Re: [COOT] HELP Coot real space refine not working.
I think Coot has always behaved this way if you don't add explicit LINKs between the ligands and the metal ion. You can add the links in Coot. Roger Rowlett On Apr 24, 2015 6:47 PM, "Kenneth Satyshur" wrote: > See enclosed png. When I try to real space refine the histidine > connected to a Zn metal, it gets sucked into the metal density. WHY? Am I > missing a lib file? I can see the Zn, but coot does not. I cannot use this > coot version anymore. There are too many errors in it. > > version 0.8.1 > > REHEL 6.6 > > > kas > > > > Kenneth A. Satyshur, M.S., Ph.D. > > Senior Scientist > > University of Wisconsin-Madison > > Madison, Wisconsin, 53706 > > 608-215-5207 >
Re: [COOT] Microscope for inspection of crystals
The Mitegen Zeiss V41 has approximately the same optical magnification range as the EMZ5, and is listed at $2050. The mag range is a little low for my taste (I like something that will go to 80-90X), especially for 96-well robotic plates, but it is a very affordable scope. I've never used one in the lab, but have seen it at meetings. It seems OK. Uses an LED backlight system. You get what you pay for. I think a quality Nikon or Olympus scope is money well spent. My SZX-12 has been a tank, standing up to constant abuse from students for 13 years. Cheers, ___ 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: (315)-228-7935 email: rrowl...@colgate.edu On 4/2/2015 1:14 PM, Adeba Mohammad wrote: Hello all, I am looking into getting a microscope for the inspection of crystals with a large stage. I currently have the Meiji EMZ5 microscope with PBH stand and a special acrylyc cover to make the stage large. However, the company that made the cover for me no longer makes those covers. What other microscope can I use? or is there a place that makes custom covers for meiji microscopes? I would like to get a microscope for no more than $2000 for the sole purpose of crystal inspection. Thanks, Adeba
Re: [COOT] Removing atom labels permanently
Is this a machine running integrated Intel graphics on Linux? I think that issue was recently discussed, and is a problem with the graphics driver. The simplest solution for a desktop would be to install a cheap Nvidia graphics card and the proprietary driver. My Linux boxes work great with any GeForce card. Laptops may have no good solutions. Roger Rowlett On Apr 16, 2014 9:54 PM, "Grant Mills" wrote: > Dear all, > > You may have read my concerns on the CCP4BB however I'm still looking for > an answer to turn off atom labels permanently. I've tried various drivers, > installs and updates and all I really want to do is get back to work. The > labels cause coot to grind to an almost halt but it runs smoothly without > them. If you have some time to help, it would be greatly appreciated as > I've been struggling with this issue for about 6 months or so. > > Thanks you for your time, > Grant >
Re: [COOT] how to modify initial settings in .coot file
This can be easily done in the .coot file. If you look at the scripting functions of coot in the documentation at http://www.biop.ox.ac.uk/coot/doc/coot.html you will see you can adjust all sorts of things. Here is the .coot file I give my students to open up refmac data on a 24" 1920 x 1080 monitor: ;; Roger's coot startup file (no-coot-tips) (set-graphics-window-size 1150 900) (set-graphics-window-position 720 25) (set-model-fit-refine-dialog-position 470 25) (set-go-to-atom-window-position 70 25) (set-ramachandran-plot-dialog-position 20 550) (set-map-radius 15.00) (set-symmetry-size 15.00) (set-smooth-scroll-steps 50) (set-smooth-scroll-limit 10.00) (set-default-bond-thickness 3) (set-show-symmetry-master 1) ;; default contour levels for 2FoFc and FoFc maps (set-default-initial-contour-level-for-map 1.0) (set-default-initial-contour-level-for-difference-map 3.5) ;; open commonly used windows (post-model-fit-refine-dialog) (post-go-to-atom-window) Cheers, ___ 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: (315)-228-7935 email: rrowl...@colgate.edu On 5/6/2013 2:44 PM, Joe Batchelor wrote: Hello, Coot is working wonderfully for us. I was hoping to get guidance on how to modify initial settings using the .coot file. Apologies if this already has been addressed elsewhere. I specifically would like to add lines to the .coot file with these results - 1 - Change initial map radius (Edit -> Map Parameters) to 20/Å /2 - Load coot with Hardware stereo on (Draw -> Stereo -> Hardware stereo) 3 - Load showing symmetry atoms (Draw -> Cell & Symmetry -> Master Switch:Show Symmetry Atoms: Yes) I would greatly appreciate advice on how to modify the .coot file to change these settings when coot starts up. Thank you, Joe Batchelor
Re: [COOT] favorite linux flavor, or as most of you would say, flavour ;)
IMO, unless you just like upgrading your OS on a frequent basis and the migraines that go with it, choose some sort of LTS (long-term-support) release. Currently I'm using Ubuntu 12.04 LTS (good for 5 years), but CentOS or Mint would be good choices, too, and that is what I considered when I upgraded from my last LTS distribution. Ubuntu (at least for now) makes it easy to configure hardware and is a popular known quantity for protein crystallographic software. I had too many hardware compatibility issues with Fedora about 5 years ago and gave up trying to maintain it. Cheers, ___ 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: (315)-228-7935 email: rrowl...@colgate.edu On 1/17/2013 11:33 AM, David Roberts wrote: I'm sorry to re-hash this issue, but I just wanted to know what the present general consensus is on linux flavors. I teach a crystallography class every 2 years, and I have a small cluster of computers running fedora, but the deal is that by the time I get around to my class, fedora has routinely gone up at least 2 levels since my last upgrade, meaning that the latest software and things are difficult at best to load on. I'm OK with any linux, I just want one that will be able to run the majority (if not all) of the typical crystallography packages (cns, ccp4, coot, etc...). I also would like one that works well with nfs and local file sharing. I can upgrade fedora, no problem, but I thought I may branch out if others think there are better flavors out there. Thanks so much Dave Roberts
Re: [COOT] coot ubuntu 12.04
Which version of Ubuntu do you have, 32 or 64 bit? I'm running the Ubuntu 10.04 Coot 0.6.2 binary on a system running 64 bit Ubuntu 12.04. You will have to install some additional packages to get it to run. I believe you missing packages are in ia32-libs, the 32 bit compatibility libraries for 64 bit Linux. I found I also had to install libgnomecanvas2-0 to satisfy Coot in Ubuntu 12.04. You will want to disable global menus as well by removing 3 appmenu-xxx packages. Google 'disable global menus in Ubuntu' to get the exact package names to be removed. Roger Rowlett On May 29, 2012 7:13 PM, "Eugenio De la Mora" wrote: > When trying to run Coot (under ubuntu 12.04) I get this message: > > COOT_PREFIX is ./coot-Linux-i686-ubuntu-8.04.4-gtk1 > ./coot-Linux-i686-ubuntu-8.04.4-gtk1/bin/coot-real > ./coot-Linux-i686-ubuntu-8.04.4-gtk1/bin/coot-real: error while loading > shared libraries: libXmu.so.6: cannot open shared object file: No such file > or directory > ERROR: In procedure dynamic-link: > ERROR: file: "libguilegtk-1.2", message: "libXext.so.6: cannot open shared > object file: No such file or directory > > If i understand porperly libraries are contained in the coot folder or I > need to install some specific package? >
Re: [COOT] Coot 0.6.2 libraries in Ubuntu 12.04
I have this version of Coot running in Ubuntu 12.04 LTS 64 bit with no problems. No missing library errors. You need to put /usr/local/xtal/coot-0.6.2/bin (or whatever) in your path, or start it with the following batch file which you can name coot or coot-0.6.2 or whatever: #! /bin/tcsh set path=(/usr/local/xtal/coot-0.6.2/bin $path) coot Then the coot script file sets all the appropriate paths, etc. and starts the program. Cheers, ___ 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: (315)-228-7935 email: rrowl...@colgate.edu On 5/9/2012 12:54 PM, Nat Echols wrote: On Wed, May 9, 2012 at 8:07 AM, Michele Vigolo wrote: I installed Coot 0.6.2 from "coot-Linux-x86_64-ubuntu-10.04.2-gtk2-python" but when I launch it from the terminal I get this warning: What is the exact command you are using to start Coot? -Nat
Re: [COOT] Coot Fedora and bashrc
Here is how I run it on my Ubuntu 9.04 machines (and also in Fedora 8): Put the coot executables in /usr/local/xtal/coot-0.6 and make this directory world readable and executable (755 permissions) (You can choose a different path if necessary.) Make sure /usr/local/xtal is in your default path Put the following script file in /usr/local/xtal and name it "coot": #!/bin/tcsh set path=(/usr/local/xtal/coot-0.6/bin $path) coot Type coot and go. SUBSCRIBE CCP4BB Anonymous wrote: Hi, I can run Coot by typing: sh /home/me/Documents/ccp4/Coot-0.5.2/bin/coot I'd like to be able to just type Coot and have it run. Normally I'd just add it to bashrc but I don't believe Coot is set up for this - it needs to be a .sh file for this to work I think. How do I go about adding it to bashrc? Thanks! -- Roger S. Rowlett Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@mail.colgate.edu
Re: [COOT] karmic
FYI, I have found that Ubuntu 9.04 (Jaunty Jackalope) is capable of running Coot, CCP4i, and Pymol flawlessly with an NVidia GeForce 9000-series card with compiz and all the whiz-bang desktop effects enabled on my Intel DG35EC motherboard. The only thing I have discovered so far that does not run correctly with compiz enabled is MLB-TV in full screen mode. (Sacrifices must be made.) This is an improvement over Fedora 8, which I was running before. I'm waiting to upgrade to Karmic Koala until some of the Gnome and PulseAudio bugs are worked out. It's still a little flaky on both real and virtual machines for me right now, even with a fresh install. Cheers. Ed Pozharski wrote: In Ubuntu 9.10, coot appears to be fully compatible with compiz when running on Intel graphics card. So there is no need to disable the visual effects anymore. -- Roger S. Rowlett Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu
[COOT] difference map contour settings
I have not been able to change the default difference map coutour levels in .coot. The entry (set-default-initial-contour-level-for-difference-map 3.5) does not have any effect for me in any version of coot I have used (currently using 0.6-pre-2008). The difference maps always start up with a default setting of 3.0 after auto-open MTZ. Is the setting command mis-formatted, or is this a bug? Cheers, Roger Rowlett Professor Department of Chemistry Colgate University
[COOT] Coot crashing on Pentium 4 machines
Is anyone out there running Coot 0.5.2 or later on a Pentium 4 box? I am finding that Coot 0.5.2 or later crashes on startup on all of my P4 machines running Fedora 8 with the latest kernel. Coot 0.5 runs fine. My quad-core machines, also running Fedora 8 and the same kernel, run the later versions of Coot (0.5.2 or 0.6-pre1) just fine. Is it just me, or is this problem reproducible on P4 processors running Linux? All my machines have some sort of Nvidia graphics card and the latest drivers (9600GT for quad-core, Quadro 980XGL for P4 machines), which I assume is pretty typical. Thanks, -- Roger S. 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 email: rrowl...@mail.colgate.edu
[COOT] Coot crash issue
I am experiencing a strange Coot crash issue on some of my Linux workstations. Coot 0.5.2 or 0.6-pre1 crashes with an identical failure mode with the following Coot output (last few lines): [...] load "tips.scm" load "americanisms.scm" load "group-settings.scm" (set-display-lists-for-maps 0) load "tips-gui.scm" /usr/local/bin/coot-0.6-pre1/bin/coot: line 124: 14996 Illegal instruction $coot_real $* coot-exe: "/usr/local/bin/coot-0.6-pre1/bin/coot-real" coot-version: /usr/local/bin/coot-0.6-pre1/bin/coot-real platform: /bin/uname core: #f No core file found. No debugging I can run Coot 0.5.2 or 0.6-pre1 with no issues on my Q9300 quad-core machine, but on any of my Pentium 4 workstations I get this crash on startup. Coot 0.5.0 runs fine on the Pentium 4's, so it's an issue that developed with 0.5.2 and later. I'm a bit mystified. Running Fedora 8, using Fedora 6 (0.5.X) or Fedora 8 (0.6-pre1) binaries. "uname -a" gives: Linux jalapeno 2.6.26.8-57.fc8 #1 SMP Thu Dec 18 19:19:45 EST 2008 i686 i686 i386 GNU/Linux Cheers, -- Roger S. 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 email: rrowl...@mail.colgate.edu
Re: [COOT] coot install on redhat
FYI, coot installs and runs just fine in many flavors of RedHat and Fedora. I've had it running in RH8 & 9 as well as Fedora 1-8, all of which can be obtained at no cost. 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 email: [EMAIL PROTECTED] -Original Message- From: Charlie Bond <[EMAIL PROTECTED]> Date: Wednesday, Apr 30, 2008 12:07 am Subject: Re: [COOT] coot install on redhat To: "COOT@JISCMAIL.AC.UK" Reply-To: Charlie Bond <[EMAIL PROTECTED]> William Scott wrote: > I was in a similar situation. A couple of years ago I ditched the Red > Hat Menace for Ubuntu, which is completely free, and all the libraries > you need are available in a nice up-to-date form. Then all my problems > disappeared (well, Linux problems). > > More propaganda: http://tinyurl.com/5npgrg Seconded. -- Charlie Bond Professorial Fellow University of Western Australia School of Biomedical, Biomolecular and Chemical Sciences M310 35 Stirling Highway Crawley WA 6009 Australia [EMAIL PROTECTED] +61 8 6488 4406
