Why dont you try CCP4MG ?
Eleanor
On 22 April 2014 22:37, Xiaoming Ren xiaomingre...@gmail.com wrote:
Dear all:
I am facing a display issue in pymol. In my structure, there is a nucleic
acid chain with some monomers which are modified nucleotides built in
scketcher of ccp4 suite. However,
Hi evey
This discussion is very informative to fresher like me. Moreover, with most of
the reading suggested in this discussion I read about the positively charged
metal ions like Na, Ca, Mg and many more. I am curious about Cl in specific
which could occur as a result of salt used in different
Hi,
I have inquired at Schrodinger about the licensing for PyMol. I was surprised
by their answer. The access to PyMol is only through a yearly licence. They do
not offer the option of purchasing the software and using the obtained version
without time limitation. This policy is very different
To the best of my knowledge the source code is still available on
Sourceforge: http://sourceforge.net/projects/pymol/
You should be able to compile binaries for the OS of your choice from there.
That being said, CCP4MG has been coming along nicely in recent years - at
this point I'm 50:50
Hi
Since this is the CCP4 BB, I'd give ccp4mg a try...
On 23 Apr 2014, at Wed23 Apr 16:43, Cygler, Miroslaw wrote:
Hi,
I have inquired at Schrodinger about the licensing for PyMol. I was
surprised by their answer. The access to PyMol is only through a
yearly licence. They do not offer the
No one is keeping you from downloading the source code and compiling.
It's straightforward and free.
Andreas
On 23/04/2014 4:43, Cygler, Miroslaw wrote:
Hi,
I have inquired at Schrodinger about the licensing for PyMol. I was
surprised by their answer. The access to PyMol is only through a
On Wed, Apr 23, 2014 at 8:43 AM, Cygler, Miroslaw
miroslaw.cyg...@usask.cawrote:
I have inquired at Schrodinger about the licensing for PyMol. I was
surprised by their answer. The access to PyMol is only through a yearly
licence. They do not offer the option of purchasing the software and
I'd like to add the under-underdog then, Tim Fenn's povscript+
https://sites.google.com/site/timfenn/povscript. Makes really clear and
nice figures and is rather simple to compile. For the most part you do
not even need a mouse to use it ...
Michael
On 23.04.2014 18:21, mark.x.brooks wrote:
And to stick up for the underdog, try Chimera from UCSF, which also has been
coming along nicely (understatement!): http://www.cgl.ucsf.edu/chimera/
Mark
On 23 Apr 2014, at 17:48, Jim Fairman fairman@gmail.com wrote:
To the best of my knowledge the source code is still available on
Hi,
if one is hesitant to compile it it, pymol is easily installed on a
Linux box via yum ;
enable EPEL repo ( in Redhat derivatives e.g. fedora, Centos, SciLinux)
yum install pymol will install version 1.6 (latest version by
Schrödinger is 1.7)
Best, Guenter
Hi,
I have inquired at
On Wed, Apr 23, 2014 at 6:15 AM, World light bsub...@btk.fi wrote:
This discussion is very informative to fresher like me. Moreover, with
most of the reading suggested in this discussion I read about the
positively charged metal ions like Na, Ca, Mg and many more. I am curious
about Cl in
In addition to what has been mentioned by others, Open-Source PyMOL
installation instructions for various platforms are available on the PyMOL Wiki:
http://pymolwiki.org/index.php/Linux_Install
http://pymolwiki.org/index.php/MAC_Install
http://pymolwiki.org/index.php/Windows_Install
Cheers,
To find Cl its worth looking at anomalous maps, especially for home source
data, since even with partial occupancy Cl is easily located. Also, for well
ordered Cl ions, B-factor will often refine to lower value than coordinating
atoms when its incorrectly refined as water. Finally, in a subset
On Apr 23, 2014, at 11:43 AM, Cygler, Miroslaw miroslaw.cyg...@usask.ca wrote:
They do not offer the option of purchasing the software and using the
obtained version without time limitation. This policy is very different from
many other software packages, which one can use without continuing
Hi Mirek,
If you happen to be using OS X, Fink makes it very easy to install recent
open-source pymol.
Best regards,
Dmitry
On 2014-04-23, at 11:43 AM, Cygler, Miroslaw miroslaw.cyg...@usask.ca wrote:
Hi,
I have inquired at Schrodinger about the licensing for PyMol. I was surprised
On 4/23/14, 1:53 PM, Francis Reyes wrote:
Office 365 is $10 a month, Adobe Creative Cloud (what used to be their Creative
Suite) is $50 a month with an annual commitment.
Licensing the use of software on a time-limited basis as a business model seems
like it's going to stick around.
And
Hi,
I have a collection of books that I would gladly give away to someone who may
cherish them. The list is enclosed.
:) Ewa SJ
Ewa Skrzypczak-Jankun, PhD
DH r.2250
Prof. emerita
Well as s/w improvements don't necessarily happen on a yearly basis, but people
like being paid each year, I think the model is not unreasonable, as long as
the cost is reasonable - which, for instance, the Adobe s/w isn't. As one can
tell from the profit margins of s/w companies. So I do pay
Hey,
Are you giving them away or selling them? ;)
Cheers
Joana Pereira
--
PhD student
Lamzin Group
EMBL Hamburg ℅ DESY
Notkestrasse 85
DE-22603 HAMBURG
GERMANY
Tel:+49 40 89902-276
On 23 Apr 2014, at 21:33, Skrzypczak-Jankun, Ewa
ewa.skrzypczak-jan...@utoledo.edu wrote:
Hi,
I have a
Hi all,
You may not have noticed, but 19 March 2014 was VR Day - the day that new
style wwPDB validation reports for all X-ray structures were made publicly
available - see
Hi all,
You may not have noticed, but 19 March 2014 was VR Day - the day that new
style wwPDB validation reports for all X-ray structures were made publicly
available - see
Hi all,
You may not have noticed, but 19 March 2014 was VR Day - the day that new
style wwPDB validation reports for all X-ray structures were made publicly
available - see
Applications are invited for a three-year University of Leeds 110-year
Anniversary Ph. D. studentship to work in the Goldman and Muench groups.
The project will involve structural and functional studies of integral membrane
pyrophosphatases, focussing on ones from pathogenic parasites such as
Hi all,
You may not have noticed, but 19 March 2014 was VR Day - the day that new
style wwPDB validation reports for all X-ray structures were made publicly
available - see
If N goes to infinity, i.e. at high or very high data multiplicity Rmerge
approaches Rmeas (Rrim).
Sure. And there is nothing incorrect, because the formulas are identical.
0.8*sd(i)/I = 0.8/(I/sd(i))
But if you sum also over a shell of hs, that notation is incomplete losing the
(or Mn).
That's not quite correct. If N goes to infinity, i.e. at high or very high
data multiplicity Rmerge approaches Rmeas (Rrim).
At this point it does not matter whether you write Rmerge or Rmeas
equals 0.8 * sd(I) / I
For low multiplicity
Rrim (or Rmeas) = 0.8*sd(i)/I
is the correct expression.
Applications are invited for a three-year University of Leeds 110-year
Anniversary Ph. D. studentship to work in the Goldman and Muench groups.
The project will involve structural and functional studies of integral membrane
pyrophosphatases, focussing on ones from pathogenic parasites such as
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