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 into one molecule, which then can be written in a nicely
formatted PDB
...@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't write non-coordinate records to disk. You'll need to
write
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
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 display
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]
Cc: pymol-users
...@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 you please show us exactly what you're typing?
Also
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
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 does not load PDBs from command line
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.
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
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
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
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
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
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
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
AM, Schubert, Carsten [PRDUS]
cschu...@its.jnj.com 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
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
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
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,
-- Jason
On Tue, Jan 4, 2011 at 8:22 AM, Schubert, Carsten [PRDUS]
cschu...@its.jnj.com wrote:
Hi
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
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
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
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
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
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
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
://www.mail-archive.com/pymol-
us...@lists.sourceforge.net/msg05888.html
Best regards,
Folmer Fredslund
2009/9/24 Schubert, Carsten [PRDUS] cschu...@its.jnj.com:
Hi,
Does anyone know how to get a hold of the viewport dimensions from
within a
script? I vaguely remember some posts about
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 their
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
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
Subject: RE: [PyMOL] object
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.
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
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
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-
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?
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
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
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
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
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
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
your python code here
python end
This works with all newer version of pymol (1.0) and enhances readability of
the code quite a bit.
HTH
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
]
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-defined
scenes stored in a session file. Users
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:
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
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,
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
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
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
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
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