Hi Adiphol,
> electron density map. First, I only have .mtz file at a hand so could
> anyone suggest me how can I convert this .mtz-file to the map or any file
> that support to PyMol. Second, this is quite not so involve with the PyMol
> program - sorry, if I would like to have an electron densit
> Finaly I succesfully installed the .NET framework, the Platform SDK, and so
> on... a lot o stuff indeed!
I'm not clear on why you'd need the .NET framework (pymol/python stuff is
generally compiled to machine code, not CLR bytecode). One thing to check
is that you're using the correct compiler
> I know that as well... what I don't know is how to install it under PyMOL.
> If I were using simply python, than that would be no big deal, I did that
> a
> 1000 times: setup.py --build; setup.py --intall
>
> Presently I'm using the windows version of PyMol, and installing a
> separate
> python
> a mystery to me. Why is there a difference bewteen contour levels of FFT
> electron density maps displayed in Xfit vs pymol? When using the command
> for example :isomesh mesh1, fo-fc, 1.0, etc..., in pymol what does 1.0 in
> terms of sigma level really mean. I was under the assumption that 1
Hi,
> I have a problem with set_key() that appeared when I executed two scripts
> sequentially. In both scripts I set the F1 key to do something different
> (ok, not a very smart move...). I thought that the newest set_key() would
> take precedence over the latest and overtake its adressing, but
>
Scott,
> I have had this problem for the past few weeks, and it has been
> difficult to diagnose the cause. The problem is that in the X11 version
of pymol run on my mactel osx laptop does not interpret my three button
mouse click properly. When I click on a given atom in the UI, it
selects some
You could also try to add sys.path.append(dllpath) to your python script,
where dllpath is the full path to the location of the pymol dll's.
Of course, this approach might run into problems with different python
versions; but depending on what you're trying to do it might be worth a
shot (if ther
Warren,
> Right now, I would only buy a straight Linux desktop for ideological
rather
> than practical reasons. If you instead buy a Mac "Pro", you get the
ability
> to run all three operating systems simultaneously, at native CPU speeds,
and
> on an as-needed basis thanks to virtualization. Rig
Well, I've managed to get pymol-0.99rc6 (with ext-0_99rc1) almost working
on suse 10.2/amd64 and figured I'd post my work-arounds so that next time
someone searches the list archives they won't have to figure them out
again (sorry if I'm duplicating things...I wasn't able to find anything);
as well
>Is there a good way to calculate and color residues by hydrophobicity
> in
> pymol? A google search showed only a very simple script that was based
> entirely
> on a single-residue lookup table. I'm looking at a set of structure
> predictions, and it would be nice to easily see that a fold
Terry,
> Method 1.
> -
>
> In the most straightforward effort, I download pymol-0_99rc6-src.tgz and
> run
>
>python setup.py install
>python setup2.py install
>./pymol
>
> as instructed. The first two commands run fine. The ./pymol gets me
>
> Fatal Python error: Interpreter
Albion,
> Is there any way in Pymol to change the color of the fog? I want dark
> fog on a white background.
As far as I know, fog works by setting transparency based distance from
the view center (clipping planes? I'm not sure of the specifics). You
might be able to do this in a post-processing
Hi,
> parseInput
> self.parseLines(file.readlines())
>File "/usr/local/apbs-0.4.0/tools/manip/psize.py", line 116, in
> parseLines
> self.q = self.q + float(words[3])
> ValueError: invalid literal for float(): 1.00119.63
>
>
> Any clues ?
It looks like it's reading from a pdb file w
> i install pymol via svn ebuild (attached). It crashes with a segfault but
> only
> if i am inside my home directory. If i am outside, everything works fine.
>
> Any ideas what this could be related to?
This may be a long-shot, but do you have any python scripts in your home
directory? If so, th
As far as I know, there isn't currently a way to do this within pymol. It
does seem like an interesting idea though.
For a poster, you'd probably have to go with the two-color stereo scheme,
which would mean losing color depth (as far as I know). You could try
generating the initial image with c
Hi Yehuda,
> I'm doing a movie script and my boss wants me to add labels,
> I know how to write the cmd command but i because i'm using cmd.mdo i
> can't
> add more ' " ' then the one in begging and one on the end.
> the line with the problem is:
> cmd.mdo (691," hide spheres,ERYTHROMYCIN;show car
Hi,
> We are, for the first time, using pymol to make figures that show
> electron density in addition to the model. No problem making the
> figure, but when we go to ray-trace the image, pymol crashes. This
> only seems to happen when electron density is present in the figure.
> We are using cc
> Thanks for the reply. "Irretrievably crashing" means that everything
stops dead. The screen freezes, mouse/keyboard become unresponsive, the
machine becomes unreachable (via ssh or even ping) from other
> workstations. Background processes instantaneously halt. A 'proper'
crash in other words!
Hi,
> I have tried 0.99 rc6 and rc7, and the 1.00 beta 01 that is described as
> "for testing on 64-bit linux", all with the same result. PyMOL appears
> to start normally
Good troubleshooting procedureI've had no problems w\ 0.99rc9 on suse
10.0 (single cpu though...so smp/threading issues w
Hi,
Based on your mapman info, it looks like this map is centered on the
origin of your unit cell. One possibly explaination is that your model is
in the center of the unit cell, and that Chimera is using symmetry to
generate density around the region you are centered on (I have never used
Chimer
Hi,
> I want to align two structures (worked fine in pymol) then generate
symmetry related molecules for each to compare crystal packing contacts
(did not). Both structures are for same dna each with different
ligand. One structure has one molecules/AU (generates symmetry fine).
The other 2/AU
>
> for i in range(2):
>
> print i
>
>
> What am I doing wrong? It doesn't matter what kind of indent (tabs,
> spaces) or filetypes (DOS/Unix) I use.
I ran into the same problem a while back. Try:
for i in range(2): \
print i
the EOL needs to be escaped for some reason...
Pe
Hi Noel,
Which version of gcc are you using? A quick check of google for the
unterminated argument list in macro error makes it look like that could be
an issues (on my systems, it works for gcc-3.4.5 and 4.0.2; but that's
using make instead of python distutils). It looks to me like a c
preproc
Ron,
> I'm not sure I fully understand your suggestion. It sounds to me
> like what you're saying is that I should add code (e.g. a dictionary)
> to the importing.py load() function which saves the file information
> of objects as they're loaded. But then instead of just distributing
> my plugin
Hi,
> I'm working on a plugin that reads information appended to the end of
PDB files to draw CGO objects. Right now, I have the user specify the
filesystem path to the currently loaded objects through the
> plugin GUI so that I know where to go to find the file. For one object,
this isn't so ba
Hi,
> 'D:\Program' is not recognized as an internal or external command,
operable program or batch file.
> ObjectMapLoadDXFile-Error: Unable to open file!
>
> - something wrong in assigning a correct path name. How to fix this
error?
> I appreciate for your valuable suggestions to overcome this pr
The easiest way I'm aware of to do this would be to use the ccp4 program
pdbset, but there are numerous other ways/programs that will do this (if
pymol has this capacity, I'm not aware of it; but someone else will
correct me).
Pete
>> I've been looking through the PyMol reference and wiki page
> 2) filelist:
>
> get a kind of temporary script which would be run on each file in the list
> when you opened it. A kind of frozen view (or a curried one?).
>
> Maybe I should just make it. Then I wouldn't have to explain the idea.
Ok, I was confused on what you meant before. I've been in s
> which I already have anyway, and I want to have pymol for multiple
> flavours
> of UNIX in the same directory on a shared network file system if possible.
> Now I'm hitting that famous bit:
> $ ./pymol
> Traceback (most recent call last):
> File "/{my PYMOL_PATH}/modules/pymol/__init__.py", lin
Tech:(650)-872-0834
> . Fax:(650)-872-0273 Cell:(650)-346-1154
> . mailto:war...@delsci.com
>
>
>> -Original Message-
>> From: pymol-users-ad...@lists.sourceforge.net
>> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
>> Peter Adrian Mey
Hi all,
For complex scenes, I've noticed that pymol 0.99rc6 (with ext0.99rc1) on
linux appears to use more memory when started from a pse file than it does
when loading the models/maps manually or from a pml script (based on the
fact that I get out of memory errors during ray-tracing after startin
Fei,
The easiest way would be to use get_view/set_view.
1. Move your first frame pdb around until you're happy with the view
2. type get_view (pymol viewer window, or pymol gui window), and save the
output in a new text file (I'd call it view.pml, but that's just me)
3. Load all of your frames in
There are two ways to do this. Either start pymol from the command line
in your working directory, or use .pymolrc to automatically change to this
directory (something like os.chdir('~/working_directory') should do it).
Pete
> Would it be possible to add setting to pymol for a default working
di
Hi Nick,
This sounds vaguely similar to the msvcr71.dll issues that were recently
discussed on the list (searching the list archives will give you more info
on this, but the quick fix is to search the hd for msvcr71.dll and copy it
to the pymol install directory).
If that doesn't resolve the prob
> 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 makes it ve
> same here, how big are your map files in MB, how much ram and swap space
> do you have?
~5MB/map, 512MB RAM, ~2GB swap. I'd expect a segfault (or an exception at
least) if I was overloading the memory/swap, and CPU would drop if it was
running out of physical RAM and swapping too much.
> I ha
Point Blvd., Suite 213
> . South San Francisco, CA 94080 USA
> . Biz:(650)-872-0942 Tech:(650)-872-0834
> . Fax:(650)-872-0273 Cell:(650)-346-1154
> . mailto:war...@delsci.com
>
>
>> -Original Message-
>> From: pymol-users-ad...@lists.sourceforge.net
>&
Hi everyone,
Has anyone else run into cases where pymol will freeze the X-server (pymol
doesn't repond to mouse or keyboard input; keyboard non-responsive to
caps-lock on/off)? The system is still stable, I'm able to login remotely
and see that pymol is running at 100% CPU. Killing pymol results
>
> I would like to change the current path for stderr to /dev/null by
> example.
>
> I have a plugin which creates a legend box from a fake (empty) apdb map.
> Instruction, which loads the map, sends an error message and I would
> like to hide it.
>
> How can I do ?
Create a new script (pymol.bas
Hi all,
I noticed today that when reading a png file using load_png, the alpha
channel does not appear to be respected (regions of the png that should be
transparent are not transparent but show up as white).
Does anyone know if this by design, a bug, or something I'm doing
incorrectly setting my
Daniel,
> I just tried to install the latest version of Pymol on a XP laptop. The
> installation completes but when I try to launch the program I get
Are you trying the latest release version or one of the betas? In any
event, it might be possible to install an older version (although this may
Hi all,
I've run into a small glitch that I was wondering if anyone else had seen
(or knew of a way to fix). At somewhat unpredicatable intervals, the
reinitialize command doesn't actually clear the viewer display (objects
show as deleted, but are still visible).
Any ideas?
Pete
Pete Meyer
Fu
> 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,
> 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
Hi Marcus,
> The surface rendering in PyMOL is quite nice, but I cannot separate the
> "branches" of the surface. That is, I would like to view a large cavity
> inside of a protein independently from the outer, solvent accessible
> surface. Is anyone aware of a means to do this?
The easiest way
Should anyone else ever need to try this, there turns out to be a very
easy way to do it, assuming that your solvent mask is in ccp4 mask format.
1. use mapmask mskin $MASKFILE mapout $CONVERTED_FILE
2. load $CONVERTED_FILE into pymol, treating it as a normal map.
Contouring at 1.0 will display
Hi pymol users,
Has anyone had any sucess in loading and displaying solvent masks in
pymol? Checking the list archives and wiki didn't result in anything;
neither did google. "help mask" within pymol seems to be talking about
selection stuff.
It seems like the best way would be to modify the cc
> hi,
> In pymol how to increase the box size of electron density map. By default
> it is opening with an square box of some value. I want to increase the
> size. How to do that?
> Thank you for your help in advance!
> sidhu
>
By default, pymol shows the entire map range. The easiest way to incre
> Or you can dump to povray and render at whatever resolution you want,
> but the image will not resemble exactly what is seen in the pymol viewer
> window.
>
I've noticed problems with the clipping planes (z axis) whenever I've
tried this. Specifically, the near clipping plane is apparently not
> multiple structura alignment. I pointed out three structures for further
> processing within all 12 structures. However, when I try to ray the
> structural
> resolution (only 3 of all 12 structures) to 2000x2000 with 'ray 2000,
> 2000', I
> always received a low resolution (as screen resolution o
> Can someone tell me wether it is possible to use a stand-alone python
> installation alongside the latest PyMol releases? I have a few things
> set up in my main python installation which an older (python free)
> version of Pymol was happy to use, having installed the newer version it
> uses it's
Hi Dirk,
> a protein structure. Is there a way in PyMOL to export the individual
frames for a movie from scenes? If not, this would be my most desired
missing feature in PyMOL!
Yes. What I do is to use a script to step through each frame of the movie
(rotation by 1 degree, zoom in slightly, chan
Simon,
> I then tried to follow Peter Myers instructions by adding the cctbx
Meyer, not Myers (not that it matters much).
> directory to the sys.path, however as I have two directories called
cctbx_build and cctbx_sources was not sure which should be added?
>
Probably cctbx_build. If in doubt,
Hi Anna,
I generally run apbs seperately (due to difficulties with Alphas), but use
the plugin to display with pymol. apbs will produce two output files,
acc.dx and pot.dx. acc.dx is the electrostatic potential mapped to the
solvent accessible surface; pot.dx is the electrostatic potential over
> Why don't we? Because we do most PyMOL development on Mac OS and Linux,
> using free or open-source tools, such as GCC, GDB, and Apple's wonderful
> XCode, with CHUD and OpenGL profilers. Even on Windows, we are now
> bypassing Microsoft Visual Tools altogether and using MingW and GCC to
> bui
> I am trying some of pymol scripts from Prof. Robert L. Campbell, which
require cctbx module. but I don't know how to put pymol and cctbx
togther.
> I download window version of cctbx/python2.4 bundle. and I download
pymol-0_98rc5-bin-win32-py24.zip. Installation of cctbx is fine, but I
got
> an e
> I have been trying to coax Pymol to raytrace or output to pov
> (make_pov.py) some very large surfaces and I am unable to. It works for
> ~33,000 atoms, but chokes on ~61,000. I would like to get up to >100,000.
>
> Anybody have some good tips? I have tried adjusting hash_max, but I
> think this
Hi All,
In case anyone was interested, I was recently able to install pymol on
tru64 and figured I'd post how I did it.
This isn't as straightfoward as a linux build, but most of the difficulty
comes from building the extensions. For ext-0.95 and pymol-0.97, follow
the generic instructions, except
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