Re: [COOT] Updated SGI dial box driver
Great Stuff, Winfried! I remember trying to get the previous incarnation of the dial box driver (Dave Gohara's) to work on RHEL years ago. I failed and subsequently acquired a PowerMate, which was just a poor imitation. My dial box has since disappeared. Does anyone have spare dial boxes collecting dust somewhere? I'd like to trade one or more for gratitude beer or the like. Best. Andreas On 10/07/2014 2:36, Winfried Meining wrote: Dear Coot community, In an effort to be able to use SGI dial boxes on 64-bit Centos 6.5 systems, I have rewritten an existing dial box driver and removed all dependencies on the Xfree86 library. The modified driver can be downloaded from http://xorgx11dialbox.sourceforge.net. Currently, only the source code and a rpm for Fedora/Redhat EL/Centos systems are available. Installation files for 32 bit systems or other OSes may follow, if users with access to these systems contribute installables. Support for input devices like the dial boxes would be a nice feature even in Coot. Are there plans to implement this? kind regards Winfried Meining -- Andreas Förster Crystallization and X-ray Facility Manager Centre for Structural Biology Imperial College London
Re: [COOT] delete alternative conformation
Select Delete - Residue/Monomer from the Model/Fit/Refine and click on the conformation you'd like to remove. Andreas On 08/07/2014 9:49, Tim Gruene wrote: Hello, is there a way in coot to remove one (or more) of a multiple conformation residue so that I am left with, say, conformation A only? Thanks, Tim -- Andreas Förster Crystallization and X-ray Facility Manager Centre for Structural Biology Imperial College London
[COOT] pango error no fonts
Dear all, I'm a bit baffled about this one. I have the latest coot (Coot 0.8-pre (revision 4996) [with guile 1.8.8 embedded] [with python 2.7.5 embedded]) installed on a CentOS 5.6 64-bit box. Coot starts up with a Pango WARNING about no modules and no shape engine. Expect to find ugly fonts. I don't find fonts at all. The menus and pop-up windows don't have readable text in them, only rectangular placeholder boxes. Coot 0.6 runs just fine. The solution suggested by coot is: You should create this file by running: pango-querymodules '/lmb/home/pemsley/autobuild/coot-build-64-bit-CentOS5-enhanced-ligand-pre-release-gtk2-python/etc/pango/pango.modules' Paul? Thanks. Andreas PDB file /usr/local/xtal/coot-0.8pre/share/coot/standard-residues.pdb has been read. Spacegroup: P 1 (coot-real:17195): Pango-CRITICAL **: No modules found: No builtin or dynamically loaded modules were found. PangoFc will not work correctly. This probably means there was an error in the creation of: '/lmb/home/pemsley/autobuild/coot-build-64-bit-CentOS5-enhanced-ligand-pre-release-gtk2-python/etc/pango/pango.modules' You should create this file by running: pango-querymodules '/lmb/home/pemsley/autobuild/coot-build-64-bit-CentOS5-enhanced-ligand-pre-release-gtk2-python/etc/pango/pango.modules' (coot-real:17195): Pango-WARNING **: failed to find shape engine, expect ugly output. engine-type='PangoRenderFc', script='latin' (coot-real:17195): Pango-WARNING **: failed to find shape engine, expect ugly output. engine-type='PangoRenderFc', script='common' (coot-real:17195): Pango-WARNING **: failed to find shape engine, expect ugly output. engine-type='PangoRenderFc', script='greek' initalize graphics molecules...done. -- Andreas Förster Crystallization and X-ray Facility Manager Centre for Structural Biology Imperial College London
Re: [COOT] [ccp4bb] Coot's hidden talents!
Surely Sir Paul! Andreas On 11/01/2013 3:27, Bosch, Juergen wrote: Surprised Mercedes didn't sued him for that :-) @Mr. Emsley I assume you soon will be Sir Emsley after that marvelous painting.mentioned in Harry's email. Jürgen
Re: [COOT] Which binary for RHEL 6?
Dear Dirk, I've installed coot-0.6.2-binary-Linux-x86_64-centos-5-python-gtk2.tar.gz with no problems. Andreas On 01/08/2011 1:34, Dirk Kostrewa wrote: Dear Cooters, before I spend some time with trial-and-error - could you please tell me, which coot binary is properly working under RHEL 6 (Scientific Linux 6)? Best regards, Dirk. -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk
[COOT] latest coot on rhel 5 32-bit
Hey cooters, I'm trying to replace my current coot (centos4 binary, version 0.6, revision 2540 with guile 1.8.7 and python 3.6.0 embedded) with a more recent binary. The OS is RHEL 5.2 to 5.4, 32-bit. I download version 0.6.2, revision 2939, python, unpack but can't start the program because of a library conflict. Error while loading shared libraries: libldap-2.2.so.7. This library is apparently provided by openldap-2.2.xx. On my machines, openldap-2.3.xx is installed, providing libldap-2.3.so.0 and the like. How to make this work? And why does the new coot use the old library when the old coot used to use a more recent one? Andreas -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk
[COOT] ramachandran fit error
Hey all, I have a structure with three chains in the asymmetric unit. When I select Refine/Improve Ramachandran Plot from Extensions/All Molecule, coot does its thing until it reaches the end of the second chain, then stops with the errors pasted below. It says something about alternate conformations, but they have all been removed. When I execute (stepped-refine-protein-for-rama 2), coot seems to do the same thing, but finishes the entire protein. (It even checks every water molecule...) Any ideas why the coot extension should fail while the scheme function executes happily? Oh, I should say I'm using coot 0.6-pre-1 rev. 2189 on RHEL 5.4beta). Thanks Andreas Little window with error message: In /csb/soft/Linux/src/coot0.6pre/share/guile/gtk-2.0/gtk.scm: 147: 0* [apply #procedure #f () ()] In unknown file: ?: 1 [#procedure #f ()] In /csb/soft/Linux/src/coot0.6pre/share/coot/scheme/fitting.scm: ... 216: 2 (let* ((imol-map #)) (func (car *multi-refine-spec-list*) imol-map) ...) 217: 3* [fit-protein-rama-fit-function (4 B -1 #f) 1] 176: 4 (let ((imol #) (chain-id #) (res-no #) ...) (let (# #) (map # #) ...)) 180: 5 (let (# #) (map # #) ...) 182: 6* [map #procedure #f (alt-conf) ... 191: 7* [residue-alt-confs 4 B -1 #f] In /csb/soft/Linux/src/coot0.6pre/share/coot/scheme/coot-utils.scm: 1497: 8 [reverse ... 1498: 9* [f ... 1498: 10*[residue-info 4 B -1 #f] /csb/soft/Linux/src/coot0.6pre/share/coot/scheme/coot-utils.scm:1498:21: In procedure SWIG_Guile_scm2newstr in expression (residue-info imol chain-id ...): /csb/soft/Linux/src/coot0.6pre/share/coot/scheme/coot-utils.scm:1498:21: Wrong type argument in position 1: #f In shell where coot was started: INFO:: replace_coords: 15 atoms updated. INFO:: graphics_info_t::clear_up_moving_atoms... DEBUG:: in safe_python_command_with_return() pValue is 0x897e86c clearing intermediate object... ERROR! --- moving_atoms_asc_type not known: 0 ERROR! --- INFO:: graphics_inf -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk
[COOT] fink remove old packages
Hey all (especially Bill, I guess), I was bushwhacking through the fink jungle on my MacBook Pro (10.5.8) today and realized just how vast it it. There are 18GB in /sw. As examples (and to make this email uncannily on-topic), there are 18 coot_0.6-pre-1-revision--?_darwin-i386.deb packages and 14 coot_0.5-pre-1-*_darwin-i386.deb packages in /sw/fink/10.4/unstable/main/binary-darwin-i386/sci. Is this necessary? How do I clean fink up? I should say that I compile everything from source. Thanks. Andreas -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk
[COOT] change size of gui
Hey all, is there a way to change the size of the coot viewer? Background: I open a coot session (previously shown on an external screen) on my laptop. The laptop screen is smaller by half than the external screen - thus the coot viewer does not fit. This being an OSX machine, I'd need access to the bottom right corner of the window for resizing. This corner is not on the screen. Clicking on the + button on the top left of the X window changes the size of the window but doesn't make it small enough to fit on the screen. I guess you wouldn't expect that from a plus button anyway. I cannot outsmart the computer. When I try to decrease the size of the coot viewer (restored from an earlier auto-save state file) on the external screen before closing the session, I fail. I can only increase the size, but not decrease it. To rephrase my question. Is there a coot equivalent to the PyMOL viewport command? Thanks. Andreas OSX 5.2, X 2.1.4, coot 0.50 pre889. -- I am not stupid. I have read several books. Salman Rushdie - Midnight's Children
Re: [COOT] Is there anything I can do to make X11 stable enough to use on 10.5.2
Hey, you can always go to the coffee shop, surf the web and impress all the other life-stylers out there with your slick machine, even though you might have to buy a MacBook Air to keep with the times. I have problems similar to what Bill described when I run coot (0.4.1 with OSX v5.2 and X 2.1.1). The computer never freezes entirely (knock on wood), but coot is completely useless. Good think my Fedora Thinkpad has forgiven me my betrayal. It is, in fact, quite happy mercilessly spanking this shiny lifestyle machine of mine. What I'm most annoyed about with all this X11 business is that there are many places to get fixes from but no one has a solution. It's not unlike trying to get a FireGL to run properly under linux, but not exactly what you expect from a company that can't stop professing its godlike superiority. Let's see if 2.1.4 changes things for me in any way. If not, there's always my beloved ThinkPad. Andreas hari jayaram wrote: We just got our brand new leopard running mac pro , we have been having frequent crashes and freeze ups as well Leopard version : 10.5.2 X version: 2.1.4 Coot version:0.5.1 Intel Mac Pro Most downright crashes where I had to resort to the power button came when i was runing coot. When running ccp4i , it seems understandably less taxing on X. But even with that I always have the gui windows bleed through into other windows. Not to mention the fact that spaces is entirely unuseable. To think that linux has had outstanding spaces like multiple desktop functionality for years.. Just my rant against leopard and X and I agree with Bills sentiment..makes me want to go back to gentoo-linuxbut then we just spent almost 3K on this machine and I am sure hoping these problems will soon disappear A willing guinea pig Hari Jayaram On Sun, Mar 23, 2008 at 6:19 AM, Phil Evans [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: Bill I've been using 10.5.2 plus the X11 2.1.4 update from the Xquartz site, I haven't had problems with freezing lately, I _think_ not since this update. The main problem is that Exposé doesn't work properly not much help ... Phil (looking at a white Easter outside the bedroom window) On 23 Mar 2008, at 01:01, William Scott wrote: Hi Folks: I know I've asked before, but it is so frustrating to lose an hour of work, trying to convince myself that I won't get reamed this time. But I keep going back, like to some sort of abusive codependent relationship, to put it into California terms. I'm using a molecular graphics model building crystallography program called coot, but this happens with enough other X11 applications that I don't think it is the fault of coot. Prior to OS X 10.5, I never ever had a problem with X11. If I try to resize a window while the program is loading, it is a guarantee that the Xserver will freeze. However, if I try to be real careful, I can start to get work done, but then when some window or pop-up menu appears, a half hour or an hour into a session of work, I'll get a random freeze. I'm running 10.5.2 on intel (but this happens on all my 10.5.2 computers, ppc and intel) and the latest X11 from the update page, and when I sample the frozen processes I get this as output: Sample of X11.txt x11_hosing.txt My kids want to know why I swear at the computer so much. I'm almost ready to reformat the disk and install ubuntu linux. Thanks. Bill Scott -- I am not stupid. I have read several books. Salman Rushdie - Midnight's Children
Re: [COOT] coot-0.5-pre-1-852 installation problem
Hey Raj, you forgot to upgrade your operating system. After all, OSX is not XP that you can use for eight years just fine. It requires continual purchase of upgrades that introduce major new features and breathtaking innovations and, at the same time, mercilessly kick all prior versions into the dustbin of computer history, better to be forgot, like everything before OSX (shudder!). But it's the best system for crystallography, so what can you do? Andreas S. Shanmuga Sundara Raj wrote: Hi, coot-0.5-pre-1-852 installation using fink ends up with the following error. I am using Mactel running 10.4. I have updated all packages using selfupdate followed by update-all. Any suggestions? Thanks Raj
