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kandi X-RAY | vmd Summary
kandi X-RAY | vmd Summary
Preview markdown files in a separate window. Markdown is formatted exactly the same as on GitHub. Features | Installation | Usage | Examples | Command-line options | Configuration.
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Top functions reviewed by kandi - BETA
- Adds application menu menu menu .
- Adds context menu to context menu .
- Convert a text node to emoji nodes .
- Get link type .
- Archive the manifest .
- Convert an object with MDAST table .
- Upload an asset to a release
- Transform the front matter .
- Create menu item item
- handle link
vmd Key Features
vmd Examples and Code Snippets
Community Discussions
Trending Discussions on vmd
QUESTION
I was making a small script in tcl for VMD:
...ANSWER
Answered 2022-Mar-09 at 12:47Try: set path [file tail [pwd]]
QUESTION
I want to sequentially update a series of file, from a tmp file distTmp.RST to sequentially dist1.RST, dist2.RST, etc..
For me, the fileutil package in vmd text interface is not working as follows:
My tcl code (add.tcl):
...ANSWER
Answered 2021-Nov-04 at 15:30The
fileutil
package is part of tcllib. Check that your variableauto_path
includes a path where Tcl can find tcllib and fileutil.Your list for
string map
is in curly braces, so it's using a literal dollar sign for$M
instead of the value of the variable named M.
Change curlies to double quotes or use thelist
command, as answered in a comment already.$$M
is usually not okay in Tcl. Are you trying to do double interpolation? If so, I recommend usingset
with one argument, to retrieve a value instead of to set a value. You can use$$
in asubst
command, but that's not my preference.
QUESTION
So I am creating task in a TaskGroup and am trying to add them in my dag sequence of tasks but it is throwing this error:
...ANSWER
Answered 2021-Oct-29 at 12:17AttributeError: 'NoneType' object has no attribute 'update_relative'
It's happening because run_model_task_group
its None
outside of the scope of the With
block, which is expected Python behaviour.
Without changing things too much from what you have done so far, you could refactor get_task_group()
to return a TaskGroup
object, like this:
QUESTION
I've been trying to run MMPBSA calculations using CAFE, however, when I use -pb_rad charmm. VMD prints the following error when it begins to run PB calculations: "Unmatched open quote in list "
I suspect that the error originates from the following section of the cafe_mmpsa script:
...ANSWER
Answered 2021-Oct-08 at 05:09You're building a string that is a tcl
command, and evaluating it. Part of what you're doing is adding quotes around arguments, which handles things like spaces in the arguments, but if they themselves have quotes, you have to take special action to avoid issues.
A demonstration of the sort of thing you're likely running into:
QUESTION
I have two div elements whose display property is set to inline-block inside a div and width: 49.5%. It is rendering side by side. That's fine but in the case of different content heights, the one which has content with less space leaves space on the upside. What I want is that it doesn't leave space and fills that space and might increase padding-bottom. How to accomplish the
...ANSWER
Answered 2021-Oct-04 at 10:33You can use flex
instead of inline-blocks
. And first thing you need to do is target the parent element and assign it display: flex
property. Rest all falls in order with the browser defaults.
QUESTION
I have a Linux subsystem installed on my Windows machine. I've transferred a tar.gz file I want to access by finding the location of my subsystem and dragging the files over. But when I run the command:
...ANSWER
Answered 2021-Feb-20 at 14:37For starters, this belongs on Super User since it doesn't deal directly with a programming question. But since you've already provide an answer here that may be slightly dangerous (and even in your question), I didn't want to leave this unanswered for other people to find inadvertently.
If you used the first method in that link, you are using a WSL1 instance, not WSL2. Only WSL1 made the filesystem available in that way. And it's a really, really bad idea:
There is one hard-and-fast rule when it comes to WSL on Windows:
DO NOT, under ANY circumstances, access, create, and/or modify Linux files inside of your
%LOCALAPPDATA%
folder using Windows apps, tools, scripts, consoles, etc.
Opening files using some Windows tools may read-lock the opened files and/or folders, preventing updates to file contents and/or metadata, essentially resulting in corrupted files/folders.
I'm guessing you probably went through the install process for WSL2, but you installed your distribution before setting wsl --set-default-version 2
or something like that.
As you can see in the Microsoft link above, there's now a safe method for transferring and editing files between Windows and WSL - the \\wsl$\
tmpfs mounts. Note that as a tmpfs mount stored in memory, it's really more for transferring files over. They will disappear when you reboot or shutdown WSL.
But even if you'd used the second method in that article (/mnt/c
), you probably would have run into permissions issues. If you do, the solution should be to remount the C: drive with your uid/gid as I describe here.
QUESTION
I'm trying to write a script in tcl to execute some analysis on VMD. First I'm creating an atom selection inside a procedure, then I'm trying to use it on another procedure.
The atom selection from VMD is implemented as a Tcl function. The data returned from atomselect
is the name of the function to use. You can read more here.
When I create the atom selection outside a proc
I can use it inside one just passing it as global
. But now that I'm creating it inside one, when I try to use it it's just a string with the procedure name.
This works:
...ANSWER
Answered 2020-Dec-05 at 22:32The problem is that the command created by the atomselect
command is being deleted when the procedure returns. I strongly suspect that this is being done using a local variable deletion trace (on some variable that is otherwise unused). When atomselect
is run in the global scope, there's no such natural deletion event (unless the global namespace is deleted, and that's an interpreter-ending event) so the trace never gets called and the created command persists indefinitely.
If we rewrite your create like this:
QUESTION
I am new in development with mule, i am using java 7 to develop an application that uses mule.
The problem is that i am not able to start mule, i am not sure but looking to the logs, i think that there is a problem with my spring configuration and mule.
in the log there is a code error: MULE_ERROR-71999 !!!.
here is the log:
...ANSWER
Answered 2020-Nov-20 at 21:23Are really sure Java 7 is used to start Mule 3.4? Probably that version is not compatible with Java 8 and that can cause this error. If you are using Anypoint Studio, or the older Mule Studio, be sure that the execution environment is pointing to a Java 7 SDK.
If you are using the command line you need to check that wrapper.conf points to the right java executable for Java 7 (example wrapper.java.command=/path/to/jdk7/bin/java
).
3.4 is absolutely end of life and ancient, same as Java 7. I recommend to migrate to current versions as soon as possible.
QUESTION
im quite new to Ansible and eager to learn how much it can do. I have a task to do the following:
- Run command bpps -a to get a list of running NetBackup processes.
- Go through each string of output (we're interested in strings having 'bpbrm -backup' in them)
- Extract following data from those strings: Policy name (field after -cl key), Backup Schedule (field after -sched key), Hostname (field after -c key) ( I assume regex with capturing groups will do the trick? )
- Put this data into data structure we can iterate over
- Iterate over this data structure and run the bpbackup -i -p policy_name -s schedule_name -h hostname command to restart backup jobs for the client that were running backups at the time when we've collected data with bpps -a
I can do it with my eyes closed on Python, however i'd like to be able to do such tasks using Ansible alone to improve my skills if it takes sane amount of time and code :)
I would very appreciate if you will give some explanation on how it works, also could you please share some resources where i can find some Ansible tasks to practice on?
Its super easy for Python but I wasn't able to find some practice for Ansible yet. Thanks in advance and sorry for lame question :)
The output:
...ANSWER
Answered 2020-Oct-17 at 19:22Q: "1) It's super easy for Python but I wasn't able to find some practice for Ansible yet. 2) I'm not asking for a fish I need a net."
A: Let me provide you with the "net". In this case, the best option is custom filter plugin. For example, the playbook below
QUESTION
I am trying to create a dynamic java agent, but when the agent is loaded this error is thrown:
...ANSWER
Answered 2020-Aug-23 at 04:03signer information does not match signer information of other classes in the same package
This happens when classes belonging to the same package are loaded from different JAR files present on the classpath, and those JAR files have signatures signed with different certificates - or, perhaps more often, at least one is signed and one or more others are not. So either make sure all JARs (or at least those which contain classes from the same packages) are signed using the same certificate or remove the signatures from the manifest of JAR files with overlapping packages.
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