Thank you so much for the info! :) El mié, 17 ene 2024 a la(s) 7:11 p.m., Elaine Meng (meng@cgl.ucsf.edu) escribió:
Hello Francisco, There is no option to save CSV from what is shown in the Check Waters tool.
You can write out the information that you mentioned into text files, but you would have to write your own script to make the CSV file, which would need to collate H-bonds per water and combine them with B-factor values (and density values if you have a map) written separately.
(1) To write out H-bonds to a file you would need to use the H-Bonds tool or hbonds command instead of Check Waters to run the H-bonds calculation. With either one you can specify to limit the calculation to waters only so you don't have to look through all the results for everything else.
In the tool, you would turn on the File option near the bottom of the dialog: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/hbonds.html>
In the "hbonds" command, you would use the "saveFile" option: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/hbonds.html#options>
(2) To write out B-factor values to a file, see "info atoms" with "attribute bfactor" and the "saveFile" option, for example:
info atoms solvent attribute bfactor saveFile ~/Desktop/water-bfactors.txt
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/info.html#atoms>
(3) I don't know if you had a density map. If you also had a density map, then you could write out the density values at water positions using the "measure mapvalues" with the "attribute" option to assign an atom attribute. Then use "info atoms" to save the attribute values similarly to bfactor as shown in #2 above except using the name of your new attribute instead of "bfactor" and also a different output file name, of course:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#mapvalues>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 17, 2024, at 4:52 PM, Francisco Murphy Pérez via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
In chimerax ... tools -> structure analysis -> check waters Can we get the information from this analysis into a csv file? Can we add also the bfactor?
Thanks