Hi all,
Can somebody please help me to generate high resolution movie files for
secondary structure of proteins? After I ray a model with high resolution in
pymol and then save it as movie frames, the high resolution and ray seem
lost. I have tried the command likes ray 2000,2000 and it does
Hi,
There are detailed instructions on the net but as far as I can
remember all you need before starting to generate the frames is the
following command:
set ray_trace_frames, 1
Also, why do you need such a high resolution. I know that computers
have a lot of power to burn but if you
Hi Warren CCP4ers,
first of all, it is great that at least one application, MacPyMOL,
works again in stereo under Leopard! It is good if developers like you
and users like us tell Apple how important a working stereo 3D is.
Personally, I consider stereo 3D as VERY important and would like
ALMN can plot the rotation function as a map - although I challenge
anyone to make much sense of it! More or less the same methodology as
MOLREP.
More useful - it lists all peaks generated by the symmetry operators in
Eulerian, and polar angles and gives the direct cosines of the rotation
Remember, there's a whole mailing list wiki dedicated to PyMOL, so no need to
clutter up CCP4bb with PyMOL-specific questions!
https://lists.sourceforge.net/lists/listinfo/pymol-users
http://pymolwiki.org
More complete answer:
# assuming that movie has already been defined in PyMOL
#
Hi all,
Using the 6.0.2 distribution of CCP4, the top program keeps failing
because it just can't see the pdb files. The files can be accessed by
the text viewer of CCP4. (the button VIEW)
I have tried to put them in other directories to make the path string
shorter, etc. None of those helped.
Hi Jan
We had this problem, I think it's because the character strings used to
store pathnames are only 80 chars long, so if you have a long pathname
(you didn't show your full pathname!) then it has a problem. You can
either fix the program, or do as we did make a soft link in the current
All - I've been trying to track down a paper (or papers) where it was
shown that the epsilon values (symmetry factors) for space groups with
pure rotation axes are not integers as is usually assumed (but still
integers for screw axes). It's almost certainly in Acta Cryst.,
probably in the 60's or
Sorry I should have copied this to the BB as it may be of general
interest:
-Original Message-
From: Ian Tickle
Sent: 17 September 2008 11:05
To: 'Jan Dohnalek'
Subject: RE: [ccp4bb] Topp fails: TOP: Open failed: File:
/people/./myfile.pdb
OK try this one: looking at the program I
I think that you are looking for A.J.C. Wilson, Acta Cryst. 17 (1964)
1591-2.
George
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-22582
On Wed, 17 Sep 2008, Ian
On Sep 16, 2008, at 5:26 PM, Warren DeLano wrote:
Also, do crystallographers still consider stereo 3D to be a
high-priority or must-have feature in a graphics workstation?
Hi Warren:
I'd put lack of stereo 3D in the same categories as lack of grant
support or involuntary celibacy.
I'm
On Sep 16, 2008, at 5:26 PM, Warren DeLano wrote:
Also, do crystallographers still consider stereo 3D to be a
high-priority or must-have feature in a graphics workstation?
Yes, I do. Really, how can you do without?
As for LCD stereo: yes, please!
Dear CCP4ers,
I am compiling ccp4-6.0.99e from source and get the errors listed
below when the compilation gets to lib/ccif/libccif.a. I re-ran
configure with the --with-rxdispencer option as recommended but the
error persists.
My system is a Fedora Core 8
Linux xtal2.itqb.unl.pt
Hi all,
We' ve just encountered a problem concerning the installation of MrBump on our
Linux machine. MrBump needs Fasta35 for operation, but during installation
does not recognise the already installed Fasta35, even if Fasta35 is placed in
the ccp4i bin. Under the same location the recognition
Hi Daniel,
Sorry to hear about your problem with mrbump. You say that you put the
Fasta35 executable in the ccp4i bin directory(note the i). This
directory is probably not in your system PATH. I would recommend that
you put it into the $CCP4/bin which should be in your system path
provided
Very well phrased Steve, and I do agree - however stereo is helpful
e.g. looking at binding pockets etc.
I think it depends very much on your workflow what you are actually
doing if you really need lots of stereo. In my case I run everything
on my MacbookPro but I occasionally walk over to
I would agree with this statement, my preference is VERY STRONG. We mostly
work on Nucleosome and Nucleosome-nuclear protein complexes. By definition
these are low-resolution structures. They are very difficult to interpret, even
with stereo and I could not imagine even trying to work on
Hi folks:
My apologies to those who will find this irrelevant, but hopefully
they didn't read beyond the subject line. I've gotten many questions
about this, so ...
After the update to 10.5.5, you have to update (again) X11, preferably
to 2.3.1.
Why Apple didn't include this in the
Just to put my two cents in on this as I would fall into that new generation
so to speak:
I started out with the SGI and linux systems with stereo, O, and dials about
eight years ago. Never used the dials and rarely seen anyone else use
them. Over the past few years I have transition to coot,
I find that depth-cue/fog is a sufficient cue for me to determine the
3-dimensionality of what I am viewing on my 2-dimensional monitor,
and I find that most 3D systems tend to give me a headache long before
I would get one without them.
Even when the depth-cue/fog isn't enough, simply
My use goes back to Evans and Sutherland workstations, FRODO, SGI's with
O, Duncan's graphics program suite, and COOT, on multiple platforms.
I don't use dials at all, and multiple uses with a three-button mouse are
far more favorable.
I still prefer O to COOT for a number of reasons. The main
Hi Nat:
On Sep 17, 2008, at 11:14 AM, Nathaniel Echols wrote:
those of us who came of age (technologically speaking) in an era of
ubiquitous bright, high-contrast (and increasingly massive) LCD
screens
can't bear to look at a CRT display any more.
The day I stopped using CRTs in the
Dear all,
I would like to continue the discussion on the availability of 3D-LCD monitors
that work with Linux or Mac (started in the discussion
Progresss with Stereo 3D under Mac OS X Leopard).
(We do have a running stereo capable system with Linux-PC SGI-CTR-monitor
CrystalEyes.)
Now we
Dear all,
following this discussion and enjoying AGAIN 3D on a Mac - at least
in Pymol -, I'd like to add my two cent opinion.
Whether or not stereo is important in research might be a matter of
debate, true! But, we are focussing on membrane proteins and normally
these structures are
Hi All,
I am trying to make a quite classic demonstration of electron density
map
sliced and contoured as (smoothed) isoheight curves. The sliced
section is
random and NOT along any main cell axes. I am curious if there is any
crystallographic software can handle this, which will save me
if you have bad/poor experimental phases and you are building de novo/
from scratch by hand,
in my opinion stereo is very handy and makes map interpretation much
easier.
-tommi
On Sep 17, 2008, at 6:02 PM, Steve Lane wrote:
Warren et al.:
The following is based largely on a survey
Dear Steve,
despite your survey/perception, bottom line is, comes paper writing
time, nothing beats stereo viewing of the molecules or the packing of
them in the crystal lattice: facts become apparent that are otherwise
easily overseen in two dimensions!
Stereo-free macromolecular
Christian,
I think it would be great to continue this discussion on CCP4bb, especially as
we learn more about all the new stereo-capable display products now hitting the
market.
It would be even more wonderful if a few volunteers could monitor this
discusson and then summarize their
From another member of the new generation...
I could not agree more with Scott. Stereo is not essential, my lab of
thirteen crystallographers does not even have the capability, and noone
has ever asked for it (including our older PI). And I have refined and
built in one year one 3.9 A and
An advantage with stereo viewing is that you can increase the slab in
a crowed active site and still make sense of it. In my experiance,
valuable for understanding structure function relationships in
flexible proteins.
Paula Lario
On 17-Sep-08, at 8:21 PM, Engin Ozkan [EMAIL PROTECTED]
Hi All,
In the portion of the MOREP logfile where it lists the RF peaks, what does
Rf and Rf/sigma mean? Is Rf - peak height and Rf/sigma - peak heights
measured as deviations from mean? Looking into the CCP4 tutorial on MOLREP
(http://www.ccp4.ac.uk/dist/examples/tutorial/html/mr-tutorial.html)
Ironically as this stereo discussion ensues, it seems NVidia is
pushing 3d glasses once again (http://tech.slashdot.org/tech/08/09/17/1530202.shtml
) . Those 120Hz LCD's are welcome reprieve from the bulky SGI
monitors in our x-ray core now.
More on topic, however, as a 'newer' generation
On Sep 17, 2008, at 8:21 PM, Engin Ozkan wrote:
As a grad student we had access to stereo, I did not use it much. I
have to say I do not know why new students would be swayed just by
them. As a young grad student, I was amazed by chemistry in action
(and I still am), and did not need
33 matches
Mail list logo
