Re: [COOT] change size of gui
Andreas, try (set-graphics-window-size x y) in the command input. Replace x, y with the desired dimensions. Works in the .coot file, no reason why not interactively (FLW). Cheers, Carsten > -Original Message- > From: Mailing list for users of COOT Crystallographic Software > [mailto:[EMAIL PROTECTED] Behalf Of Andreas Förster > Sent: Friday, April 04, 2008 3:39 PM > To: COOT@JISCMAIL.AC.UK > Subject: [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 > >
[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
Re: [COOT] Problems with display - wincoot
I'm having exactly the same problem, but with mandriva 2007 does anybody know how to solve it? thank you! txino !.!.
Re: [COOT] Reply to Rotate/Translate Multi-chain complex
Oh, I think I see what you mean now. You want to do the rot/trans by hand - and in coot you can only move a residue range (up to a whole chain). No. There is no way to do that. It's on the list :) A work-around is to by hand rot/trans a fragment and then LSQ match the moving molecule on to the fragment. Bleugh. It should be better. Paul. Daniel Pomeranz Krummel wrote: Paul and Adam, Thanks for the comments. I am actually trying to rotate/translate or position the complex into a map, thus not to do lsq. Adam's approach is quite arduous. Is there a simpler way, Paul? 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
Hi Robert: I meant it seems random what platform/machine it appears on. When it does, it is 100% reproducible. So, for example, on my colleague's intel imac running 10.4.11, I get this error, but not on my intel imacs running 10.5.2. I (like you) can't trace it to any other sed. Also I did say I do not think the new compiler is responsible for it, but was just noting that it also introduces problems (specifically, when compiling gfortran). If you want to use the debian packages I compiled, they are here: http://sage.ucsc.edu/fink_intel/10.5/unstable/main/binary-darwin-i386/sci/ Sorry for this. I've reported the problem (including forwarding your email to the coot bb) and as soon as i figure out what to do I will fix it. Bill On Apr 4, 2008, at 6:57 AM, Robert T Wyatt wrote: 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
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
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
[COOT] Reply to Rotate/Translate Multi-chain complex
Paul and Adam, Thanks for the comments. I am actually trying to rotate/translate or position the complex into a map, thus not to do lsq. Adam's approach is quite arduous. Is there a simpler way, Paul? > 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] 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)))
[COOT] Rotate/Translate Multi-chain complex
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? Daniel
