hah! On Fri, Mar 21, 2025, 6:44 PM Harry Powell < 0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> 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/ > ######################################################################## 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/
