Hi Gottfried (and Karl!, and Andrew Gnann off-board) Many thanks. It seems that if I don’t have the “set_view()” as the last thing I do before I save the picture, then I get my “almost but not quite right” images. So it looks like some of my other commands were modifying the view after I’d used the set_view().
I knew this was the place to come if I wanted to get the (word to avoid) orientation correct… Harry > On 21 Mar 2025, at 11:07, Palm, Gottfried > <0000b793af054fc6-dmarc-requ...@jiscmail.ac.uk> wrote: > > Maybe this procedure is too naive: > load your molecule > get_view > save the resulting set_view text snippet in a text file > do all your manipulations for picture 1 > use the set_view command (example below) > set_view (\ > 0.917584956, -0.307915270, -0.251439005,\ > -0.064036198, 0.509748638, -0.857936978,\ > 0.392342955, 0.803332448, 0.448020160,\ > -0.000433061, 0.000110999, -56.563850403,\ > 98.031951904, 22.916479111, 45.273895264,\ > -25.373046875, 138.503067017, -20.000000000 ) > save picture 1 > do all your manipulations for picture 2 > use the same set_view command as above > save picture 2 > > Greetings > Gottfried > > Am Freitag, den 21-03-2025 um 11:07 schrieb Harry Powell: > Hi > > I’m trying to generate images from PyMol because it has an easy-to-use CLI - > I’m not at all interested in how to do this with the GUI. > > I have a protein PDB file, and I have “pockets” in PDB format from pyKVfinder. > > What I want to do is to generate separate PNGs for each protein/pocket pair > that have the protein _exactly_ overlapped (i.e. with the centre of the > protein in the center of the image, in the same orientation, with the _only_ > difference being where the pocket is drawn). > > I can produce images where the protein is _almost_ in the same place with > _almost_ the same orientation, but they are not quite the same (looks to me > as if they are using the centroid & orienttion calculate for the protein+hole > pair ineach case) - examples attached (if you open these with, say, Preview > on a Mac, you can see that the models jump around from one image to the next). > > Presumably this is really easy, but I haven’t worked out how to do it. > > I’m almost certain that somone here can help! > > Harry > > <KAE_and_protein.png><KAG_and_protein.png><KAB_and_protein.png> > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
