Thank you so much. it worked. (I used this command for 2-1-60-61 dihedrals : sel @/serialNumber=2 | @/serialNumber=1 | @/serialNumber=60|@/serialNumber=61) Thank you again. Baris

Eric Pettersen pett@cgl.ucsf.edu, 7 Eyl 2022 Çar, 19:44 tarihinde şunu yazdı:

Hi Barış, The RMSD plot only plots all atoms if none are selected. Is the problem that you don't know how to select the desired atoms -- maybe because they have duplicate names? There are several alternatives. If we are talking about a very small number of atoms, you could just select them with the mouse -- control-click the first, then shift-control-click the second, third, fourth, etc. Obviously, for any large amount of atoms this would be tedious. You can also use commands to select by element type or atom serial number. Here are example commands:

Select elements Pd, Cl, and C:

    sel @/element=Pd | @/element=Cl | @/element=C

Select atom serial numbers 7 through 10:

    sel @/serialNumber>=7 & @/serialNumber<=10

The '|' in the first command forms the union between its left and right sides. Conversely, the '&' in the second command takes the intersection of its left and right sides.

--Eric

    Eric Pettersen
    UCSF Computer Graphics Lab

...

On Sep 7, 2022, at 6:26 AM, Barış KURT via Chimera-users <

chimera-users@cgl.ucsf.edu> wrote:

...

Hello, my intention is to plot RMSD chart for only Pd,Cl,Cl,C atoms (their

numbers are 1,2,3,4). But I couldn't find a way to do it.Also II want to plot dihedral RMSD for all atoms except C,H,Cl,P atoms.How can I do that?

...

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Hi Marco, (a) In our tests the matchmaker superpositions were slightly better if we recomputed secondary structure, so that is why it is the default. However, you can say to use only the input secondary structure (do not run ksdssp) with "computeSS false", for example:

mm #0 #1 computess false show true

https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html

In ChimeraX, we improved matchmaker so that by default it uses a recomputed secondary structure but also keeps the original assignments on the structure. However, this feature is not available in Chimera.

(b) I'm not sure what you mean by "whole alignment" -- more than 2 sequences? The matchmaker process only creates pairwise alignments. If you want to compute a multiple (>2) sequence alignment from the superposition, there is a separate tool Match->Align (in menu under Tools... Sequence). https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchalign/matchalign.html

There is no command for that tool, so it may be difficult to script -- somebody else would have to advise on that.

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Sep 26, 2022, at 1:19 AM, Marco Sette via Chimera-users chimera-users@cgl.ucsf.edu wrote:

Dear all, I would like to write a script to compute structural alignment and show the actual, not the calculated by ksdspp, secondary structure of some pdb files.

My problems are:

a) mm #0 #1 show true

shows the predicted secondary structure, not the actual. How this can be modified to show the actual secondary structure?

b) how the typical script provided in

https://www.cgl.ucsf.edu/chimera/current/docs/ProgrammersGuide/basicPrimer.h...

for fn in file_names: replyobj.status("Processing " + fn) # show what file we're working on rc("open " + fn) rc("mm #0 #1 ... ?") #

has to be modified to have the whole alignment in the same window? Thanks for your help, Marco Sette