to support this option. Lets
hope for future releases.
Carsten
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net]on Behalf Of William
Scott
Sent: Tuesday, October 11, 2005 11
Hi
I am trying to combine a scene with annotations spanning several lines.
So far something like
> scene new, store, message="Line1\nLine2"
would produce some nice coloration effects but not a newline character.
I was able to use the api function to do the trick
>mesg="line1\nline2"
>cmd.scene(
Hi
I was wondering if it is possible to save a carved out section of a map and
the read it back into pymol as a separate map. The background is that I'd
like to distribute .psw files with a couple of maps, but they get rather
large (>50 MB) since the map data is not compressed in pymol. I am only
Just for the sake of the uninitiated
What are .p1m files and how do they differ from regular .pml files. I took a
quick look at Sebastians file and it looked pretty much like a regular .pml
file to me.
Cheers,
Carsten
-Original Message-
From: Ezequiel H Panepucci [mailto:
Hi All:
just a quick follow up on Warren mentioning the Sharp 3D LCD display. After
a couple of trials with various drivers I got the LCD to work under the
following setup:
Nvidia Quadro FX1100 with driver V67.22
Windows XP with all the latest SPs and patches installed (may not matter)
One head o
Hi all:
I am trying to benchmark our graphics cards or more specifically different
versions of the Linux NVidia drivers with pymol. I cobbled together a short
python script, which I thought would do the trick but it did not. The intent
was to rotate a representation a certain number of degrees in
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