Is there any way to color by secondary structure? I know of other
programs that do this (Molmol, for example- though its colors are
hideous); I'd be happy using a scripted solution if that's easiest. I'm
guessing there's some easy way to loop through residues or atoms and
determine what their
the Quadro 2 from a machine we bought as
a server. Would I see any actual performance gain? Which chip is
actually faster, at least for what I'd be using it for?
thanks,
Nat Echols
Gerstein Lab
Yale University
0. Upgrade to 10.2.3 if you have not already done so.
On a side note, did they fix NIS compatability again after breaking it in
10.2? I dropped OS X as soon as I discovered that, since that made it
nearly useless for the environment I work in. If they got it working
again, that and the new X
They are different, especially at the ends of the helixes ... the web SS
seems to have longer helixes than the pdb HELIX info. Is one more
'correct' than the other?
If in doubt, obtain DSSP (it might be installed locally already) and go
with whatever it tells you:
workstation (O2, Octane, Fuel, Onyx)? I've got an old Pentium III PC with 450
MHz and a (non-stereo) Nvidia GeForce2 MX440 graphics card side-by-side with
an SGI O2 with a R12000 processor: a simple pymol (0.86) movie of a protein
sketch at 800x800 resolution and maximum display quality
Pymol at least *compiles* under a vast amount of processor
architectures, if only under Linux:
http://buildd.debian.org/build.php?arch=pkg=pymol
Nothing wrong with testing your code on as much platforms as possible of
course :)
It's harder than you think. I have a *really* old SGI, which
I'm new with Pymol and I would like your help in the following problem:
I have a receptor image that I want to emphasize the ligand in its interior.
I'm a big fan of transparent surfaces for this, e.g.:
http://bioinfo.mbb.yale.edu/people/nat/mbp.mpg
Its a nonpeptidic ligand that I would like
I have one object showing the surface of a protein and another object showing
a ligand inside the protein.
Is it possible to use the clip command to define different clipping planes
for the 2 objects.
I want so cut the proteinsurface using clip, but the Ligand inside the
protein should
Has anyone been succesful in depicting a membrane surface in pymol? The
archives showed a similar question from John Maynes but no answer.
I would like to render my protein above a membrane surface as cover art for a
soon-to-be published paper.
I'm not entirely sure I understand the
This looks terrific. However, I'm having problems building on both Linux
and Irix (using the Intel cc and SGI cc, respectively). It compiles fine,
but './pymol.com -c' fails with Fatal error: can't initalize module
sglite. It's still right where it should be in contrib/sglite - any idea
why
I'm trying to make some figures for a review, and I'm seeing weird little
partial spheres show up when I try to ray-trace a polymerase structure:
http://bioinfo.mbb.yale.edu/people/nat/weird.png
They're in the bottom third of the picture, and seem to show up in
the same location in the structure
I'm stuck using some OS X computers that do not allow installation of
software. Does anyone have (or can quickly build) PyMOL 0.9 as a single
directory that I can launch pymol.com from without having to make any changes
to the system? Given the circumstances, I probably need to work out of
I just got a shiny new Gateway laptop - essentially a ripoff of the 15
Apple (but cheaper), with NVidia chipset. I installed RedHat 9.0, NVidia
drivers, and the PyMOL rpm for rh9, but I get segfaults when I try to run
'pymol'. The tar.gz file works perfectly, so it's not a problem for me,
but I
What's been added? I didn't see a changelog. . .
(the 'dss' command, by the way, looks unbelievably awesome.)
On Sat, 25 Oct 2003, Warren L. DeLano wrote:
(in a whisper)
I'm still in the process of building binaries, but pioneers are welcome
to start downloading 0.92, if your platform is
I am not suggesting at all that users should now start coding for PyMOL
in BASIC - naturally, the best way to extend PyMOL remains to write
additional program modules in Python. Nevertheless, for people who
already write code in languages other than Python, the above strategy
might represent
Hmmm, I've been wanting to do the exact same thing, and I'd reached the
conclusion that the only way to do it would be to write a Python script.
I'd be happy to share it when (if) it gets written (perhaps this week,
since I'm stuck without real work for now).
Ideally, it'd be nice to have even
The downloaded script is then executed by Pymol, which can uses Python's
socket abilities to download PDB files and run Pymol commands on them.
H, I like this idea. Can PyMOL open files directly over the web? It
would be nice to simply type
PyMOL load http://server/1cll.pdb, calmodulin
I'm very curious about this dial all of a sudden - I just started doing
refinements, and I'd love to use my laptop as much as possible instead of
our slow old SGIs. Has anyone used it on Linux? How's it work with O?
Could it theoretically be programmed to, say, flip through rotamer
libraries or
I know this has come up before and I can't remember what the solution was.
PyMOL is drawing bonds between the protein I'm interested in, the ATP
analog, and the bound metal ions, presumably because the metals are close
enough to the protein and analog for bonds to be autodetected. Is there a
way
areas of the protein that undergo movement and show general trends. There is
also a server at Yale (http://www.molmovdb.org/molmovdb/ ) that will perform
simulated annealing while morphing between two structures, thereby producing
intermediate structures that violate fewer protein restraints.
I'm trying to use Robert Campbell's draw_axes script with PyMOL 0.97 on
Linux. Is there a simple way to get stock PyMOL to recognize stock CCTBX?
I'm not having any success here. (If I have to I'll use the special
distribution on the lab's Mac, but I'd rather just get it going on my
computer.)
I just downloaded the beta the other day and this is the first time I've
tried it out. When I'm typing commands in the graphics window or using
the menus on the internal interface, the display frequently breaks apart -
a large rectangular portion literally gets clipped off from the rest of
the
Thanks to the poewrful software I was able to create some protein
animations using Python. As a mac user I have the option to save
directly the animation for quick time player. From the options I have
upom save, I tried 'movie' and 'animation' and both formats show a
reduced performance when
There is a well documented bug in Powerpoint 2004 for mac regarding
movie playback performance which seems to be the problem. There are
hundreds of posts on Microsoft's support forums. Actually when you
build the slide in PPT 2004 in edit mode the preview of the movie plays
fine but not in
Please revise, extend, and embellish.
- structure alignment (pretty simple, but a lot of people don't know how
to use the various commands)
- as part of movies, a large section on available 3rd-party apps and
codecs would be very useful (as well as workarounds for PowerPoint
madness)
-Nat
You can't just do:
set stick_radius, .5, name n+ca+c+o
set stick_radius, .2, ! name n+ca+c+o
because both selections belong to the same object and the whole object
is affected by the setting change.
On the other hand, you CAN do this:
show lines
show sticks, name n+ca+c+o
set stick_radius,
On a second note (and sorry to open up this debate again), What is the
consensus for displaying a pymol movie in a presentation package such as
powerpoint? i've tried avi and mpeg but i find that there is a loss in
the quailty when compared to the sharpness of a animated gif.
I'm pretty sure
Fit only works with objects that are identical in terms of atom number,
chainID, atom name and what not. This is not the case for a protein on
one side and a protein plus ligand on the other.
I've gotten away with some differences between chains. Sometimes you need
to force it to fit using
you can set the number of cycles of refinement on the command line.
change this:
align 1kjg i. 1-99 n. ca, 1kjh i. 1-99 n. ca
to this:
align 1kjg i. 1-99 n. ca, 1kjh i. 1-99 n. ca, 0, 0
I forget what the first 0 means; the second means don't refine. It'll
use all matching atoms this
Apologies if this has been asked/answered already. My rotation student
just showed me how PyMOL animates the transition between scenes, which
makes for some beautiful zooming effects. Is it possible to capture these
in a movie?
thanks,
Nat
Any body know how to fix this. Have people tested this driver? Should I load
an earlier driver?
When dealing with NVidia cards, I've found this is always the first thing
to try whenever a problem arises. Their Linux drivers are updated to
support new hardware and fix old bugs, but they often
I'm trying to make a high-quality figure showing ligand binding in a
cleft, incorporating sticks, electron density, and some combination of
cartoon/surface/lines for the protein. Ray-traced shadows make the
perspective much clearer but also add visual noise - for instance, the
electron
This is a new pet peeve of mine: it's too easy to select a residue instead
of bringing up the menu of actions. I still haven't figured out what the
difference is, but I keep selecting by mistake. Is there any way to
either control the sensitivity of the clicking, or turn off mouse
selections
unfortunately I've already tried that server and I've seen that also in
that case, the ligand is stripped out.I obtain movies with only the
protein movements. I don't know if i have problems with my pdbs:
I have 245 residues + 1 ligand (246). it has the ATOM and not the HETATM
indication, could
On Fri, May 28, 2010 at 10:49 AM, Thomas Juettemann juettem...@gmail.comwrote:
Hi Chris,
the emails are only sent to you because you subscribed to the pymol-users
list.
If you don't want them anymore you need to unsubscribe.
Click on Show details at the top of this email. Click then on:
Sort of an obscure question, but I've run into problems with a plugin I
wrote - based on what I've seen so far, I'm pretty sure it isn't in 0.99,
but it would be helpful to know what the minimum required version is.
thanks,
Nat
On Tue, Dec 21, 2010 at 2:42 PM, Jason Ferrara ja...@discordia.org wrote:
I've been using the pymol2 interface to run pymol inside Qt widgets. There
doesn't seem to be any documentation for it, but once you figure it out it
seems to work well.
Do you think you could put a quick summary of
On Thu, Jan 27, 2011 at 9:54 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
Is there a way to select specific insertion codes - or rather, their
absence? I'm automatically building up selections like chain A and ((resi
1:5) or (resi 10) or (resi 13)), and I want to ignore insertions, which
tend to duplicate residue numbers. help selection didn't turn up
anything, and
On Tue, Feb 15, 2011 at 2:07 PM, Jason Vertrees
jason.vertr...@schrodinger.com wrote:
Interesting question. PyMOL's wildcards can help here:
select allButInsertionsA, not (i. *A)
This will look for all residue NUMBERS that end in A and select
everything but that.
Thanks, that definitely
I've never found a clean way to do this - what I do is to save a PDB file
with the original model and the relevant symmetry mates, which I then use
for the alignments. There may be a way to do is with object groups,
however. (FYI, you'll probably also need to rename the chain IDs for the
On Mon, Nov 21, 2011 at 8:55 PM, Donnie Berkholz dberkh...@gentoo.org wrote:
I always wonder, are there actually people who feel they gain some sort
of competitive advantage by having access to PyMOL features first?
Doesn't seem to make sense because anyone else can pay for the same
level of
On Tue, Jan 3, 2012 at 10:43 AM, Francis E Reyes
francis.re...@colorado.edu wrote:
Is there anyway to change the carboncolor for coloring by atom type to deep
purple?
http://www.pymolwiki.org/index.php/Advanced_Coloring#Coloring_by_atom_type
shows that i only have a limited set of util.cba*
On Tue, Jan 3, 2012 at 11:08 AM, Francis E Reyes
francis.re...@colorado.edu wrote:
Seems like the pymolwiki doesn't show you can use util.cba in that way . In
fact help util.cba is ambiguous.
Anyway to specify an object or selection with that? util.cba(deeppurple,
(selectionhere))
On Mon, Jan 23, 2012 at 12:42 PM, Simon Becker
simon.bec...@uni-konstanz.de wrote:
I would like to visualize the intermediate structures my program
produces during the computation cycle. Every iteration it generates a
new structure. Is there a way to display this structure in pymol, using
e.g.
On Mon, Jan 23, 2012 at 12:42 PM, Simon Becker
simon.bec...@uni-konstanz.de wrote:
I would like to visualize the intermediate structures my program
produces during the computation cycle. Every iteration it generates a
new structure. Is there a way to display this structure in pymol, using
e.g.
I have a weird problem: we have a cluster of Linux computers (managed
by Sun Grid Engine) running at least three different distributions of
Fedora. I compiled PyMOL on the head node (Fedora 8) and I want to
invoke it on the command line to generate images as part of some other
computations. I'm
I'm trying to figure out how to launch PyMOL automatically from a
script on Windows. I'm stuck with the 0.99 build for now, where the
.exe is
C:\Program Files\DeLano Scientifc\PyMOL\PyMOL.exe
Is this now
C:\Program Files\Schrodinger\PyMOL\PyMOL.exe
in the newer versions, or somewhere else?
On Wed, May 23, 2012 at 10:20 AM, Rituparna Sengupta rsengu...@wisc.edu wrote:
Sorry about the lack of description in the previous post.
The chemicals show incorrect bond connections. Some of the rings go missing.
In all, the structure changes and just by looking at it, its possible to tell
On Fri, Jul 13, 2012 at 2:12 PM, Jason Vertrees
jason.vertr...@schrodinger.com wrote:
It would be nice if publishers required a common CSV format for
specifying contacts and annotations. Then we could easily pull the
data from reliable resources. But, alas, this doesn't exist.
One possible
On Fri, Oct 26, 2012 at 10:37 AM, joseph Lyons josephaly...@gmail.com wrote:
I currently source cctbx from /usr/local/xtal/cctbx/cctbx_build/setpath.sh
with pymol in /usr/local/xtal/pymol_1.41/pymol
I have tried the getting pymol to recognise the cctbx.python however I have
run into
On Mon, Nov 26, 2012 at 8:28 AM, Per Larsson per.lars...@sbc.su.se wrote:
I'm running a pml-script file to render some images on a remote server, using
pymol 1.4, but I do not get any output at all. And no error message, so it is
hard to troubleshoot, unfortunately.
To reduce the complexity
On Mon, Dec 10, 2012 at 12:02 PM, Alex Truong atru...@bu.edu wrote:
I was just wondering if it was possible to shrink the sidebar width so I
have more viewing space? I regularly work with multiple windows open,
usually splitscreen (vertically split). Since I do most of my work on a
laptop with
On Wed, Jan 30, 2013 at 8:33 AM, H. Adam Steinberg a...@steinbergs.us wrote:
Is there anyway to change the default settings in PyMol so that when I open
the program, it is using my specified defaults? or perhaps there is a way a
script can automatically be run at startup? Or automatically run
On Wed, Jan 30, 2013 at 10:43 AM, H. Adam Steinberg a...@steinbergs.us wrote:
This is great, but looks like it's only for Windows? Where would one put this
pymolrc.pym file on a Mac?
http://www.pymolwiki.org/index.php/Pymolrc
Quoting the wiki:
On a linux-type system, this file will be
On Wed, Jan 30, 2013 at 10:56 AM, H. Adam Steinberg a...@steinbergs.us wrote:
You are correct, if I put the pymolrc.pym file in the user folder, MacPyMol
does try to read it when it starts up.
However, it errors every time.
If I put just this one command in the file and start up PyMol, it
On Wed, Feb 20, 2013 at 2:21 PM, Yarrow Madrona amadr...@uci.edu wrote:
When I display ccp4 maps in pymol they look a bit larger than I am used to
seeing in coot for a given sigma setting. Is it common for users to
increase the sigma setting when displaying maps in pymol?
Have you tried:
set
On Fri, Jan 24, 2014 at 11:55 AM, Schubert, Carsten [JRDUS]
cschu...@its.jnj.com wrote:
I am trying to get the roving density features to work from a scripting
level w/o invoking the Density Wizard. Setting up the following script
loads fine, but does not enable roving. Is there anything else
I'm getting the same error for a completely unrelated SourceForge
repository (but strangely, another works fine). I suspect they're having
server problems - it wouldn't be the first time.
-Nat
On Wed, Apr 30, 2014 at 1:39 PM, Andreas Förster docandr...@gmail.comwrote:
Dear all,
trying to
On Fri, Oct 3, 2014 at 11:17 AM, PC patrick.coss...@inbox.com wrote:
Sorry its me again. Can someone tell me where I can find the code for
the align command?
It seems the RMSD differs from other online tools I found.
Are you running it with default arguments? If you do this:
align
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