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
