diff --git a/_data/keywords.yml b/_data/keywords.yml index a0c6c3f..bd65228 100644 --- a/_data/keywords.yml +++ b/_data/keywords.yml @@ -144,7 +144,7 @@ runtype: - cmd: --msreact type: MSREACT tool descript: > - Use the mass spectral fragment generator + Use the mass spectral fragment generator. MSREACT has several individual runtypes. See url: text: MSREACT keywords. diff --git a/_data/msreact.yml b/_data/msreact.yml index 5c550a4..45bbdef 100644 --- a/_data/msreact.yml +++ b/_data/msreact.yml @@ -14,7 +14,7 @@ msreactkeywords: - cmd: ---msnoattrh descript: > - deactivate attractive potential between hydrogen and LMO centers. + deactivate attractive potential between hydrogen atoms and LMO centers. - cmd: --msmolbar descript: > @@ -28,7 +28,7 @@ msreactkeywords: descript: > do not remove temporary files and MSDIR with constrained optimizations and write directories for isomers and fragmentpairs, as well as seperated fragment structures in - individual directories. The nomenclature of the directories is `p` for isomers and productpairs. + individual directories. The nomenclature of the directories is `p` for isomers and product pairs. For fragments, it is `pf`. - cmd: --chrg diff --git a/assets/images/msreact-algo.png b/assets/images/msreact-algo.png new file mode 100644 index 0000000..27946df Binary files /dev/null and b/assets/images/msreact-algo.png differ diff --git a/page/examples/msreact-example_1.md b/page/examples/msreact-example_1.md index c83feb4..adf3123 100644 --- a/page/examples/msreact-example_1.md +++ b/page/examples/msreact-example_1.md @@ -25,7 +25,7 @@ permalink: /page/examples/msreact/example_1.html {% include image.html file="msreact-example-1-1.png" alt="Bacillaene at GFN-FF level" caption="Most stable gas-phase structure of 2-pentanone at charge +1 with GFN2-xTB." max-width=400 %} -We want to investigate the fragmentation reactions of 2-pentanone in an EI-MS experiment. Therefore, we provide the lowest conformer found by `CREST` at charge +1 as input <2-pentanone.xyz>. We only want to get unique fragments so we use the -msmolbar flag to sort out duplicates with `molbar`. Before starting crest, we should make sure that `molbar` is properly installed and in our path. +We want to investigate the fragmentation reactions of 2-pentanone in an EI-MS experiment. Therefore, we provide the lowest conformer found by `CREST` at charge +1 as input <2-pentanone.xyz>. We only want to get unique fragments so we use the -msmolbar flag to sort out duplicates with `molbar`. Before starting crest, we should make sure that `molbar` is properly installed and can be executed globally. {: .text-justify } @@ -700,6 +700,5 @@ CREGEN> running RMSDs ... done. {% include defaulttab.html %} -CREST produces 25 unique products and writes them sorted according to their relative energy to -to the file `crest_msreact_products.xyz`. Isomers are also written to `isomers.xyz`, fragmentpairs to `fragmentpairs.xyz`. +CREST produces 25 unique products and writes them sorted according to their relative energy to the file `crest_msreact_products.xyz`. Additionally, isomers are written to `isomers.xyz`, fragmentpairs to `fragmentpairs.xyz`. {: .text-justify } \ No newline at end of file diff --git a/page/overview/workflows.md b/page/overview/workflows.md index 9ef52f8..7818508 100644 --- a/page/overview/workflows.md +++ b/page/overview/workflows.md @@ -168,6 +168,8 @@ action products. {: .text-justify } +{% include image.html file="msreact-algo.png" alt="MSREACT fragment generation workflow." caption="Basic concept of the MSREACT fragment generation workflow with the 2-pentanone molecule as an example." max-width=1000 %} + [Go to the MSREACT keyword documentation ]({{site.baseurl}}/page/documentation/msreact.html){: .btn .btn-blue }