Right, thank you very much! And yes, I've just double checked the problem with double labels was due to the my pdb so I ould solve it via selection only of the side chains for the labels: label @@display & sideonly height 0.8 color gold Keep in touch Enrico пт, 21 янв. 2022 г. в 17:37, Elaine Meng <meng@cgl.ucsf.edu>:
Different resolution should not be a problem, only different height/width ratio. So if your window is 500 x 700 pixels, you could save anything with 5 x 7 ratio (1000 x 1400, 750 x 1050, etc.).
You can adjust the size of the window with "windowsize". In "save" command just give either "width" (which will automatically fix height) or "height" (which will automatically fix width), but do not give both unless they match the ratio of your window. I explained all of these before, but maybe it was not clear.
see help <https://rbvi.ucsf.edu/chimerax/docs/user/commands/windowsize.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#image>
Elaine
On Jan 21, 2022, at 1:02 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
Thanks a lot, Elaine! It was exactly due to the mismatch between resolutions. So for the simplicity I have to avoid indication of the resolutions in the save command in order that it could be taken automatically? Cheera Enrico
чт, 20 янв. 2022 г. в 21:39, Elaine Meng <meng@cgl.ucsf.edu>:
Hello, There is something weird about your PDB file so that ChimeraX thinks there are two residues that are both Glu-166. Since I don't know exactly what is weird about it, I don't know you would fix it, but maybe your idea of hiding the backbone would work.
As for the 2D labels, I have never had this problem. It uses the xpos and ypos I give in the command. However, I am always using it interactively (not in batch mode) and I always save an image that has the same aspect ratio as the graphics window of the display.
So my only idea is that maybe you are saving an image with different aspect ratio than your graphics window (e.g. graphics window is horizontal rectangle but the image you are saving is a square). I would not recommend saving a different aspect ratio. If you want a square image then make the graphics window square beforehand, e.g. with "windowsize" command. However, that applies to interactive use. I don't know if/how it works in nogui. But maybe you are using the GUI even though scripting it like a batch mode.
I don't have gothic font and it looks from the image you sent that you do not have it either. You can see the list of possible fonts in ChimeraX with command "2dlabels listfonts" (on the same machine you are making the images, of course).
See 2dlabels help <https://rbvi.ucsf.edu/chimerax/docs/user/commands/2dlabels.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 20, 2022, at 1:35 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
Please see the picture enclosed (as you see there is a duplicate name of glu-166). I've just checked my script- there is always one model used for the visualization, so I believe it may be due to my pdb. Actually to produce this pdb I fused dockins poses with pdb of protein. Since I did flexible docking the side chain of Glu-166 is present in each frame of the ligand and the backbone of the same residue is in each frame of the protein (now everything within the same multi-model PDB file). I've just check in pym**l and it recognizes the contacts without the duplications, so may be as a trick I have to hide backbones in chimeraX ?
The second question about labels: as you may see on the screenshot there are two labels placed using: 2dlab create title text "DOLCE (pdb XRAY), rep 1th" color red font gothic xpos .02 ypos .99 size 40 2dlab create title2 text "Created by Enrico Martinez, 2022" color indigo font Avenir xpos .02 ypos .02 size 33 I can not understand why they are always in the middle of the image (on Y coordinates!) since the first label should be always on the top (xpos .02 ypos .99 size 40) and the second one in the bottom (xpos .02 ypos .02 size 33). At least I see it like this in chimeraX gui. The same is for the electrostatic diagram (-10.. 10), which emerges in the central part of the image ... Many thanks in advance! Enrico
ср, 19 янв. 2022 г. в 21:13, Elaine Meng <meng@cgl.ucsf.edu>:
As far as I know, there would only be one label for the same residue. Maybe you have open/displayed more than one Glu-199, possibly in different chains or different models. So if it is multiple models, make sure you close or at least hide any extra models. If it is multiple chains in the same model, then specify only the chain you want to label in the labeling command.
Yes you can attach images, sessions, etc. to messages sent here. Elaine
On Jan 19, 2022, at 3:27 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
Thank you very much Elaine! Regarding my first question (about the displayed layer of the amino-acids involved in the contact with the ligand): I mean the displayed names (like Glu-199) in the graphical windows (what I see on the screen-shot!), which resulted from the command "contacts". So some amino acids are mentioned tvisely in the same graphical visualization. P.S. may I attach a PNG file directly to the message ?? Cheers, Enrico
<test.png>