Re: [COOT] Rotate/Translate Multi-chain complex
In message [EMAIL PROTECTED] [EMAIL PROTECTED] writes: Hello I would like to rotate/translate a multi-subunit complex, each subunit having a different chain name. Is there a way (maybe a script) that allows this to be done in Coot without attempting to change to a single chain name? I presume that the rotation/translation matrix (m in this case) is given by a LSQ match. If so, you can use the following. If not, you can supply the rotation/translation matrix directly to the transform-coords-molecule function. a rotation/translation matrix is a (list (list m11 m12 m13 m12 m12 m23 m31 m32 m33) (list t1 t2 t3)) Paul. ;; Set these for your case: ;; ;; match residues 10 to 20 in B chain of moving molecule to residues ;; 11 to 21 in chain A of reference molecule. The final 2 means CA ;; match 0 means all atom) (define match-params '(11 21 A 10 20 B 2)) (define ref-mol0) (define moving-mol 2) (clear-lsq-matches) (apply add-lsq-match match-params) (let* ((rc (copy-molecule moving-mol)) (m (apply-lsq-matches ref-mol rc))) (delete-molecule rc) (if m (transform-coords-molecule moving-mol m)))
Re: [COOT] coot-0.5-pre-1-906
Yes, I've seen this appear essentially at random. I don't have it on 10.5.2 intel but do on 10.4.11 intel. Moreover, 0.4.2 compiles ok but the newer one on that platform does not. I have not been able to figure out what is going wrong. There are some bugs in the iphone SDK -supplied compiler, but I don't think this is responsible for it. On Apr 4, 2008, at 6:28 AM, Robert T Wyatt wrote: Hi all (maintainer cc'd), I'm staying home from work today so I finally have a little time to mention a couple of problems. I'm on Mac OS 10.5.2 with the latest iPhone SDK (same error occurred prior to installing this) and an Intel MacBookPro. With the latest coot, similar to the immediately preceding version, I get a bunch of these: sed: 42: ./confstatKgEf4A/subs-3.sed: unescaped newline inside substitute pattern ... and then: +/var/tmp/tmp.2.BPOqWx:22 touch c-interface-database.hh +/var/tmp/tmp.2.BPOqWx:23 make coot_wrap_guile.cc make: *** No rule to make target `coot_wrap_guile.cc'. Stop. Complete output is available here: http://63.246.166.35/~robertwyatt/fink/coot-0.5-pre-1-906.txt The immediately preceding version had similar problems: config.status: creating auxil/vectors/Makefile sed: file ./confstatqsItQP/subs-3.sed line 42: unterminated `s' command config.status: executing depfiles commands +/var/tmp/tmp.2.e3xTi9:20 /bin/rm -f src/coot_wrap_guile.cc src/ coot_wrap_guile_pre.cc src/coot_wrap_python.cc src/ coot_wrap_python_pre.cc +/var/tmp/tmp.2.e3xTi9:21 cd src +/var/tmp/tmp.2.e3xTi9:22 touch c-interface-database.hh +/var/tmp/tmp.2.e3xTi9:23 make coot_wrap_guile.cc make: *** No rule to make target `coot_wrap_guile.cc'. Stop. Complete output is available here: http://63.246.166.35/~robertwyatt/fink/coot-0.5-pre-1-874.txt I get these errors with and without fink's sed and/or ssed. Happy to test potential solutions, Robert
Re: [COOT] coot-0.5-pre-1-906
Just a comment: it's not random for me; it's consistent. Also, the same error occurred prior to installing the new SDK, so I also think it's unrelated. However, I'm not sure that another recent update (say to Apple's sed...?) isn't to blame. --rtw William G. Scott wrote: Yes, I've seen this appear essentially at random. I don't have it on 10.5.2 intel but do on 10.4.11 intel. Moreover, 0.4.2 compiles ok but the newer one on that platform does not. I have not been able to figure out what is going wrong. There are some bugs in the iphone SDK -supplied compiler, but I don't think this is responsible for it. On Apr 4, 2008, at 6:28 AM, Robert T Wyatt wrote: Hi all (maintainer cc'd), I'm staying home from work today so I finally have a little time to mention a couple of problems. I'm on Mac OS 10.5.2 with the latest iPhone SDK (same error occurred prior to installing this) and an Intel MacBookPro. With the latest coot, similar to the immediately preceding version, I get a bunch of these: sed: 42: ./confstatKgEf4A/subs-3.sed: unescaped newline inside substitute pattern ... and then: +/var/tmp/tmp.2.BPOqWx:22 touch c-interface-database.hh +/var/tmp/tmp.2.BPOqWx:23 make coot_wrap_guile.cc make: *** No rule to make target `coot_wrap_guile.cc'. Stop. Complete output is available here: http://63.246.166.35/~robertwyatt/fink/coot-0.5-pre-1-906.txt The immediately preceding version had similar problems: config.status: creating auxil/vectors/Makefile sed: file ./confstatqsItQP/subs-3.sed line 42: unterminated `s' command config.status: executing depfiles commands +/var/tmp/tmp.2.e3xTi9:20 /bin/rm -f src/coot_wrap_guile.cc src/coot_wrap_guile_pre.cc src/coot_wrap_python.cc src/coot_wrap_python_pre.cc +/var/tmp/tmp.2.e3xTi9:21 cd src +/var/tmp/tmp.2.e3xTi9:22 touch c-interface-database.hh +/var/tmp/tmp.2.e3xTi9:23 make coot_wrap_guile.cc make: *** No rule to make target `coot_wrap_guile.cc'. Stop. Complete output is available here: http://63.246.166.35/~robertwyatt/fink/coot-0.5-pre-1-874.txt I get these errors with and without fink's sed and/or ssed. Happy to test potential solutions, Robert
[COOT] change size of gui
Hey all, is there a way to change the size of the coot viewer? Background: I open a coot session (previously shown on an external screen) on my laptop. The laptop screen is smaller by half than the external screen - thus the coot viewer does not fit. This being an OSX machine, I'd need access to the bottom right corner of the window for resizing. This corner is not on the screen. Clicking on the + button on the top left of the X window changes the size of the window but doesn't make it small enough to fit on the screen. I guess you wouldn't expect that from a plus button anyway. I cannot outsmart the computer. When I try to decrease the size of the coot viewer (restored from an earlier auto-save state file) on the external screen before closing the session, I fail. I can only increase the size, but not decrease it. To rephrase my question. Is there a coot equivalent to the PyMOL viewport command? Thanks. Andreas OSX 5.2, X 2.1.4, coot 0.50 pre889. -- I am not stupid. I have read several books. Salman Rushdie - Midnight's Children
