Project

General

Profile

Actions

Bug #1732

closed

Add publication reference boxes to single and multi model refinement pages

Added by Amber Herold about 12 years ago. Updated about 10 years ago.

Status:
Closed
Priority:
High
Assignee:
Amber Herold
Category:
Web interface
Target version:
Start date:
04/16/2012
Due date:
% Done:

0%

Estimated time:
Affected Version:
Appion/Leginon 2.1.0
Show in known bugs:
No
Workaround:

Description

Currently, these do not include references.

Dmitry, can you point me to the correct references for these? I can add them to the code.

These are the generic references. Can I use these or are there more specific ones?

    return referenceBox("EMAN: semiautomated software for high-resolution single-particle reconstructions.", 1999, "Ludtke SJ, Baldwin PR, Chiu W.", "J Struct Biol.", 128, 1, 10600563, false, false, "img/eman_logo.png");

    return referenceBox("FREALIGN: high-resolution refinement of single particle structures.", 2007, "Grigorieff, N.", "J Struct Biol.", 157, 1, 16828314, false, "10.1016/j.jsb.2006.05.004", "img/grigorieff_lab.png");

    return referenceBox("XMIPP: a new generation of an open-source image processing package for electron microscopy", 2004, "Sorzano CO, Marabini R, Velázquez-Muriel J, Bilbao-Castro JR, Scheres SH, Carazo JM, Pascual-Montano A.", "J Struct Biol.", 148, 2, 15477099, false, "10.1016/j.jsb.2004.06.006", "img/xmipp_logo.png");


Related issues 1 (1 open0 closed)

Related to Appion - Test Case #1662: Run Multi-Model Refinement: XMIPP ML3DFailDmitry Lyumkis03/15/2012

Actions
Actions #1

Updated by Dmitry Lyumkis about 12 years ago

for ML3D, I would also add:

Scheres, S. H., H. Gao, et al. (2007). "Disentangling conformational states of macromolecules in 3D-EM through likelihood optimization." Nat Methods 4(1): 27-29.

and:

Scheres, S. H. (2010). "Classification of structural heterogeneity by maximum-likelihood methods." Methods Enzymol 482: 295-320.

Actions #2

Updated by Amber Herold about 12 years ago

  • Status changed from Assigned to In Code Review
  • Assignee changed from Dmitry Lyumkis to Anchi Cheng
  • Priority changed from Immediate to High

I'm not really satisfied with this code...I really want to refactor the whole reference box thing...but I will resist for now.

Actions #3

Updated by Anchi Cheng about 12 years ago

  • Status changed from In Code Review to In Test
  • Assignee changed from Anchi Cheng to Amber Herold

code reviewed.

Any recommendation of sessions that have preparedRecon for testing?

Actions #4

Updated by Amber Herold about 10 years ago

  • Status changed from In Test to Closed
Actions

Also available in: Atom PDF