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Changes for page Extended ISPyB (EXI)

Last modified by hakanj on 2025-11-24 09:34
From version 9.1
edited by tabermah
on 2024-12-06 09:31
Change comment: There is no comment for this version
To version 7.3
edited by tabermah
on 2024-12-06 09:10
Change comment: There is no comment for this version

Summary

Details

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Content
... ... @@ -8,7 +8,6 @@
8 8  * Select the proposal you want to work with. Make sure you work with the proposal with scheduled beamtime. Sample information entered under the wrong proposal cannot be accessed during the experiment.
9 9  * If your proposal is not listed
10 10  
11 -
12 12  = Creating a contact at the user's institution =
13 13  
14 14  The first step to set up the shipment is to assign a contact from your home laboratory. This is the person whose name will appear in the shipping labels and who will receive notifications about the dewar.
... ... @@ -16,7 +16,6 @@
16 16  * On the top menu bar, select **Manage shipping address** from the **Shipment** drop down menu. Select **List** to show the existing contact address card list – it will open to the left of the window.
17 17  * Look for your name in the list (the information is taken automatically from DOOR) and click anywhere on the card to verify that all the information is up to date and complete. If this is not the case, click on the **Edit** button, enter the correct information and **Save**.
18 18  
19 -
20 20  = Create a shipment =
21 21  
22 22  The next steps are to generate the ID and shipping labels for your dewars, list the containers and samples in the dewars and send a notification to DESY P11 staff. Even if you plan to transport the dewars to DESY yourself, creating the shipment is useful to provide the required sample information to be used in synching to MXCuBE.
... ... @@ -30,11 +30,11 @@
30 30  ** If you wish to review or edit the information after saving the form, select **List** under **Shipments** in the Shipment dropdown menu. That will show a list of your shipments in the left side of the window in inverse order of creation -sometimes you may need to refresh the page to show the newly created shipment. Click anywhere on the shipment card to open the shipment information.
31 31  * Set up the parcels (dewars) and sample list contained in the shipment as explained in the following section
32 32  
33 -
34 34  = Create new samples and provide a sample list =
35 35  
36 36  This section describes how to enter information about the parcels, containers and samples present in the shipment. Adding the parcels must be done in order to generate the shipping label for the dewars, as described  in the **Send shipment**section in this document. However, filling up the sample details can be done while the dewars are in transit or even when they are already at DESY. Once the Unipucks are loaded in the sample changer dewar (shipment status set to “processing”) it will not be possible to change the shipment contents any longer.
37 37  
35 +
38 38  == Creating a new sample ==
39 39  
40 40  If you are sending crystals of a new protein, it is important that you create an entry for the protein, since you will not be able to upload or save information from an unknown sample. To create a protein follow these steps:
... ... @@ -46,14 +46,15 @@
46 46  
47 47  == Fill the sample information in a CSV file ==
48 48  
49 -A practical way to enter information about the parcels, containers and samples included in the shipment is by uploading a CSV file. The upload menu is accessed by clicking the **Import from CSV** button in the shipment card. The example file below will generate a parcel called Dewar1 containing seven Unipucks fully loaded with crystals of different proteins.
47 +A practical way to enter information about the parcels, containers and samples included in the shipment is by uploading a CSV file. The upload menu is accessed by clicking the **Import from CSV** button in the shipment card. [[This example file>>url:https://lu.box.com/s/c4bpgc9ygm03wt9jhh8lu9x0rt67gh2m]] will generate a parcel called Dewar1 containing seven Unipucks fully loaded with crystals of a single protein . The example spreadsheet also contains a diffraction plan (data collection parameters that can be used for automated experiments). It is possible as well to include more than one parcel in the same file or upload separate files for different Unipucks.
50 50  
51 51  After saving the sample list, you can edit the information by going to the shipment page, clicking on the containers and selecting **Edit**. That will display the sample list for that container. You can also make corrections to the CSV file, then delete the parcel by clicking on the “Edit” icon to the right of the parcel pane and clicking on **Remove**, and finally reload the corrected CSV again.
52 52  
53 -You can now find the filled up parcel in the shipment page. Use the icons to the right to add extra Unipucks, edit/remove the parcel, print the shipping labels. To import a CSV file, use the link above the parcel pane.
51 +For more information about the contents and format of the CSV file, please see [[Importing sample information list as a CSV file>>url:https://www.maxiv.lu.se/beamlines-accelerators/beamlines/biomax/user-information/prepare-sample-shipments-with-exi-at-max-iv/importing-sample-information-list-as-a-csv-file/]].
54 54  
55 -[[attach:Shipment.csv||target="_blank"]]
53 +Filled up parcel in the shipment page. Use the icons to the right to add extra Unipucks, edit/remove the parcel, print the shipping labels. To import a CSV file, use the link above the parcel pane.
56 56  
55 +
57 57  == Fill the sample information online ==
58 58  
59 59  * Click the **Add parcel** button.
... ... @@ -67,24 +67,22 @@
67 67  ** None of the other fields are used at P11.
68 68  ** After filling up the sample information, click on **Shipment** button above the spreadsheet and reply **Yes** to save the changes to the container.
69 69  
70 -
71 71  = Send the shipment to DESY =
72 72  
73 73  * Click on the **Print labels** icon to the right of each parcel to generate a PDF file with the shipping and return EXI labels. Make sure that the information on the labels is correct. If not, go to the “Shipping addresses” list and correct the information.
74 74  * If everything is correct, print the labels. Please attach the dewar label and the shipping label on your dewars, and enclose the return label within the dewar box with other return forms (courier waybill or invoice
75 75  * If you are sending to and from **outside EU** and need customs declarations:
76 -** You need to fill in a Proforma invoice to send along with the shipment.
74 +** You need to fill in a Proforma invoice to send along with the shipment. This can be retrieved from DHL or from here: **Pro Forma Invoice to MAX IV: [[customsDeclarationProForma_sendToMAXIV.pdf>>url:https://lu.box.com/s/mzrdll406uup441g02ks9fop42wp2ypt]] **and **Pro Forma Invoice from MAX IV: [[customsDeclarationProForma_returnFromMAXIV.pdf>>url:https://lu.box.com/s/bgb7uxxza304kwoy3jzj6m4q0tc9jho7]]**
77 77  ** Be sure to use a proper description of the content of the shipment, as an example: “Dry shipper containing small frozen protein crystals for scientific experiments. Crystals are non-hazardous. Dewar contains non-flammable gas (liquid N2).”
78 78  ** Value cannot be 0, use any other small value instead (eg. 1).
79 -* The button **Send Shipment to the facility** will activate once you print the labels. When you click it, the status of the dewar will change to “sent to the facility”. This will let beamline staff know that the shipment is on its way.
77 +* The button **Send Shipment to DESY** will activate once you print the labels. When you click it, the status of the dewar will change to “sent to DESY”. This will let beamline staff know that the shipment is on its way.
80 80  * When the dewar arrives at DESY, staff will scan the EXI label, and the shipment status will be set to “Arrived”.
81 81  * You will be able to modify the shipment in EXI after shipping the dewars. However, once the Unipucks are assigned a position in the dewar and the status changes to “processing” you will not be able to make more changes. If you need to amend or update the sample information once the sample unipucks are loaded and assigned, follow these steps:
82 82  ** Create a new shipment, containing the Unipucks with the correct sample information.
83 83  ** Click on “print labels” -you do not need to actually print them, this is just to activate the “send to DESY” button.
84 84  
85 -After “sending the shipment” go to the **Prepare experiment** tab and assign the corrected Unipuck information to the actual Unipuck position in the sample changer dewar.
83 +After “sending the shipment” go to the **Prepare experiment** tab and assign the corrected Unipuck information to the actual Unipuck position in the sample changer dewar. Consult [[the MXCuBE documentation on mounting samples>>url:https://www.maxiv.lu.se/beamlines-accelerators/beamlines/biomax/user-information/mxcube3-at-biomax-user-guide/]] for more help on this step.
86 86  
87 -
88 88  = Arrange the return of dewar(s) =
89 89  
90 90  You are responsible for organizing the courier for the transport of both incoming and departing dewars. Please be prepared to order the return shipment before the beamtime, and be sure to attach the return papers from your courier to the dewar in addition to the EXI-generated shipping dewars; if the courier will not supply you with a return waybill at the moment you ship the dewar, please enclose a note in the dewar explaining when the dewar will be picked up and that you will e-mail the return waybill to the local contact as soon as you receive it. This is specially important for remote experiments. Failure to include all the required return information will result in delays shipping the dewar back.
... ... @@ -101,7 +101,7 @@
101 101  
102 102  For remote users, all the previous steps will be taken care of by staff, provided that you have enclosed the courier return papers in the dewar case.
103 103  
104 -If you are sending to and from **outside EU** please enclose the Proforma invoice**.**
101 +If you are sending to and from **outside EU** please enclose the Proforma invoice**: **[[customsDeclarationProForma_returnFromMAXIV.pdf>>url:https://lu.box.com/s/bgb7uxxza304kwoy3jzj6m4q0tc9jho7]]
105 105  
106 106  
107 107  
Shipment.csv
Author
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1 -XWiki.tabermah
Size
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1 -4.5 KB
Content
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1 -#parcel name,container name,container type,container position,protein acronym,sample acronym
2 -Dewar1,CPS-5474,Unipuck,1,HUMA,H10Fum_1
3 -Dewar1,CPS-5474,Unipuck,2,HUMA,H10Fum_2
4 -Dewar1,CPS-5474,Unipuck,3,HUMA,H11Succ_1
5 -Dewar1,CPS-5474,Unipuck,4,HUMA,H11Succ_2
6 -Dewar1,CPS-5474,Unipuck,5,HUMA,H11Succ_3
7 -Dewar1,CPS-5474,Unipuck,6,HUMA,H11refold_1
8 -Dewar1,CPS-5474,Unipuck,7,HUMA,H11refold_2
9 -Dewar1,CPS-5474,Unipuck,8,HUMA,H11refold_3
10 -Dewar1,CPS-5474,Unipuck,9,HUMA,H11refold_4
11 -Dewar1,CPS-5474,Unipuck,10,HUMA,H11refold_5
12 -Dewar1,CPS-5474,Unipuck,11,JAVI,J1295_1
13 -Dewar1,CPS-5474,Unipuck,12,ANDRE,GPX4_1
14 -Dewar1,CPS-5474,Unipuck,13,ANDRE,GPX4_2
15 -Dewar1,CPS-5474,Unipuck,14,ANDRE,GPX4_3
16 -Dewar1,CPS-5474,Unipuck,15,ANDRE,GPX4_4
17 -Dewar1,CPS-5474,Unipuck,16,ANDRE,GPX4_5
18 -Dewar1,CPS-5473,Unipuck,1,BW,Nsp_Q204K_1
19 -Dewar1,CPS-5473,Unipuck,2,BW,Nsp_Q204K_2
20 -Dewar1,CPS-5473,Unipuck,3,BW,Nsp_Q263K_1
21 -Dewar1,CPS-5473,Unipuck,4,BW,Nsp_Q263K_2
22 -Dewar1,CPS-5473,Unipuck,5,BW,Nsp_Q250K_1
23 -Dewar1,CPS-5473,Unipuck,6,BW,Nsp_Q250K_2
24 -Dewar1,CPS-5473,Unipuck,7,HUMA,H10Succ_1
25 -Dewar1,CPS-5473,Unipuck,8,HUMA,H10Succ_2
26 -Dewar1,CPS-5473,Unipuck,9,HUMA,H10Succ_3
27 -Dewar1,CPS-5473,Unipuck,10,HUMA,H10Succ_4
28 -Dewar1,CPS-5473,Unipuck,11,HUMA,H10Fum_3
29 -Dewar1,CPS-5473,Unipuck,12,HUMA,H10Fum_4
30 -Dewar1,CPS-5473,Unipuck,13,HUMA,H10Fum_5
31 -Dewar1,CPS-5473,Unipuck,14,HUMA,H10Mal_1
32 -Dewar1,CPS-5473,Unipuck,15,HUMA,H10Mal_2
33 -Dewar1,CPS-5473,Unipuck,16,HUMA,H10Mal_3
34 -Dewar1,CPS-5472,Unipuck,1,HUMA,H10_1
35 -Dewar1,CPS-5472,Unipuck,2,HUMA,H10_2
36 -Dewar1,CPS-5472,Unipuck,3,BW,ICCG_L50Y_1
37 -Dewar1,CPS-5472,Unipuck,4,BW,ICCG_L50Y_2
38 -Dewar1,CPS-5472,Unipuck,5,BW,ICCG_L50Y_3
39 -Dewar1,CPS-5472,Unipuck,6,BW,ICCG_L50Y_4
40 -Dewar1,CPS-5472,Unipuck,7,BW,ICCG_L50Y_5
41 -Dewar1,CPS-5472,Unipuck,8,BW,ICCG_L50Y_6
42 -Dewar1,CPS-5472,Unipuck,9,BW,ICCG_Y61E_1
43 -Dewar1,CPS-5472,Unipuck,10,BW,ICCG_Y61E_2
44 -Dewar1,CPS-5472,Unipuck,11,BW,ICCG_Y61E_3
45 -Dewar1,CPS-5472,Unipuck,12,BW,ICCG_Y61E_4
46 -Dewar1,CPS-5472,Unipuck,13,BW,Nsp_Q204K_3
47 -Dewar1,CPS-5472,Unipuck,14,BW,Nsp_Q204K_4
48 -Dewar1,CPS-5472,Unipuck,15,BW,Nsp_Q204K_5
49 -Dewar1,CPS-5472,Unipuck,16,BW,Nsp_Q204K_6
50 -Dewar1,CPS-5471,Unipuck,1,HUMA,H11_1
51 -Dewar1,CPS-5471,Unipuck,2,HUMA,H11_2
52 -Dewar1,CPS-5471,Unipuck,3,HUMA,H11_3
53 -Dewar1,CPS-5471,Unipuck,4,HUMA,H11_4
54 -Dewar1,CPS-5471,Unipuck,5,HUMA,H11_5
55 -Dewar1,CPS-5471,Unipuck,6,HUMA,H11_6
56 -Dewar1,CPS-5471,Unipuck,7,HUMA,H11_7
57 -Dewar1,CPS-5471,Unipuck,8,HUMA,H11_8
58 -Dewar1,CPS-5471,Unipuck,9,JP,PINK_1
59 -Dewar1,CPS-5471,Unipuck,10,JP,PINK_2
60 -Dewar1,CPS-5471,Unipuck,11,AZEEM,A631_1
61 -Dewar1,CPS-5471,Unipuck,12,AZEEM,A631_2
62 -Dewar1,CPS-5471,Unipuck,13,AZEEM,A631_3
63 -Dewar1,CPS-5471,Unipuck,14,HUMA,H10_3
64 -Dewar1,CPS-5471,Unipuck,15,HUMA,H10_4
65 -Dewar1,CPS-5471,Unipuck,16,HUMA,H10_5
66 -Dewar1,CPS-5470,Unipuck,1,HUMA,H11_9
67 -Dewar1,CPS-5470,Unipuck,2,HUMA,H10_6
68 -Dewar1,CPS-5470,Unipuck,3,HUMA,H10_7
69 -Dewar1,CPS-5470,Unipuck,4,HUMA,H10_8
70 -Dewar1,CPS-5470,Unipuck,5,HUMA,H10_9
71 -Dewar1,CPS-5470,Unipuck,6,HUMA,H10_10
72 -Dewar1,CPS-5470,Unipuck,7,HUMA,H10_11
73 -Dewar1,CPS-5470,Unipuck,8,HUMA,H10_12
74 -Dewar1,CPS-5470,Unipuck,9,HUMA,H10_13
75 -Dewar1,CPS-5470,Unipuck,10,HUMA,H11_10
76 -Dewar1,CPS-5470,Unipuck,11,HUMA,H11_11
77 -Dewar1,CPS-5470,Unipuck,12,HUMA,H11_12
78 -Dewar1,CPS-5470,Unipuck,13,HUMA,H11_13
79 -Dewar1,CPS-5470,Unipuck,14,HUMA,H11_14
80 -Dewar1,CPS-5470,Unipuck,15,HUMA,H11_15
81 -Dewar1,CPS-5470,Unipuck,16,HUMA,H11_16
82 -Dewar1,CPS-5469,Unipuck,1,HUMA,H10_14
83 -Dewar1,CPS-5469,Unipuck,2,HUMA,H10_15
84 -Dewar1,CPS-5469,Unipuck,3,HUMA,H10_16
85 -Dewar1,CPS-5469,Unipuck,4,HUMA,H10_17
86 -Dewar1,CPS-5469,Unipuck,5,HUMA,H11_17
87 -Dewar1,CPS-5469,Unipuck,6,HUMA,H11_18
88 -Dewar1,CPS-5469,Unipuck,7,HUMA,H11_19
89 -Dewar1,CPS-5469,Unipuck,8,HUMA,H11_20
90 -Dewar1,CPS-5469,Unipuck,9,HUMA,H11_21
91 -Dewar1,CPS-5469,Unipuck,10,HUMA,H11_22
92 -Dewar1,CPS-5469,Unipuck,11,HUMA,H11_23
93 -Dewar1,CPS-5469,Unipuck,12,HUMA,H11_24
94 -Dewar1,CPS-5469,Unipuck,13,HUMA,H11_25
95 -Dewar1,CPS-5469,Unipuck,14,HUMA,H11_26
96 -Dewar1,CPS-5469,Unipuck,15,HUMA,H11_27
97 -Dewar1,CPS-5469,Unipuck,16,HUMA,H11_28
98 -Dewar1,CPS-5468,Unipuck,1,JAVI,J1299_1
99 -Dewar1,CPS-5468,Unipuck,2,JAVI,J1299_2
100 -Dewar1,CPS-5468,Unipuck,3,JAVI,J1299_3
101 -Dewar1,CPS-5468,Unipuck,4,JAVI,J1295_2
102 -Dewar1,CPS-5468,Unipuck,5,JAVI,J1295_3
103 -Dewar1,CPS-5468,Unipuck,6,JAVI,J1295_4
104 -Dewar1,CPS-5468,Unipuck,7,JAVI,J1295_5
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107 -Dewar1,CPS-5468,Unipuck,10,JAVI,J1295_8
108 -Dewar1,CPS-5468,Unipuck,11,JAVI,J1299_4
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113 -Dewar1,CPS-5468,Unipuck,16,JAVI,J1295_11