From 370ee7fe57d302cbd7f0958a50a1e889040e2d4a Mon Sep 17 00:00:00 2001 From: Modesto <57681431+mredrejo@users.noreply.github.com> Date: Fri, 7 Feb 2025 11:28:33 +0100 Subject: [PATCH] fix pymol mistakex --- .DS_Store | Bin 12292 -> 12292 bytes docs/pymol.html | 2 +- docs/search.json | 2 +- pymol.qmd | 4 ++-- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.DS_Store b/.DS_Store index 499ed3b202a719f8bc6c8d4d35afd052dc8422ed..ef019353de37f795c9f19429eebeda11a9e1d975 100644 GIT binary patch delta 168 zcmZokXi36kwdJuO>UWT6qey zCzIFYXX5gVK9hZvcWh?iQ08Eq3evhcPGue=U?2I77%}@ zi6Cv3e?Yl!DcZpkM+M}hI%*^@g(ynB)JMnZJYA$=x=HsaLC@(eeWXwHnZD2uq$3Lg za-c^(CSwY$5K)c_RH7D*XhJg z#SqRRj_bICM|g|`USJe2@d_XC72oik>6nq_F%v6gcIIX^te!Qn78(n~c+;w6CyTXq z1|&Z(Kq)IOh(|L9IoCi(uqz;k9gZhpX`1v285}=RtIM>`o4;UT!`~?u|A8Vul9esw z=yMImJd>@cw9H*utvofiDZ!$39<6BAar{HGWm0~XN2e1sg3OQ4ni=Y(9P}smoLZ|@ z;DlQo$4&h|Be&@RjnF8)SB?CH20Y9tLM$4es)NN?ik2}CUe&@H_^|=q zs)>;5Vk@>|Cw5^s_TvD0aY*&ik0Yv)6F60k(>Q}cT);3c;WDn^DsJGe>g5?;kK_GK zy(yJC-o&rzYcu0oTXu%R3_S*?yF#=%-R^CoE$VSPL|b{4OX)SZltf8E*22-<6a4~2SGL^% diff --git a/docs/pymol.html b/docs/pymol.html index 9ea51d3..a68a719 100644 --- a/docs/pymol.html +++ b/docs/pymol.html @@ -438,7 +438,7 @@

2.3 3. Create new object and/or get rid of what you don’t want

If we want to work only with some objects or chains in the PDB file, you can do it in several ways. There are several options but you need to show the sequence (Menu Display or button S on the botton-right corner).

You can remove objects (Option 1A or 1B) or copy a selection to a new object (Option 2A or 2B). You can test all with the instructions below, but I find more convenient to use command line alternatives (1B and 2B).

-

Note: The options below are alternative ways to get the same results. Try only one option each time starting over from 6KI3 structure.

+

⚠️️ Note that the options 1 and 2 below are alternative ways to get the same results. Try only one option each time starting over from 6KI3 structure.⚠️❗️

  • Option 1A: select in the sequence panel the sequence you want to remove and remove it

    remove sele
    • diff --git a/docs/search.json b/docs/search.json index 884429b..55eb3d6 100644 --- a/docs/search.json +++ b/docs/search.json @@ -766,7 +766,7 @@ "href": "pymol.html#create-new-object-andor-get-rid-of-what-you-dont-want", "title": "Pymol Practice", "section": "2.3 3. Create new object and/or get rid of what you don’t want", - "text": "2.3 3. Create new object and/or get rid of what you don’t want\nIf we want to work only with some objects or chains in the PDB file, you can do it in several ways. There are several options but you need to show the sequence (Menu Display or button S on the botton-right corner).\nYou can remove objects (Option 1A or 1B) or copy a selection to a new object (Option 2A or 2B). You can test all with the instructions below, but I find more convenient to use command line alternatives (1B and 2B).\nNote: The options below are alternative ways to get the same results. Try only one option each time starting over from 6KI3 structure.\n\nOption 1A: select in the sequence panel the sequence you want to remove and remove it\nremove sele\nOption 1B: use command line\n\nStep 1: First you need to see the composition of your structure\n\nget_chains 6KI3\nselect chain A\nselect chain B\n#to see who is who\n\nStep 2: select the chains you want to remove and remove them\n\nselect kk, chain A or chain C or chain D or chain E\ndelete kk\nOption 2A: Select in the sequence panel the sequence or whole chains you want to keep: A > “Copy to object” or “extract to object” will allow to work independently with that portion without removing the rest. Just click on the object to disable.\nOption 2B: use command line\n\nStep 1: Select and create:\n\nselect kk, chain B or chain F or chain G or chain H\ncreate monomer, kk\n\nOr directly create an object with your selected chains:\ncreate monomer, chain B or chain F or chain G or chain H\n\nStep 2: Now you can remove the original object (if you wish)\nremove 6KI3\n\n\nSome interesting points about selection on Pymol:\n\nUnnamed selection are temporarily named “sele” and replaced after every select command execution.\nSelections can be renamed in the A (action menu on the left) or by command line : https://pymolwiki.org/index.php/Set_name\nMultiple selection can be also done but syntax is tricky: https://pymolwiki.org/index.php/Selection_Algebra\n\n\nCreate your own representation of the monomer ternary complex (protein + metal cofactor + DNA)" + "text": "2.3 3. Create new object and/or get rid of what you don’t want\nIf we want to work only with some objects or chains in the PDB file, you can do it in several ways. There are several options but you need to show the sequence (Menu Display or button S on the botton-right corner).\nYou can remove objects (Option 1A or 1B) or copy a selection to a new object (Option 2A or 2B). You can test all with the instructions below, but I find more convenient to use command line alternatives (1B and 2B).\n⚠️️ Note that the options 1 and 2 below are alternative ways to get the same results. Try only one option each time starting over from 6KI3 structure.⚠️❗️\n\nOption 1A: select in the sequence panel the sequence you want to remove and remove it\nremove sele\nOption 1B: use command line\n\nStep 1: First you need to see the composition of your structure\n\nget_chains 6KI3\nselect chain A\nselect chain B\n#to see who is who\n\nStep 2: select the chains you want to remove and remove them\n\nselect kk, chain A or chain C or chain D or chain E\ndelete kk\nOption 2A: Select in the sequence panel the sequence or whole chains you want to keep: A > “Copy to object” or “extract to object” will allow to work independently with that portion without removing the rest. Just click on the object to disable.\nOption 2B: use command line\n\nStep 1: Select and create:\n\nselect kk, chain B or chain F or chain G or chain H\ncreate monomer, kk\n\nOr directly create an object with your selected chains:\ncreate monomer, chain B or chain F or chain G or chain H\n\nStep 2: Now you can remove the original object (if you wish)\nremove 6KI3\n\n\nSome interesting points about selection on Pymol:\n\nUnnamed selection are temporarily named “sele” and replaced after every select command execution.\nSelections can be renamed in the A (action menu on the left) or by command line : https://pymolwiki.org/index.php/Set_name\nMultiple selection can be also done but syntax is tricky: https://pymolwiki.org/index.php/Selection_Algebra\n\n\nCreate your own representation of the monomer ternary complex (protein + metal cofactor + DNA)" }, { "objectID": "pymol.html#bonus-track-more-info-and-useful-resources-about-pymol.", diff --git a/pymol.qmd b/pymol.qmd index bdd633b..4ad1355 100644 --- a/pymol.qmd +++ b/pymol.qmd @@ -246,8 +246,8 @@ You can remove objects (Option 1A or 1B) or copy a selection to a new object (Option 2A or 2B). You can test all with the instructions below, but I find more convenient to use command line alternatives (1B and 2B). -*Note: The options below are alternative ways to get the same results. Try only -one option each time starting over from 6KI3 structure.* +*⚠️️ Note that the options 1 and 2 below are alternative ways to get the same results. Try only +one option each time starting over from 6KI3 structure.⚠️❗️* - Option 1A: select in the sequence panel the sequence you want to remove and remove it