Which is ccp4 online webserver do you use?

The CCP4-online webserver is now available. Users can make use of BALBES, MrBUMP and MoRDa, the automated molecular replacement services.
And, what is the purpose of the CCP4 Documentation wiki?
The CCP4 Documentation Wiki is a new way of documenting the CCP4 software, with the aim of being more accessible to GUI- and novice users: The focus is on how to user the software through the user interface, and the wiki is divided into two main areas:
Also Know, what should I use as an alternative to CCP4? Issues have previously been reported when using CCP4 software, while having Avast AV running on Windows systems. We therefore recommend using the default Windows Defender software as an alternative when installing or using CCP4 software. Click here for the MD5 checksums of all files.
Thereof, how do I set up my CCP4 environment?
Windows users can get a correctly set up environment by running the CCP4Console program. The CCP4 manual gives an overview of the CCP4 suite in the context of the structure determination process.
Keeping this in consideration, what is the version of windows for CCP4?
A version of the CCP4 suite is available which will run under a number of different Microsoft Windows versions: Windows ME, Windows 95/98, Windows NT V4.0, Windows 2000, and Windows XP. The installation procedure is different from the Unix/Linux platforms but is straightforward:

20 Similar Question Found

Can you use ccp4 online on internet explorer?

CCP4 online does not seem to work on Internet Explorer at the moment. Please use some other browser for the time being. Sorry for the inconvenience.

What do you need to know about ccp4?

CCP4 aims to develop and support the development of cutting edge approaches to experimental determination and analysis of protein structure, and integrate these approaches into the suite. CCP4 is a community based resource that supports the widest possible researcher community, embracing academic, not for profit, and for profit research.

Where can i download ccp4 software for pc?

The CCP4 software can be downloaded and runs on Windows, Mac OS and Linux. It provides an integrated suite of programs for determination of macromolecular structures by X-ray crystallography that can be accessed through a graphical interface on your computer, through CCP4 Online, or through CCP4 Cloud.

How is ccp4 used in x-ray crystallography?

It provides an integrated suite of programs for determination of macromolecular structures by X-ray crystallography that can be accessed through a graphical interface on your computer, through CCP4 Online, or through CCP4 Cloud. CCP4 offers a variety of workshops and courses for students, early career researchers, and project leaders.

When was the first version of ccp4 released?

The interface, christened ccp4i, was first made publicly available sometime in 1998, and has been released as an official part of the main CCP4 suite since March 1999 (CCP4 4.0). In March 2001 Liz moved on to the CCP4 3D Viewer Initiative and support and development of CCP4i has passed onto CCP4 staff.

When did liz potterton release the ccp4 interface?

Since 1997 Liz Potterton has been developing a graphical user interface for the CCP4 suite. The interface, christened ccp4i, was first made publicly available sometime in 1998, and has been released as an official part of the main CCP4 suite since March 1999 (CCP4 4.0).

Is the pointless program part of ccp4?

The pointless program (see Scaling and Assessment of Data Quality, Philip Evans, Acta Cryst D 62, 72-82) is part of CCP4 and serves to identify space group possibilities from unmerged data. HTML documentation is at http://www.ccp4.ac.uk/html/pointless.html . The pre-release version may be obtained from ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/ .

How to create a simple map in ccp4?

Use fft to create a map in CCP4. (This task can be run from the Run FFT-Create Map option under Map & Mask Utilities) You can create a simple map or a 'Fo-Fc map as you wish. CCP4i will create a 2Fo-Fc map by default. To make a Fo-Fc map, set F1=DELFWT and PHIC=PHDELWT in the task window. Select the option to cover 'asymmetric unit' .

What should the grid size be for ccp4?

You need to select structure factor (F) and phase (PHI) column data and optionally, weightcolumn data, to calculate the map. The default map grid sizeof 0.75 Å is appropriate for model building work but a higher resolution (i.e. smaller grid size) may give a better picture but slower performance.

How big is the download file for ccp4?

CCP4 Source Packages Once compiled, the CCP4 source package allows automatic updates directly from the CCP4 source code repositories. It includes suitable Python and Tcl/Tk software, and can build COOT and CCP4 Molecular Graphics. See the README file in the package, or read it online. CCP4 Program Suite 7.0 Download size: 974 MBDate: 07/01/2016

Which is the default sampling rate for ccp4?

The sampling rateis applied when generating maps from experimental data (MTZ files) and is the resolution of the map. The default value of 0.75 is quite coarse, values like 0.5 will give more attractive, but slower, pictures.

Which is the best program for ccp4 molecular graphics?

CCP4mgis the quick and easy way to create beautiful publication quality images and movies. It is also the easy way to superpose and analyse structures. See the Functionalitypage for details. The program runs 'out of the box' on Linux, MacOSX and Windows platforms.

Which is the refinement module in ccp4?

Refinement in CCP4 is usually done using the program Refmac5 , although there is also Restrain available. Before proceeding with refinement, it is important to check that there are suitable restraints in place.

How to define a link in ccp4 geometry?

To define a link you must enter the atom name, alternate indicator, the residue name, sequence number, chain ID and insertion code for two atoms. The link ID is a CCP4 specific field on the end of the LINK record which should contain the name of a type of link defined in the CCP4 geometry libraries.

How are restraint dictionaries generated in ccp4?

Restraint dictionaries for ligands can be generated and/or editted using the Monomer Library Sketcher. Multiple dictionary files can be merged with the Merge monomer libraries task. Refinement of the model can then proceed via the Run Refmac5 task, as described below. The special case of NCS Phased Refinement is treated in a separate task.

Where can i find the program documentation for ccp4?

D50, 760-763 There is a partial list of program references extracted from the individual program documentation. List of the major program changes since the previous release. This list can also be seen in function grouping. ccp4 - introduction to the CCP4 Program Suite ccp4_interface_installation - Installation of CCP4 Interface

Is the 3d mrc format compatible with ccp4?

Largely compatible with CCP4. Note that some programs will treat 3D MRC files as stacks of 2D imagess (like IMOD). This behavior is partially supported in EMAN, but be aware that it is impossible to store metadata about each image in the stack when doing this, so it is not suitable as an export format for single particle work.

How is the ccp4 interface designed to work?

The CCP4 Interface is designed with the expectation that all data files relating to one crystallographic project will be in one directory. It is simple to override this but it may be helpful to organise all CCP4 work this way. You may have more than one project, and it is easy to switch between projects inside the Interface.

Which is the reflection file format in ccp4?

Standard CCP4 programs deal with reflection files in so-called MTZ format. Files in different formats, namely ascii MTZ ('na4'), X-PLOR/CNS, SHELX, MULTAN, TNT, mmCIF and user defined ascii, may be converted to MTZ format.

What is the ccp4 software and how can i use it to determine macrom?

The CCP4 software can be downloaded and runs on Windows, Mac OS and Linux. It provides an integrated suite of programs for determination of macromolecular structures by X-ray crystallography that can be accessed through a graphical interface on your computer, through CCP4 Online, or through CCP4 Cloud.