不知不觉又陪大家过了一个月，转眼就要到 6 月了，一说到 6 月，关注本站的同学们大概...
在人工智能领域苹果已经收购了多家公司，收购的这些技术将促使 Siri 在上线 5 年后迎...
玩家能在世界各地探索，只要附近有小精灵出现，手机就会发出震动提示。
太过 Amazing 的创新往往最终不会成功，QuickTime VR 的故事告诉了我们这一点。
从阿伦德茨对 Apple Store 的一系列改造来看，苹果零售店似乎也将会逐渐沾上“奢侈”...
对于爱自拍的女性来说，不怕存储空间不够用而导致的频繁删照片了。
究竟传闻中显著改进的 iPhone 7 表现如何，我们拭目以待。
虽然最近苹果的手机业务有所下滑，但这条产品线仍然是一棵不折不扣的摇钱树。
刀塔的故事背景我想不少朋友已经很熟悉，再重复灌输难免显得有些啰嗦，详细的剧情小...
凭借着旗下众多恐怖游戏而在玩家心中留下惊悚形象的开发团队 Roman Pusnik根据目前仍...
坦克作为游戏中常见的素材，现在已经涉及到了射击、冒险等多种类型，在《巨型坦克（Me...
在刚刚过去的本周四，曾经开发过人气休闲小游《气球猫》的开发团队 C4M Prod 为全球的...
游戏采用了较为写实的一种画风，游戏中每一次比赛都是玩家与另外一辆赛车之间的较量。
新作再出，又吸引了粉丝们从四面八方赶来，和他们朝思暮想的伙伴再见一次。
音游玩家们期盼已久的雷亚第三代音乐手游《兰空VOEZ》本周四终于正式上架移动平台了。
Burkley 皮质保护壳造型非常复古，它由表面的真皮和内部的硬质塑料打造而成，将 MacBo...
Adonit 推出了一款新的手写笔，人们将之称为苹果 Apple Pencil 的竞争对手。
由于当地还没有官方零售店，库克在授权店也开了一次眼界。
这款 Otterbox 模块化保护壳的背面底部拥有一个凹槽设计，允许用户将自己需要增强的模...
苹果与飞利浦其实也是老搭档了~
耳机的造型设计借鉴了黑胶唱片标志性的圆碟造型，在享有优良音质的同时迎合时尚品味。
说得我都想天天呆厨房里做甜品了~
尽管有缺陷，但它应该称得上是一款很优秀的，适配iPhone的VR设备。
2012 Mac Mini 安装Win8 过程。。。
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白苹果, 积分 881, 距离下一级还需 619 积分
昨晚上终于拿到了2012款mac mini低配，包括触摸板，和有线苹果键盘。家里有现成的显示器。由于家里有时还需要Windows系统，所以准备安装一下。把过程记录一下，或许有网友能用到。
先罗嗦点开机的小插曲：
1. 接好电源，鼠标，键盘，显示器，按电源按钮，发现白屏幕后就没有动静了。。。。解决办法：启动时按住Option解决；
2. 第一次启动过程中，按照步骤顺利识别了触摸板，然后就提示无线蓝牙键盘（我没有）。。。解决办法：我的有线键盘接的有问题，把那根USB延长线当成普通USB转接线了。把延长线接在键盘上，再接到mini上。重新启动安装，就OK了。
安装Windows过程：我自己有正版的Win7 和Win8 Pro，以为应该能够顺利用 Boot Camp助理安装，结果还是一波三折。
1. 安装Win7结果：（1）先利用Mac制作了Win7映像光盘iso格式（自己安装了一个制作光盘转ISO的应用），并准备一个8GB U盘；（2）启动Boot Camp助理，选择刚刚制作的ISO文件和U盘，分区60GB给Win7。自动安装开始，并且自动下载了。。。，机器也自动重启了，在驱动程序选择时，卡壳了，没法进入下一步。。。。找了若干资料无果。（3）重新进入Mac，利用Boot Camp还没法恢复分区（可能是我自己在Win7安装时，用自定义方式把60GB分区删除并重新建立了一下）；（4）利用Disk Utility，把分区60GB删除（这部分空间暂时不能用了，当时也没找到办法怎么重新分配给Mac系统，暂时不管它）
2. 安装Win8过程：（1）开始步骤同Win7尝试过程，并再分配20GB给Win8，利用Boot Camp，还是恰在驱动程序那里，没法点击“下一步”，没找到解决办法；（2）利用Disk Utility把刚刚分配的20GB删除，这样分区变成了Mac 420GB，未分配80GB（前面还有60GB）；（4）重启机器，按住Option，利用刚刚生成的U盘（里面有Win8安装程序，是Boot Camp帮助格式化，并把Win8 ISO自动拷贝到上面了），在80GB分区安装Win8（会自动重新分区成2个分区），一切顺利。Win8安装好了。
待续。。。。
<p id="rate_058" onmouseover="showTip(this)" tip="很不错,学习了!&人气 + 1
" class="mtn mbn">
很不错,学习了!
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顶。。。。
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我昨天安装win7也惊险无比，其实boot camp全做好了，不要看以前的教程，直接全选3项对勾就好了。后怕一下，出现non system disk，是u盘问题。好在我用了两个优盘。
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我的昨天也做好了win7，前几天做win7不是通过cootmacp，结果悲剧在win7下做分区导致苹果无法进入，只能在线恢复，恢复了34个小时终于好了，昨天又通过bootcanp做的win7一切正常，现在win就一个C盘 我也不分区了
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iPhone5s，iPhone4s，iPad Ari，iPa
对magicpeng于 11:21在楼主发表的主题评分:人气:+1;
昨晚上终于拿到了2012款mac mini低配，包括触摸板，和有线苹果键盘。家里有现成的显示器。由于家里有时还需要Windows系统，所以准备安装一下。把过程记录一下，或许有网友能用到。
先罗嗦点开机的小插曲：
1. 接好电源，鼠标，键盘，显示器，按电源按钮，发现白屏幕后就没有动静了。。。。解决 ..很不错,学习了!
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提示: 作者被禁止或删除 内容自动屏蔽
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学习，想装WIN8.1……
估计会很少用，不知道装双系统之后对平常启动直接进IOS的速度影响大不大？
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Powered by Discuz!WinCoot download
WinCoot install and download page
How to download and install WinCoot?
Since we have an installer there is hardly any manual intervention
required to install WinCoot. However if you have a multi-user
computer you might want to change a few things. Here is how things
Download the installer for
use NEW experimental
for even more options).
Double-click the downloaded file (WinCoot-version.exe).
WinCoot is extracted and
short cuts
created on the desktop and Start
for the current user (N.B. you may want to avoid
spaces in the WinCoot master directory name, it may cause
problems. If you have Administrator privileges you will be asked
if you want to install it for all users).
That's all. You are ready to enjoy using WinCoot... Happy
(You might want to read the installation notes for
multi-user
computers .)
N.B. (1) WinCoot will save your backup structures in a coot-backup
directory, which is default under C:\yourWinCootdirectory\coot-backup.
can be changed for every user. It will accumulate a lot of pdb
files and should be 'cleaned' occasionally.
N.B. (2) You will need about 500MB of disk space for WinCoot (I hope
can reduce it somehow soon...).
Source code download
You can download the source code from here.
However, I cannot garantee that you'll be able to build it on your
MinGW system. An autobuild script help you to do so (build-it-win).
free to email me if
you have problems and are desperate to do so.
What are the different versions (stable/developer version)?
Stable releases are tested official releases (every few month). The
developer versions are build every night and are the latest coot
versions. Although these are tested they may not be fully functional
and contain unknown bugs.
Multi-user
Windows computer and single
user installation
WinCoot doesn't need to set any environment variables any more but
instead uses a .bat file which sets these in runtime. However
uses 2 directories (environment variables) which
could/should
be used individually by the user. These are COOT_HOME, which hosts
the .coot.py
file and .coot-preferences directory,
COOT_BACKUP_DIR,
where intermediate, backup pdb
files are stored. For a multi-user Windows computer the
Administrator
might want to change these environment variables in the runwincoot.bat file
(by default in C:/yourWinCoot)
individual user (you obviously need a runwincoot.bat
file for every user).
The coot state file will be saved in the directory where WinCoot is
started from (default is C:/yourWinCoot).
individual users you could change this in the Properties of the
WinCoot (desktop)
shortcut. Alternatively you start WinCoot (runwincoot.bat) from a
shell in the directory where you want to work in and the state file
environment variables.
This is a list of environment variables WinCoot uses. These are set
runtime when executing runwincoot.bat.
So there is no need to set any variables. There is no need to change
the variables, except COOT_HOME and COOT_BACKUP_DIR for
individual users, if required. Feel free to edit the runwincoot.bat file.
Environment
Variable Name
Variable Value
C:\WinCoot
where .coot.py for
personal settings is
COOT_BACKUP_DIR
C:\WinCoot\coot-backup
intermediate pdbs
are saved here
COOT_REFMAC_LIB_DIR
C:\WinCoot\share\lib
COOT_SCHEME_DIR
C:/WinCoot/share/coot/scheme
only required for guile
needs "/" instead
COOT_STANDARD_RESIDUES
C:\WinCoot\share\coot\standard-residues.pdb
COOT_PIXMAPS_DIR
C:\WinCoot\share\coot\pixmaps
COOT_RESOURCES_FILE
C:\WinCoot\share\coot\cootrc
COOT_DATA_DIR
C:\WinCoot\share\coot
COOT_REF_STRUCTS
C:\WinCoot\share\coot\reference-structures
COOT_PYTHON_DIR
C:\WinCoot\share\coot\python
COOT_REF_SEC_STRUCTS
C:\WinCoot\share\coot\ss-reference-structures
GUILE_LOAD_PATH
C:/WinCoot/share/guile/1.8; C:/WinCoot/share/
C:/WinCoot/share/guile/gtk-2.0;
C:/WinCoot/share/guile/
C:/WinCoot/share/guile/
C:/WinCoot/share/guile/site
only required for guile
Add-& needs "/" instead
C:\WinCoot\share\coot\syminfo.lib
(edit, not new)
C:\WinCoot\ C:\WinCoot\lib
this is added to
Last modified 18/02/2015
email: Bernhard.Lohkamp (at) ki.seFrom CCP4 wiki
Coot is a graphics program for building, refining and analysing macromolecular models obtained with crystallographic procedures.
There is a
with extensive . The program may be downloaded for Linux and Windows computers from the . The license of Coot is GNU GPL.
OS X install packages for nightly builds that work on 10.8.X and 10.9.X are available here:
Please refer to the
Please refer to the
Installing coot on linux is rather more straightforward than on OS X, because most linux systems are based on gnome and/or kde, and tend to have many of the required components already installed. Most of the other dependencies are also readily available.
This is the recommended way for those who do not want to delve into the mysteries of compiling and linking a great but complex piece of software. Read the (somewhat outdated, it seems)
to find "Additional Notes" for your operating system.
In short, just go to
(a mirror is at
) and pick a suitable binary, e.g.
coot-0.5-pre-1-revision-1003-binary-Linux-i386-fedora-5.tar.gz for a Red Hat Enterprise Linux 5 or CentOS-5 system (Fedora 6 corresponds to RHEL5, thus Fedora 5 binaries are OK). If you prefer a "stable" binary, these are at .
Then un-tar it under /usr/local/src (or in your $HOME), and establish a symlink (ln -s) between /usr/local/bin/coot and the bin/coot of the freshly unpacked distribution.
If you then run coot, and the loader complains that a certain library is missing, just ask
yum whatprovides &thatlibrary&
and install the library, again using yum (assuming yum is available in your distribution, otherwise use apt or whatever is there for this purpose).
First of all, SL (Scientific Linux) is a derivative of RHEL, as is CentOS. So all three OSs behave exactly the same.
The binaries with "x86_64" binaries are for 64 the "i386" binaries are for 32bit systems. Since my notebook is 64bits ("uname -a" reports "x86_64" more than once), I download
(the main server is slow, so I use the mirror). As root, I "cd /usr/local/src" and un-tar. Next, have to find out which libraries are missing. This can be achieved by (note the use of LD_LIBRARY_PATH in the second command - do not permanently modify LD_LIBRARY_PATH&#160;!):
[root@localhost]# cd coot-Linux-x86_64-centos-5-gtk2-python
[root@localhost]# LD_LIBRARY_PATH=lib ldd bin/coot-real | grep found
libssl.so.6 =& not found
libcrypto.so.6 =& not found
libssl.so.6 =& not found
libcrypto.so.6 =& not found
So only two libraries are missing! Either they can be installed using yum, or they are already available, but have a higher version.
First possibility: find out about installable RPM packages (preferred way):
[root@localhost
src]# yum provides libssl.so.6 libcrypto.so.6
Loaded plugins: refresh-packagekit
openssl098e-0.9.8e-17.el6.i686&#160;: A compatibility version of a general
&#160;: cryptography and TLS library
&#160;: sl
Matched from:
&#160;: libssl.so.6
... (the package is repeated, and libcrypto.so.6 is also mentioned)
Now don't just install the openssl098e-0.9.8e-17.el6.i686 and its dependencies - it is a 32bit library (the name ends with ".i686")! Installing it does not solve the problem - we need a 64bit library. Unfortunately "yum provides" does not tell us about the 64bit library (is that a yum bug?). By specifying just the package name (openssl098e.x86_64 would also work, and would avoid any 32bit package)
yum install openssl098e
we install both libssl.so.6 and libcrypto.so.6 in their 64bit versions - done!
Second possibility: find out if the system already has a higher version of the two libraries:
[root@localhost locate libssl.so
/usr/lib64/.libssl.so.1.0.0.hmac
/usr/lib64/.libssl.so.10.hmac
/usr/lib64/libssl.so
/usr/lib64/libssl.so.1.0.0
/usr/lib64/libssl.so.10
So the answer is: there is /usr/lib64/libssl.so which is at version 10, which is compatible with the version we need (6). For libcrypto.so the same is true. So just
cd coot-Linux-x86_64-centos-5-gtk2-python/lib/
ln -s /usr/lib64/libssl.so libssl.so.6
ln -s /usr/lib64/libcrypto.so libcrypto.so.6
The way these symlinks are made they would even work if RHEL upgrades libssl or libcrypto to higher versions. Works for me.
Final step (this does not need to be repeated for a new coot version): create /usr/local/bin/coot with
#!/bin/csh -f
setenv LANG C
exec /usr/local/src/coot-Linux-x86_64-centos-5-gtk2-python/bin/coot $*
and make it executable with
chmod a+x /usr/local/bin/coot
As an alternative, you might wish to exploit the debain dpkg/apt/synaptic package management system on Ubuntu and other Debian linux distributions using (unofficial)
. (These will be discontinued when official packages become available.)
To do so, simply download the deb files and install with the command
sudo dpkg -i *.deb
dpkg will complain if a dependency is missing rather than install a broken program.
A pre-packaged version of Coot (0.7-pre-1) for Ubuntu is available from mok0's Personal Package Archive (PPA) on Launchpad. Currently, packages for Ubuntu 10.04 (Lucid) and 10.10 (Maverick) are available.
To install the coot package on your system, you first need to install the public key for mok0's PPA:
sudo apt-key adv --keyserver
--recv-keys 1DC81A57
Next, add the PPA repository to your /etc/apt/sources.list file:
sudo add-apt-repository ppa:mok0/ppa
That's it! Now, you should be able to:
apt-get update && apt-get install coot
This version of Coot only supports the Python scripting language.
To install the coot on Mandriva 2010.0 use the ubuntu distribution:
tar zxf coot-0.6.2-binary-Linux-i686-ubuntu-8.04.1-python-gtk2.tar.gz
in the .cshrc file:
alias coot
'source /prog/CCP4/ccp4-6.1.13/include/ccp4.setup-csh&#160;; /prog/coot-Linux-i686-ubuntu-8.04.1-gtk2-python/bin/coot'
You can convert any debian package file into an rpm file using the program alien.
I have done this and have made the
available.
Installation of coot and all of its dependencies are handled automatically through the autobuild scripts. There are two versions:
- the old user interface. This script builds coot and all its dependencies.
- the new user interface. This script builds coot and most of the dependencies, excluding GTK2.
To build Coot, all you should need to do is edit a few settings in the top of the build script, or alternatively specify those settings as environment variables. For example, the following sequence of instructions will build the latest pre-release of the GTK 2 version with python support:
export AUTOBUILD_INSTALLED=${HOME}/autobuild/coot
export AUTOBUILD_BUILD=${HOME}/autobuild/
export LOGS=$AUTOBUILD_BUILD/logs
export NIGHTLY_DEST_DIR=$AUTOBUILD_BUILD
export STABLE_DEST_DIR=$AUTOBUILD_BUILD
export build_coot_prerelease=1
bash build-it-gtk2-simple python & build.log
(This script works in bash. For tcsh, replace 'export' with 'setenv' and '=' with ' '.
In some cases you may need to download additional development packages in order to build all the components.
There are also instructions for .
Coot has several options for stereographic display, ranging from cross-eyed and wall-eyed split-screen stereo, to hardware-stereo modes that work with CRT systems and most recently the new Zalman 3-D LCD monitor.
Either cross-eyed or wall-eyed split-screen stereo mode can be invoked using the "Stereo" menu item under "Draw", as is shown in the image below:
Similarly, hardware stereo can be invoked (assuming you have the CRT, correct graphics card, emitter, etc) using the same menu item, by selecting "Hardware Stereo".
The first viable LCD monitor for stereographics display is made by Zalman and costs about $300:
The attributes for this monitor have been tested and
on the PyMOL site. Please read it for important details and suggested purchasing sources.
page describes specifically how to get this to work with coot on Mac OS X, but the instructions should be generalizable to linux and Windoze.
Note that the stereo effect is very sensitive to the vertical position of your eyes relative to the screen: if you don't see stereo, try tilting the screen.
Establish an additional toolbutton "swap stereo":
Main Toolbar -& right mouse click-& Manage buttons-& select Swap Stereo
Or for the script minded:
switch_stereo_sides()
This will toggle the stereo images left and right.
Coot can be scripted in scheme (guile) or python - support for each is more or less equal these days.
Several examples of coot extensions to the language can be seen by examining the 0-coot-state.scm file that coot leaves behind when it finishes.
Coops generates a coot script from the output of molprobity, specifically probe, reduce, cluster and clashlist.
For an explanation of the principals underlying reduce and clashlist see . Get Molprobity software .
Use Coot version 0.1 or higher.
Invoke like this (from the directory in which you run coot):
$ coops myfile.pdb
The use Calculate-&Scripting to read in and run coops.scm
Get COOPS .
This example can be found in the coot scheme sources (the function name is molecule-centres-gui and is in the xxx/share/coot/scheme/coot-gui.scm file).
It is a simple function that creates a button box - a button for each coordinates molecule in Coot.
It is annotated.
Reproduced as .
This is a composite script and demonstrate reading pdb file, an MTZ file, translations, zoom, spin zooms, contour level changing, map masking, real space refinement, water addition and loop fitting.
The data files used in the example can be obtained
Put them in the directory where you start coot.
Save the script
to your disk, then use Calculate -& Run Script... to activate it.
is a Cootenization of the CN2COOT script written by Joel Bard (it is based on his csh ) and can be used to compare and contrast scheme programming
and shell script programming (the coot version is longer to some extent because it does extra error checking).
As well as doing the conversion the resulting mtz/maps are loaded into Coot.
It is part of Coot as of version 0.1.2.
To load the most recent files, do this:
which enables the scripting function: (load-latest-files)
For extra gui goodness (you will need 0.1.2):
coot -- --
Here we create a small function to save part of a molecule and add a
gui interface, it can be used in the usual way (i.e. with --script on the command line, Calculate-&Run Script... or
add the script to your ~/.coot file.
The Powermate dial can be used with coot.
One could just assign the rotations to +/-y keys and be done with it, but this script gives you a way of having positive and negative rotations in all three cartesian directions.
The F1 key is mapped to positive rotation, the F2 key to negative rotation, and the F3 key permits you to toggle through x, y, and z, on successive key presses.
I then map F1 and F2 into the ordinary rotations on the powermate (using send key equivalents) and then I map F3 into the single click on the dial, making it easy to toggle through x, y and z.
The press-and-rotate opti I map these into scroll up and down, and put them on the slowest response setting, which makes contouring density easier to control than it is from my mouse scroll wheel.
Imagine you have a file of some property (Chemical Shifts, for example) of a residue that you wish to apply to the
atoms of a particular model from a pdb file as pseudo B factors.
Here's how to do that in Coot:
We have a file "cs.tab" like this, the residue number then the chemical shift value (one for each residue in a particular chain):
Use apply-cs.scm to apply these values as pseudo temperature factors. Typical usage, where "A" is the chain id, and cs.tab the file of values per residue.
(apply-cs (read-pdb "test.pdb") "A" "cs.tab")
Imagine that you have a structure that has residues with partial occupancy. After refinement, it would be convenient to quickly navigate to all such residues.
How can that be done?
Start coot with command line arguments:
This will provide an extra menu item called "Extras", clicking on "Residues with low occupancy..." therein will lead you through the process.
Note that this will often work with SHELXL molecules, because they have atoms with negative (e.g -31) occupancies.
Note also that you will need a recent version of Coot to use this, as it stands.
This will not work on stock Coot version 0.4.x.
You can enable this for use with 0.4.x if you update/replace your xxx/share/coot/scheme/coot-gui.scm file from .
This is a simple interface to the delete-sidechain-range function, it illustrates how arguments can be transfered
from the GUI to the scripting function.
It was written in response to a question from Byron DeLaBarre.
Unfortunately (prior to 0.5) there was an error in the standard delete-sidechain-range function, which is why we over-ride it.
With this script:
Just so you get an idea of the customization by key bindings here are what Paul uses currently (add to your .coot file).
I (wgscott) wrote a
wrapper shell script that lets you convert xplor/cns maps on the fly (you need to install
first) and has a few other enhancements.
I also made a Coot OS X applet that allows you to drag and drop a cns/xplor or ccp4 mapfile or any other coot-compatable file (mtz or pdb file, for example).
Using the File & Get Info dialog, you can program this applet to open all .map and all .mtz files, if you want to, making these files double-clickable.
(requires a separate working coot installation)
Just so you get an idea of the customization by key bindings here are what Bernhard/Paul uses currently (add to your .coot file or put the file in .coot-preferences directory).
For (re-)colouring maps blue:
To (re-)colour coordinate molecules yellow:
To show NCS where NCS-related side-chains have different rotamers:
GUI to easily access jiggle fit and morphing (currently pre-release Coot required, may be moved into trunk):
Python scripting is different to (default) scheme scripting which is mainly described in Paul Emsley's documentation (although it's mentioned somewhere, fairly hidden). You have to change the commands in the following way:
GUILE scripting: (guile-command argument1 argument2 ...)
PYTHON scripting: python_command(argument1, argument2, ...)
Here some simple rules how to translate from Scheme to Python. To translate the other way around, i.e. Python to Scheme, just turn the rules around:
Replace all '-' with '_' (except in equation when you need arithmetic '-' minus signs)
Move the brackets around the argument(s)
Separate multiple arguments by commas rather than spaces
Replace 'define' with 'def' for functions and with '=' for assignments
Make sure to use indentation for the function content [Python is indentation sensitive] and a ':' after the function definition.
Some additional/advanced(?) rules:
#f -& False
#t -& True
(set! variable value) -& variable=value
In Scheme we may have the following script:
(define mol2-pdbFile "somePDBfile.pdb" )
(define mol2-model (read-pdb mol2-pdbFile))
(define (read-mol-again)
(clear-and-update-model-molecule-from-file mol2-model mol2-pdbFile))
(read-mol-again)
Which will translate into Python:
mol2_pdbFile = "somePDBfile.pdb"
mol2_model = read_pdb(mol2_pdbFile)
def read_mol_again():
clear_and_update_model_molecule_from_file(mol2_model, mol2_pdbFile)
read_mol_again()
As of Coot 0.5 (and if you have both scripting languages available) you an use the following commands to run a script or command in the other language:
(run-python-command "python_command(arg1, arg2, ...)")
[from guile/scheme]
run_scheme_command("(scheme-command arg1 arg2 ...)")
[from python]
This permits use of themes for a more OSX-like experience, among other things.
Click on the thumbnail image below to see a full-size screenshot of Coot with a gtk+2 Aqua-like theme.
To get this effect, you need the Glossy_P gtk+2 theme:
Edit a file called ~/.gtkrc-2.0 and put into it the following line:
include "/usr/share/themes/Glossy\ P/gtk-2.0/gtkrc"
Alternatively, if you use gnome or xfce4, you can open the theme manager and just make it open the downloaded Glossy_P tarball, and it should add this as a theme.
It should be noted that the answers ("A") are from Paul Emsley himself (and were maybe slightly edited).
Q: How can I get involved with Coot development?
A: Join the
project. This is a project to get new people involved in improving Coot, by acting as a clearing house for simple tasks which need doing, and providing documentation for doing them.
Q: Is it possible to deactivate the nomenclature errors check? Sometimes this check is not very useful and it becomes rather annoying when one has several molecules loaded only wants to look at the structures...
A: Add to your ~/.coot or whatever:
(set-nomenclature-errors-on-read "ignore")
Q: I am sure this exists somewhere through scripting in COOT, but can I apply NCS edits to only a subset of NCS copies? In
other words, can I tell coot which are NCS related chains, and which aren't.
I am working on this nightmarish case of asymmetrical homodimers, where the sequences are very similar, but the structures are not, so I need to tell coot which chains are actually related to each other.
A: Nightmare. If you have a recent [1632 or later for the scheme version, 1646 for the python version] Coot, you can do this:
(manual-ncs-ghosts imol resno-start resno-end chain-id-list)
imol is 0 (say)
resno-start and resno-end is the residue range for the LSQ fitting to return the NCS matrix,
chain-id-list is the list of chain-ids, starting with the master/reference chain-id and followed by the peer chain-ids that are NCS related, e.g. (list "A" "B" "D")
The python interface is similar.
There is also a GUI to activate this feature under Extensions -& NCS.
Description of problematic situation: I am using
to refine my 1.2 ? data and I am refining the hydrogen atoms. Subsequent rebuilding in coot is difficult though since hydrogens often does not "follow" when you do side chain rebuilding. For the moment I have quit transfering hydrogens to coot and add the hydrogens every refinement cycle, though it would be good I think if I could see them in coot without bothering about wrong positions. So these are my specific questions:
Specific Q1: Using "edit chi angles" does not work properly.
A: This fails because for chi angles Coot uses the Refmac dictionary to know what is connected to what (if it can).
The work-around is to rename the refmac dictionary so Coot can't find it - which will force Coot to find bond by distance criteria.
Specific Q2: Using "real space refine" does not work properly.
A: Yes this fails.
Hydrogens are named differently to SHELX hydrogens.
In principal this could be made to work if the dictionary was reworked to use SHELX hydrogen names.
This would also fix the chi angles problem too of course.
Specific Q3: I am unable to open the output pdb file from ShelXL in Coot.
A: Well, it's hard to know what's the problem without details - the console should say something. But when handling the output of shelxl, I suggest you read the .res file rather than the pdb, then the subsequent .ins file contains lots of "header" information.
Another answer to questions 1+2 is to rename the hydrogen atoms in the shelxl res-file to match the mmCIF dictionaries used by Coot. This only needs to be done once as shelxl does not modify these names. Except for a few manual editions, the renaming can be done semi-automatically using regular expressions (replacing A-&1, B-&2, etc).
Concerning question 3, the Coot -& Extensions -& Module -& SHELXL menu entry works really well now. It reads in all relevant shelxl files and provides a menu highlighting the problematic areas in the model.
Q: improvement of image quality on machines with NVidia cards?
A: After talking about antialiasing with Stuart McNicholas, I discovered a program called nvidia-settings. I found that if I do:
Antialiasing Settings -& Override Application Setting, and set the slider to 16x
then I start Coot, I see that it starts up in nice antialiasing mode (which is a lot better that the poor mode that Coot has built-in).
I don't know if this works on other/newer systems, but it works for me on my oldish GeForce 6600. (Of course the FPS takes a hit.)
Q: How to set the default to display symmetry related molecules?
A: Add (set-show-symmetry-master 1) to the appropriate file.
Q: I still have a ".coot" file in my home folder for a few coot preferences that I couldn't find in the new ".coot-preferences/coot-preferences.scm". There is a warning that I should not add commands to this file. So is a "~/.coot" still the proper place to add default commands for coot?
A: Coot does not create a ~/.coot file for you, but will read it if it exists.
Likewise, ~/.coot.py in which you can write python commands.~/.coot-preferences is a directory in which all .scm files and .py files are executed.
coot-preferences.scm and coot_preferences.py there are generated by using the Edit -& Preferences dialog (and thus it overwrites older versions - hence the warning).
If you want to create a script that will be read by everyone then put those files into a directory defined by environment variable $COOT_SCHEME_EXTRAS_DIR (for *.scm) or $COOT_PYTHON_EXTRAS_DIR (*.py). All *.scm in $COOT_SCHEME_EXTRAS_DIR and *.py files in $COOT_PYTHON_EXTRAS_DIR will be executed at start up.
So you have a variety of places. Personally I mostly use ~/.coot.
Q: How do I use "torsion general"?
A: Thanks for pointing out the lack of documentation on this. I'll make a note to add some.
You need to click on the torsion-general icon, then click 4 atoms that describe the torsion - the first atom will be the base (non moving) part of the atom tree, on clicking the 4th atom a dialog will pop up with a "Reverse" button [1].
Move this dialog out of the way and then left mouse click and drag in the main
window will rotate the moving/"top" part of the residue round the clicked atoms
When you are happy, click "Accept".
Window focus may be an issue - depending on your setting, the window manager may
eat one of your clicks as you change focus between the dialog and the main
graphics window (this I find annoying and there are instructions in the FAQ on
how to turn that off for various systems).
[1] which may not work in 0.6-pre (grumble/sigh/sorry).
If it doesn't not work,
the "Reverse" button should invert the moving and "base" part of the residue.
Q: I have some peaks in my map which take water or sodium/magnesium or chlorine atom with out giving out any positive or negative density upon further refinement. Is there any easy way of calculating the peak height / number of electrons at a given position, say a mouse click point in coot? Is there any formula to calculate the number of electrons based on sigma level and peak height, as given in difference map peaks in coot?
A: First, go to the Coot wiki and pick up the .
If you want density information at a given cursor point: point at the blob, press the 'g' key (which recentres on the biggest density under the cursor).
using the Scheme scripting window:
(apply density-at-point (imol-refinement-map) (rotation-centre))
There is no user access to the peak integration code of coot as yet.
Q: I have a pair of disulfide bonds which link two monomers in separate
asymmetric units.
There is a single monomer in the asymmetric unit, and two monomers come together to form disulfides between Cys 26-Cys45, and Cys45-Cys26. When I real-space-refine these residues, they do not form a nice disulfide, and Coot does not seem to recognize them as a disulfide.
A: For the record, you can't refine symmetry-related disulfides in Coot (as of Nov 3, 2009).
Q: How to use macros in COOT? Do they need to be written in Python or another language that I had not heard of before? Where can I find a low level description of how to write macros with some examples (I know nothing about Python, except that it is fashionable)?
A: The other language is a form of Lisp, called . You can learn about programming python in many ways of course (not least the , which is what I read first). The coot python extensions are described in the documentation. There is a standard trivial formatting change that has to be made to get the syntax right for python, see "Python Scripting" []. There is a growing collection of coot scripts in this Wiki article.
Q: Is there any similar function in COOT as lego_auto_mainchain command in O program?
A: there are 2 loop fitting tools in Coot
C alpha -& Mainchain ,
DB Loop: (No good documentation)
Extensions -& Modelling -& DB Loop...
Q: Do an LSQ superposition using specified residues in multiple chains (superposing one oligomer on another).
A: Something like this then?
clear_lsq_matches()
# specs for reference then moving
add_lsq_match(20, 90, "A",
20, 90, "A", 1)
add_lsq_match(20, 90, "B",
20, 90, "B", 1)
add_lsq_match(15, 75, "D",
15, 75, "D", 1)
apply_lsq_matches(1, 2)
which presumes that the reference molecule is in 1 and the moving molecule 2.
Q: How to do a LSQ superposition of a homologous structure onto my working structure using ± N residues about the current position, where N is a variable (not essential, could be fixed) and the current position is the last residue that I clicked on.
A: That is more involved - and more useful because it
can be dynamic. Something like the following perhaps (in Scheme, just for amusement (not tested)). You will need to set imol-ref, perhaps by reading in the reference pdb, as demonstrated below.
The function is bound to Shift-Y.
(define dynamic-lsq-range-extent 2) &#160;;; ± 2 residues either side of centre residue
(define imol-ref (read-pdb "reference.pdb"))
;; convert between the input reference chain id and the chain id of
;; the moving molecule that corresponds to that chain
(define (mov-match-chain ref-chain-id)
ref-chain-id)
(define (dynamic-lsq-match)
&#160;;; get the current residue and use that to make residue ranges for
&#160;;; an LSQ fit
(using-active-atom
(clear-lsq-matches)
(add-lsq-match (- aa-res-no dynamic-lsq-range-extent)
(+ aa-res-no dynamic-lsq-range-extent)
aa-chain-id
(- aa-res-no dynamic-lsq-range-extent)
(+ aa-res-no dynamic-lsq-range-extent)
(mov-match-chain aa-chain-id)
(apply-lsq-matches aa-imol imol-ref)))
(add-key-binding "Dynamic LSQ overlay" "Y" dynamic-lsq-match)
There is the --auto &filename& commandline option for auto-reading mtz files (mtz file has the default labels FWT, PHWT). Can this be made to work with a SHELXE .phs output file after converting with convert2mtz&#160;? - the resulting MTZ file has labels F PHI FOM.
A: use: coot --python -c 'make_and_draw_map("sad.mtz", "F", "PHI", "FOM", "/HKL_base/HKL_base/FOM",1, 0)'
Show me where NCS-related side-chains have different rotamers
(define (compare-ncs-rotamer imol chain-A chain-B)
(let ((n-residues (chain-n-residues chain-A imol))
(mismatched-rotamers '()))
(lambda (serial-number)
(let ((res-name-A (resname-from-serial-number imol chain-A serial-number))
(seqnum-from-serial-number
imol chain-A serial-number))
(ins-code-A (insertion-code-from-serial-number imol chain-A serial-number))
(res-name-B (resname-from-serial-number imol chain-A serial-number))
(seqnum-from-serial-number
imol chain-A serial-number))
(ins-code-B (insertion-code-from-serial-number imol chain-A serial-number)))
(if (not (= res-no-A res-no-B))
(format #t "sequence number for ~s do not match~%" res-no-A))
(if (not (string=? res-name-A res-name-B))
(format #t "residue names for ~s do not match~%" res-no-A))
(let ((rot-name-A (get-rotamer-name imol chain-A res-no-A ins-code-A))
(rot-name-B (get-rotamer-name imol chain-B res-no-B ins-code-B)))
(if (not (string=? rot-name-A rot-name-B))
(set! mismatched-rotamers
(cons (list imol chain-A res-no-A ins-code-A
res-name-A
(if (string=? rot-name-A "") "-" rot-name-A)
(if (string=? rot-name-B "") "-" rot-name-B))
mismatched-rotamers))))
(range n-residues))
(dialog-box-of-buttons "Mismatched Rotamers"
(cons 300 300)
(map (lambda(rotamer)
(let ((label (string-append " "
(list-ref rotamer 1)
(number-&string (list-ref rotamer 2))
(list-ref rotamer 3)
(list-ref rotamer 4)&#160;;; res-name
(list-ref rotamer 5)
(list-ref rotamer 6)))
(thunk (lambda ()
(set-go-to-atom-molecule imol)
(set-go-to-atom-chain-residue-atom-name
(list-ref rotamer 1)
(list-ref rotamer 2) " CA "))))
(list label thunk)))
mismatched-rotamers)
And one would use this something like:
;; example usage:
(let ((imol (read-pdb "test.pdb")))
(compare-ncs-rotamer imol "A" "B"))
Q: We've noticed a new behavior in real space refinement in coot 0.8.1 whereby dragged atoms are more tightly restrained to their initial positions than in earlier versions. This seems to be described in the release notes by:
o BUG-FIX: The amount that the other atoms ove with moving the picked atom has been reduced (but is configurable)
A: Add e.g. this to your ~/.coot.py file:
set_refinement_drag_elasticity(0.8)
Q: I'm wondering why this was changed. Does the optimum elasticity change with resolution, map quality, or another experimental limitation? Or does it more of a user preference?
A: Because of cis-peptides. My worry was that in the previous regime, it was
too easy to introduce cis-peptides when fitting to low resolution maps.
I believe the current default setting is much less likely to do that.
Q: I've tried various settings of refinement_drag_elasticity and I need to lower it to 0.5 or so before any semblance of earlier behavior appears.
A: It used to be 0.167, I think.
Q: I am using COOT 0.8.1 EL that comes with the CCP4 6.5.010 on my Mac OS X 10.10.2. I wanted to run molprobity but the Validate & Probe clashes button in my pull down menu is not active. Is this function available in this COOT version?
A: Reduce and probe are separate programs available from the Richardson’s lab at Duke . Download and install on your box. Then coot needs to be told in some instances where it can find these executables. I have the following lines in my ~/.coot file in Linux.
;; This file is required. As of coot 0.8pre no other mechanism for
;; enabling probe in coot works
;; This is full pathname of molprobity's probe program
(define *probe-command* &/apps/xray/bin/probe&)
;; This is full pathname of molprobity's reduce program
(define *reduce-command* &/apps/xray/bin/reduce&)
Untried: if you have Phenix installed: it comes with phenix.probe and phenix.reduce - you could insert the paths to these binaries into the above definitions.
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