Dear Pymol users!
I am using a multi-model pdb containing the 80 predicted docking
solutions as well as the receptor (the both presented in each frame).
I need to calculate all hydrogen bonds (and possible other
interactions) observed in each frame (=docking solution)? I've already
used pymol for t
Hi Pascal,
these changes are beyond the versioned source tarballs. The SVN
repository is more frequently updated to make new (often experimental)
features available to people who like to test them or need them
urgently. CIF write support was added in this commit:
http://sourceforge.net/p/pymol/cod
Hi,
Thomas pointed to me that the code for saving cif files is already
in the open source directory.
We need some help here.
The current version is 1.7.2.3.
In Sourceforge it is 1.7.2.2.
We didn't find the option for saving .cif files as indicated by Thomas
in his last reply.
___
we have imp
Hi Pascal,
we have implemented basic cif export (only atom table and symmetry header for
now), this will be available in the next PyMOL release. The cif export code is
already in the open-source repository, so if you need it urgently or want to
test it, you could compile from source.
To preser
Hello,
I was wondering if there is a way to save CIF files with pymol.
We need this for the large ribosomal PDB files that
are available in the PDB as “split” files (PDB format) or .cif files
(for example 4u3u.cif).
As a related issue, if we load a large cif file (more than 9 atoms
and two le
Hi James,
you can save multi-model PDBs with state=0:
PyMOL> save trajectory.pdb, state=0
There is also a "save_traj" function in PSICO which can write DCD format:
http://pymolwiki.org/index.php/Psico
The latter is based on the "save2traj" script by Sean Law:
http://pymolwiki.org/index.php/Save2
Dear Pymol Users!
I wounder whether it will be possible to save big ensemble of the loaded
into pymol Pdb's files as the trajectory output (like dcd format) what are
actually can be performed by vmd (e.g by means of
http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/animatepdbs/).
The pro
Dear PyMOL users,
After upgrading my notebook to Win7 from XP 'save' function started to function
differently. Before PyMOL would save everything in the directory where I'd
launch it from. Now, by default, it goes to Win32. In some cases I can use
'save as' option and after few clicks get to th
Hi James,
PyMOL itself does not install a .pymolrc file, but you can create your own and
put it in your home directory. On startup, PyMOL will search a couple of places
for the .pymolrc file (current directory, home directory, PYMOL_PATH) and take
the first that is found.
Hope that helps.
Che
Recently I've tried to find pymolrc but couldn't do it ( I have pymol
1.5 installed from binarries package manager )
own@starlight ~/Desktop $ locate pymolrc
own@starlight ~/Desktop $ locate .pymolrc
own@starlight ~/Desktop $ locate *.pymolrc
How I could locate it ?
Akso I'm looking for detailed
Hi James
Check out the information about how to load custom settings and functions:
http://www.pymolwiki.org/index.php/Pymolrc
Hope this helps,
Folmer
2012/8/16 James Starlight :
> Dear PyMol users!
>
>
> I wounder to know about possible way to save settings of the PyMol
> after LogOut from it.
Dear PyMol users!
I wounder to know about possible way to save settings of the PyMol
after LogOut from it.
E.g I've defined some basic settings like fetch_host and fetch_patch
for uploading of new pdb files as well as set new background colour.
Also I've changed some advanced settings - e.g I de
Thank you, Jason. I have a pml script that creates a fairly long (3000
states) movie. There are several morphed proteins that are loaded at
different states, and I was hoping to fine tune the camera views and
clipping planes at key points. My computer runs out of memory after
~500 states, and altho
Vitaly,
Despite the documentation, you cannot save a single state to a
session; you can, however, save a single state to a pdb:
save ~/state5.pdb, my_object, 5
Why are you deleting objects instead of hiding them (using scenes)?
Name collisions? Something else?
Cheers,
-- Jason
On Mon, Jun 18,
Hello,
I have a 60-state session file that contains three objects: one of
them has a single state, while other two have several. In the first
state of the session objects #1 and #2 are loaded, and halfway through
object #2 is deleted and object #3 is loaded.
Is it possible to save the individual s
Hi Martin,
> When I try to save an object as a PDB (after editing it slightly with
> the PyMOL edit mode, i.e. adjusting a dihedral angle),
> the "Save Molecule" dialog asks to save "all", "global" or "objects
> current" state. When saving with the last two, I get no coordinates in
> the generated
Dear List
When I try to save an object as a PDB (after editing it slightly with
the PyMOL edit mode, i.e. adjusting a dihedral angle),
the "Save Molecule" dialog asks to save "all", "global" or "objects
current" state. When saving with the last two, I get no coordinates in
the generated file onl
I don't know if there's a way to do this from within pymol, but it's
fairly straightforward to do using mapman (from ccp4) - or your favorite
map utility.
Pete
Tatyana Sysoeva wrote:
> Dear Pymol experts!
>
> I am going to make a presentation with running Pymol during it. I would like
> to sh
thanks! that is true, I may do this in Phenix... Those maps will be small
and quickly loadable.
I found out that I missed the Youtube video about the Volume in Pymol 1.4,
which is listed on Pymol wiki page, I am sorry. It seems that it might be
not available in the 1.3 version.
Thank you!
On Tu
Dear Pymol experts!
I am going to make a presentation with running Pymol during it. I would like
to show small details (ligand densities) of several ED maps in this
presentation.
I will have to keep several Pymol instances running due to setup of the
presentation to avoid loading big files on the
Thats wonderful, thanks a lot.
Martin
Am 15.08.11 09:25, schrieb Thomas Holder:
> Hi Martin,
>
> there are for sure several ways to achieve this, one might be using
> the "pop" command (there is no PyMOLWiki page, but "help pop" gives a
> quick example how to use it).
>
> fetch 2xwu, async=
Hi Martin,
there are for sure several ways to achieve this, one might be using the
"pop" command (there is no PyMOLWiki page, but "help pop" gives a quick
example how to use it).
fetch 2xwu, async=0
select _justca, byca 2xwu
python
while cmd.pop("_tmp", "_justca"):
cmd.iterate("_tmp", "sto
Dear List
I was wondering if there could be a way of having every residue of a
protein structure being saved to a separate file. How could this be done?
I believe the 'iterate' method might be useful in combination with the
'byres' identifier, but I havent figured out how to combine them in the
Hi Francois,
That information is in the view matrix you get from get_view. The
first nine numbers are the rotation matrix R. The next three numbers
are the camera position c, followed by the three numbers denoting
origin of rotation o. Then to transform your protein coordinates, as
in the PDB, to
Jason Vertrees wrote:
> Hi Francios,
>
> Someone recently asked about this and the answer was that this should
> be a setting, but isn't currently available. If I have time, I'll try
> to sneak this in the upcoming PyMOL v1.4 release.
Is there a workaround for the moment?
For example, asking Py
Hi Virasak,
In Pymol you can change the element type to match your needs:
alter n. si, elem="si"
Hope it helps,
Tsjerk
On Tue, Mar 22, 2011 at 2:44 PM, Virasak Dungsrikaew wrote:
> Hi Tsjerk,
>
> You are right. In my work, I almost working with XYZ format and all
> programs that I used is wor
Hi Virasak,
It goes a bit far to call it a bug. It's a problem with the xyz
format. It only has names for atoms, not element types, and Pymol
can't go guessing, otherwise any CA would end up as calcium :S
Cheers,
Tsjerk
On Tue, Mar 22, 2011 at 2:30 PM, Virasak Dungsrikaew wrote:
> Hi Tsjerk,
>
Dear all,
I am using PyMOL 1.2r2 on Ubuntu 10.10.
When I click 'Save Molecule...' from 'File' menu and select a molecule
that contained 'Si' atom, the output pdb will show 'S' instead of 'Si'
on the right most column.
I also try this with mol format, the result is the same.
Is this a known bug or
Jason Vertrees wrote:
> Hi Francios,
>
> Someone recently asked about this and the answer was that this should
> be a setting, but isn't currently available. If I have time, I'll try
> to sneak this in the upcoming PyMOL v1.4 release.
Please, send me an e-mail if it is done some day.
Other soft
Hi Francios,
Someone recently asked about this and the answer was that this should
be a setting, but isn't currently available. If I have time, I'll try
to sneak this in the upcoming PyMOL v1.4 release.
Cheers,
-- Jason
On Fri, Feb 25, 2011 at 3:05 AM, Francois Berenger wrote:
> Hello,
>
> Is
Hello,
Is it possible to save the Connolly surface
computed by Pymol without any rotation and translation
added compared to the PDB from which the atom coordinates were read?
I looked at the .obj file output and find there was some centering
done and also some rotation added.
Thanks a lot,
F.
-
ack together in one's favorite image handling
>> program a la panoramas in photography Is this way too complex to
>> be bothered with? I suspect parallax may be a problem...
>>
>> -Tom
>>
>>
>>
>> -Original Message-
>> From: Ev
Of course your protein and computer will be different to mine, but
just as a test I used a fully surfaced 380 residue protein with a
docked ligand and did the raytrace you suggest:
using Pymol 1.2:
Macbook Pro 2.16GHz, 2GB RAM took 10 minutes to render, 20 seconds to
write the 9000x6000 PNG
led, each frame would have a distinct
"vanishing point" (if that's the correct term).
Cheers,
Warren
From: Thomas Stout [mailto:tst...@exelixis.com]
Sent: Thu 10/22/2009 12:36 PM
To: Tsjerk Wassenaar
Cc: pymol-users@lists.sourceforge.net
Subject: Re:
er 3 | render 4 |
| | |
| | |
---
I feel like I'm missing something important here!
-Tom
-Original Message-
From: Tsjerk Wassenaar [mailto:tsje...@gmail.com]
Sent: Thursday, October 22, 2009 11:45 AM
To: Thomas Stout
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Saving high r
-Original Message-
> From: Eva Vanamee [mailto:eva.vana...@mssm.edu]
> Sent: Monday, October 19, 2009 1:51 PM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] Saving high resolution images
>
> Hi,
>
> I'd like to save an image in high resolution for a po
y, October 19, 2009 1:51 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Saving high resolution images
Hi,
I'd like to save an image in high resolution for a poster.
The requested size is 20" by 30". I calculated that it would correspond
to a 6000 x 9000 pixel image.
H
For photographs, 180 dpi is often sufficient for large prints. For
diagrams, which are less complex, you might even get by with less, maybe
even 120 dpi. You could try rendering a portion of your image at that
resolution (e.g. 540 x 540 for a 3" square) and see how it holds up at a
normal viewi
Large format prints are not usually printed at the same resolution as
normally-sized images. This compensates for the distance the viewer is
at to see the image. If a professional printer is doing the work ask
them what resolution they need.
Rich
Eva Vanamee wrote:
> Hi,
>
> I'd like to save a
PM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] Saving high resolution images
>
> Hi,
>
> I'd like to save an image in high resolution for a poster.
> The requested size is 20" by 30". I calculated that it would
correspond
> to a 6000 x 9000 pixel im
Hi,
I'd like to save an image in high resolution for a poster.
The requested size is 20" by 30". I calculated that it would correspond
to a 6000 x 9000 pixel image.
How can I create such a large ray traced image without crashing the
computer?
Many thanks in advance for the help.
Best,
- Eva
te: Friday, Mar 13, 2009 6:03 pm
Subject: [PyMOL] Saving figures for publication
To: "pymol-users@lists.sourceforge.net"
Hi,
I need to make figures in tiff format with at least 600 dpi resolution
as required by the journal. The default resolution in Pymol figures is
72. Is there a si
Dear Abhinav
2009/3/13 Abhinav Kumar :
> Hi,
>
> I need to make figures in tiff format with at least 600 dpi resolution
> as required by the journal. The default resolution in Pymol figures is
> 72. Is there a simple way to increase the resolution (and save it in
> tiff format)?
> Alternatively, I
)-228-7935
email: rrowl...@mail.colgate.edu
-Original Message-
From: Abhinav Kumar
Date: Friday, Mar 13, 2009 6:03 pm
Subject: [PyMOL] Saving figures for publication
To: "pymol-users@lists.sourceforge.net"
Hi,
I need to make figures in tiff format with at least 600 dpi resolution
Hi,
I need to make figures in tiff format with at least 600 dpi resolution
as required by the journal. The default resolution in Pymol figures is
72. Is there a simple way to increase the resolution (and save it in
tiff format)?
Alternatively, I can 'convert' from png to tiff afterwards
--
T
Hi Miguel,
This seems like a big in the program. Save the file as per usual (.pse)
Change the suffix of the file to .psw and that works fine
J
Miguel Alejandro Pabon Sanclemente wrote:
PyMOL community,
I want to assemble a short animation using the PyMOL movie-making
capabilities. I trie
PyMOL community,
I want to assemble a short animation using the PyMOL movie-making
capabilities. I tried to save several scenes as a .psw file (as previously
suggested) but by default PyMOL saves the file as .pse. How can I make PyMOL
save the file as .psw? I'm working with PyMOL version 0.
...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Warren
DeLano
Sent: Saturday, April 15, 2006 11:08 AM
To: Paulo Martel
Cc: pymol-users@lists.sourceforge.net
Subject: RE: [PyMOL] saving files in pymol
Paulo,
Thank you for the simple and helpful suggestion -- this is exactly the
o:war...@delsci.com
> -Original Message-
> From: pymol-users-ad...@lists.sourceforge.net
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
> Paulo Martel
> Sent: Friday, April 14, 2006 6:45 PM
> Cc: pymol-users@lists.sourceforge.net
> Subject: [Py
Sorry, wrong thread.
This should be my answer to laura's question about different sphere size.
Too excited to be of a little help here.
Tiger
From: "Geng Tian"
To: pmar...@ualg.pt
CC: pymol-users@lists.sourceforge.net
Subject: RE: [PyMOL] saving files in pymol
Date: S
: [PyMOL] saving files in pymol
Date: Sat, 15 Apr 2006 02:40:39 +0100
Hello,
one thing I find a little bit annoying: the "save" command in Pymol will
accept any of ., and if the is unknown,
it will simple save a pdb file. While some people may find this a useful
feature, I think i
Hello,
one thing I find a little bit annoying: the "save" command in Pymol will
accept any of ., and if the is unknown,
it will simple save a pdb file. While some people may find this a useful
feature, I think it is quite dangerous. For instance, suppose
I'm trying to save "work.pse" and mista
orge.net] On Behalf Of Alan
> Sent: Monday, March 20, 2006 12:16 PM
> To: Warren DeLano
> Cc: Pymol
> Subject: Re: [PyMOL] Saving PDB with CONECT information
>
> Thanks a lot Warren.
>
> If you allow me, my script to build sequences of 3 peptides
> is almost done.
t; From: pymol-users-ad...@lists.sourceforge.net
> > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Alan
> > Sent: Monday, March 20, 2006 11:39 AM
> > To: Pymol
> > Subject: [PyMOL] Saving PDB with CONECT information
> >
> > Hello List!
>
-Original Message-
> From: pymol-users-ad...@lists.sourceforge.net
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Alan
> Sent: Monday, March 20, 2006 11:39 AM
> To: Pymol
> Subject: [PyMOL] Saving PDB with CONECT information
>
> Hello List!
>
> Is
Hello List!
Is PyMol able to save the built protein/molecule in a PDB file with
CONECT information. If so, how to do it?
Thanks in advance for any help.
Cheers,
Alan
--
Alan Wilter S. da Silva, D.Sc. - Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road,
Marylin,
try saving using the command line instead of the pull down menu i.e
"save newfilename.pdb"
This should save everything in one file.
Brian
--
***
Brian J Goodfellow
Departamento de Química
Universidade de Aveiro
3810-193 Aveiro, Portugal
Tel:
ebruary 08, 2006 11:16 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] saving coordinates of docked molecules in
> new orientation
>
> Hi all,
>
> After manually docking a molecule to another molecule (from a
> different .pdb file), is it possible to wri
Hi all,
After manually docking a molecule to another molecule (from a different
.pdb file), is it possible to write out the coordinates of the moved and
docked molecule with it's 'new' coordinates relative to the .pdb to
which it was docked?
Marilyn
Marilyn D. Yoder
Division of Cell Biology a
If you would like appropriately scaled images then you can set up your
viewer to the appropriate dimensions eg for a square
viewport 700,700
or rectangle
viewport 800,400
If using a square I then use
ray 1800,1800
this ray traces an image larger than your pymol window and allows you to
sav
> Hi everyone,
> Each time I try to save images, Pymol writes 640x480
> pixel image to the file. I wonder if there is a way to
> save images (png format) other than 640X480 pixel that
> is default.
> Any help will be appreciated.
> Thanks.
Images are saved as either the size of the viewer window,
Hi everyone,
Each time I try to save images, Pymol writes 640x480
pixel image to the file. I wonder if there is a way to
save images (png format) other than 640X480 pixel that
is default.
Any help will be appreciated.
Thanks.
__
Yahoo! fo
05 11:45 AM
> To: kosa
> Cc: pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] saving multiple object in one pdb file
>
>
>
> > My question is: how to save multiple objects from pymol as one nice
> > pdb file, for instance with each object with different chain nam
> My question is: how to save multiple objects from pymol as one nice pdb
> file, for instance with each object with different chain name?
alter SymgenObject,chain 'X'
and repeat as needed for all objects (changing the chain as needed). Then
use all of your objects as the selection for save (ak
Dear users,
I had generated many symmetry mates of my structure using pymol symexp
command. I got many objects generated. Each contains one symmetry
related molecule. Now I want to save all objects in one pdb file. I do
"Select all", create new object from this selection and save the object
a
ol-users-ad...@lists.sourceforge.net
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Tim Fenn
> Sent: Saturday, August 13, 2005 11:38 AM
> To: Schubert, Carsten [PRDUS]
> Cc: pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] Saving a carved section of a map.
>
> On
On Fri, Aug 12, 2005 at 02:48:16PM -0400, Schubert, Carsten [PRDUS] wrote:
>
> 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.
Pymol won't do it, but if its something thats urgent, povscript+ saves
maps in GTS format (in
Original Message-
> From: pymol-users-ad...@lists.sourceforge.net
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
> Schubert, Carsten [PRDUS]
> Sent: Friday, August 12, 2005 11:56 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] Saving a carved
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
ack! the code i sent works with some simple functions, but not with
everything. i'll toy around with it some more, but i'll still have the
same question: would it be possible for pymol to save the results of
cmd.extend in session files and restore them if security is turned off?
thanks,
-mi
hi,
i have some scripts that load a bunch of files and do various smart things to
make it easy to work with my data. in particular, they define functions and
use cmd.extend() to register those functions. the setup takes a long time, and
is therefore inconvenient. i'd like to go through it o
rincipal Scientist
DeLano Scientific LLC
Voice (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
> steve Alam
> Sent: Friday, September 24, 2004 8:52 AM
Dear Pymolers,
I've been using pymol to superimpose NMR ensembles. The Align FXN
works great and would look something like:
load /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_1.pdb, MOL1
load /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_2.pdb, MOL2
load /Users/alam/Documents/nzfcom
Hi Greg,
So when you say that sticks don't look very good I assume you mean they
are too thick? If this is the case you know that you can change the
stick thickness by changing the stick_radius value
set stick_radius, 0.1
Ciao,
Scott
On Sep 13, 2004, at 10:56 AM, Greg C wrote:
Thanks Scott.
ol-users@lists.sourceforge.net >Subject: [PyMOL] saving images >Date: Mon, 13 Sep 2004 09:38:45 -0700 > >Hi Greg, >You might need to display your sidechains as sticks rather than >lines in order for them to be visible when you write out your image >file. Or perhaps, if you are not
Hi Greg,
You might need to display your sidechains as sticks rather than lines
in order for them to be visible when you write out your image file. Or
perhaps, if you are not already doing it, you should raytrace your
scene by hitting the "ray" button before you write out your image file.
Scott
Hello all,
I'm having a problem saving the pymol output as an image. I'm working with asingle alpha helix (~25 residues) with the residues displayed as lines, the backbone as a ribbon, and one or more of the residues as spheres. When i go to save the image, the lines are no longer present in the
"Warren L. DeLano" wrote:
>
> You've got choose either real-time manipulation with OpenGL-quality
> rendering or prerendered movies without manipulation. We need another
> 100-1000 fold increase in CPU performace before real-time raytracing will
> become possible.
>
> -Warren
Dear Warren,
Do
On Sun, 2 Jun 2002 kkli...@gate.sinica.edu.tw wrote:
> Now here comes another question.
> I prepared a long movie by running the script I wrote.
> I use a very good desktop to generate the movie and
> the speed of rendering is fast.
> But if I want to demonstrate the same movie with pymol on a
> n
Dear pymolers,
Yesterday I asked the question about selection.
After studying python manual I figure out what I should do.
> I can select some residues in my protein in the command prompt
> by saying for example
> select prot = (VAL or PRO or GLY)
> but now I have trouble translating
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