an Intel i3 CPU.) An Intel Chromebook might be an attractive option for
undergrads for biochemistry classes and/or protein crystallography research
projects. You can install Pymol in Windows with pip as well.
Roger Rowlett
Gordon & Dorothy Kline Professor, Emeritus
Department of Chemistry
Col
-protocols/home/model-building-and-validation
Roger Rowlett
On Mon, Apr 12, 2021, 2:35 AM shubhashish chakraborty <
cshubhash...@gmail.com> wrote:
> Hello,
> I am not able to align my pdb file with its respective electron density
> map generated by CCP4i. Kindly let me know what
fetch 6h07, type=pdb1
Roger Rowlett
Gordon & Dorothy Kline Professor, Emeritus
Department of Chemistry
Colgate University
On Tue, Jan 14, 2020, 3:42 AM Clelia Canova wrote:
> Hi!
>
> I’m studying the file *6H07. pdb *for a project, download for rcsb.com.
> How can I se
You are using d = sqrt(dx^2 + dy^2 + dz^2), right? (Where dx = x2 - x1,
etc.)
___
Roger S. Rowlett
Gordon & Dorothy Kline Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346
tel: (315)-228-7245
ofc: (315)-228-7395
fax:
Clarisa,
Depending on what you want to do with the file, you may not need to save
a new PDB at all.
You could for example,
* Issue the command symexp ,,(all),4.0 to generate nearby
symmetry mates, then remove the objects you don't need to form the
proper dimer. ( is your
You can also do this locally on your own machine if you arrange to get
the CNS morph_dist.inp script. (You need CNS to run it, of course.) The
nice thing about this method is that it minimizes the structures of the
intermediate morphs into something sensible. I don't know how
sophisticated
How about,
color measure01, red
color measure02, yellow
etc.
Roger Rowlett
On Dec 24, 2013 8:51 AM, Li Xue me.li...@gmail.com wrote:
Hello all,
Is it possible that I could use *different* colors for the dashes for the
distance measurements?
I know I can use set dash_color, red to set all
You can try installing the ATI proprietary driver (fglrx, Catalyst)
instead of using the open source driver that come with Ubuntu. Check to
see if this driver is compatible with your card.
I've had nothing but trouble and bad luck getting ATI graphics cards to
work under linux. If building
What about the following commands:
select mystuff, resi 1-3 and m1
select otherstuff, resi 7-9 and m2
Cheers,
___
Roger S. Rowlett
Gordon Dorothy Kline Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346
tel: (315)-228-7245
script and symlink works fine. Running Ubuntu
12.04 LTS.
Any ideas?
Cheers,
___
Roger Rowlett
Gordon Dorothy Kline Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346
tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
ImageMagick can easily append/adjoin animated gifs.
Roger Rowlett
On Nov 24, 2012 8:38 PM, Jordan Willis jwillis0...@gmail.com wrote:
Hi,
I have 3 different conformations of the same structure and I was wondering
what is the easiest possible way to morph 3 conformations.
Morpheasy works
I'm using an older DepthQ-WXGA system and Quadro FX3700(?) graphics card
in a classroom setting and it seems to work fine. Stunning, really. It
uses a VGA cable and the 3-pin mini-DIN on the graphics card. I mount
the IR emitter on top of the projector and everyone in the room can sync
with it
I think the isomesh command will let you set
whatever contour level you wish, e.g.:
isomesh map, mymap.map, X.X, maparea
Where map is the name of the mesh object, mymap.map is the map
file name, X.X is the desired contour level, and maparea, is the
Lina,
If you want to create an "omit" map for your ligand using CCP4i, you
can find instructions here for both Fo-Fc and 2Fo-Fc maps:
http://capsicum.colgate.edu/chwiki/tiki-index.php?page=Model+Building+and+Validation#Creating_Omit_Maps_for_Ligands_using_Refmac
To display an omit map in
Pymol-ers,
I am writing to alert the Pymol community that I will be
co-organizing (under the auspices of the Council on Undergraduate
Research) a session at the 2012 American Crystallographic
Association meeting (July 28-Aug 1) devoted to practical
. See the pymol wiki for how to select atoms to link with the bond
command. You will have to show sticks to see the bond. Waters are usually
visualized as spheres, and you may want to modify their vdw radius to
0.5-1.0 A to make them small enough.
Cheers,
Roger Rowlett
On Apr 18, 2011 5:48 PM
This appears to be a common problem with 1.4 and Jason is aware of it. The
same issue exists in Ubuntu 9.04 with Nvidia 180.xx drivers, 32 bit. The Win
version works OK.
Roger Rowlett
On Mar 29, 2011 7:53 AM, Schubert, Carsten [PRDUS] cschu...@its.jnj.com
wrote:
Joachim,
I'm running
Has anyone else noticed that Pymol (v 1.3 or
1.4) will no longer fetch data from the pdb server? If I issue
'set fetch_host, pdbe' I can fetch data OK, but if you 'set
fetch_host, pdb' I'm getting a fetch error for any accession
number.
--
Thanks, all. Looks like I'll have to investigate local issues with our
institutional firewall. Sigh. Not the first time...
Roger Rowlett
On Mar 22, 2011 12:58 PM, Jason Vertrees jason.vertr...@schrodinger.com
wrote:
Great, thanks, David. Just ensuring the problems been isolated.
Cheers
When Pymol 1.4 is started in Ubuntu 9.04 with
the latest available Nvidia driver for this OS (version 180) I get
the following startup error (and strange window rendering where
bits of the pymol rendering window are transparent):
"Detected OpenGL version
In pymol 1.4, I get a strange error in Ubuntu
10.04 (VM):
"pymol.exe: error while loading shared libraries: libtk8.5.so:
cannot open shared object file: No such file or directory"
The file is there, and is readable. Any ideas? I have run
David,
Use double quotes or start typing and autocomplete with the
tab key.
Cheers.
On 9/20/2010 11:20 AM, David A. Horita wrote:
Hi,
How
does one change directories in Windows when the directory
FYI, the ionic radius of Ca(2+) is 1.14 A. A
calcium atom is 1.80 A. After issuing the "alter elem ca,
vdw=1.14" command, you may have to execute the "rebuild" command to
change the previously displayed sphere radius.
Cheers.
On 3/16/2010 11:31 AM, Jason Vertrees wrote:
Raluca,
Here's
Two items come to mind:
1. A Powerpoint plugin for live Pymol viewing in presentations.
2. A simpler method of doing structure morphs in Pymol. Intelligent
morphing is incredibly powerful for visualizing protein conformational
changes based on "endpoint" protein structures, or just
Has anyone on the board configured a DepthQ
projector for classroom use, i.e. using a ceiling-mounted projector.
Our IT department has recently installed a DepthQ projector in a
classroom-type setting, and it displays stereo Pymol images for about
20 seconds, then loses sync. My configuration
Has anyone got the Caver 2.0.003 plugin working in Ubuntu 9.04? I can
install the plugin in pymol, load the example pdb (1MJ5) and open the
dialog box, which seems to have the correct paths to the plugin .jar and
lib directory. I can even select the correct starting point and have it
displayed
How do you disable cartoon_highlight_color once it
has been enabled? The command "set cartoon_highlight_color, off" does
not work in 1.2b3, as suggested by the Pymol wiki. Pymol just reports
that "off" is not a color.
Cheers,
--
Roger S. Rowlett
Professor
Department of Chemistry
Colgate
Is there a relatively simply way to get pymol to
populate a unit cell with exactly the correct number of copies of the
asymmetric unit, i.e., similar to the Uppsala software factory utility
XPAND or the "Build Crystallographic Symmetry" command in SPDBV?
Ideally, it would be helpful to perform
, for example, you will need
to provide an image of 1800 x 1800 pixels to achieve the required 600 dpi.
Roger Rowlett
Professor
Colgate University Presidential Scholar
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346
tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
Robert Campbell wrote:
Hi,
On Fri, 27 Jun 2008 13:25:02 -0400, Michael Lerner mgler...@gmail.com
wrote:
This is probably a fairly basic question, but I'm stumped. I want to
visualize electron densities along with my PDB file. So, say I'm interested
in 2DJX. I go to the PDB and download
Buz Barstow wrote:
Dear All,
I'm considering purchasing a new graphics workstation for molecular
graphics and macromolecular refinement. I'm considering buying a
machine with 2 quad core xeon processors, and a nVidia Quadro FX
graphics card with 1.5 Gb of memory.
Can the current generation of
Gary Hunter wrote:
I am displaying pdb files of metalloenzymes, and like to show the
metal ions as spheres.
I select the metal and use showspheres
Fine
Somehow recently I must have done something to reset the vdw radius of
manganese (MN in the pdb), as Mn atoms now display as small spheres (a
Try the command png filename.png, 1200, 1600, -1, 1 to create an
output image 1200 pixels wide by 1600 pixels tall, raytraced. To disable
raytracing, change the last argument to zero.
Cheers,
--
Roger S. Rowlett
I kind of like using Slerpy (found on the Pymol Wiki) to assemble highly
controlled movies of static structures. The resulting PNG frames can be
assembled into an animated GIF using ImageMagick, and if the GIFs are
too big (they are lousy in Powerpoint) they can be converted to smaller
more
bg_color white should do it.
Nagarajan wrote:
Hello all,
I am having some doubts in command line argument in pymol. Can anyone tell
me the command to change the background to white using command line..! I
can use it in a movie script.
Thanking you
Nagarajan.P
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