Menu
▾
▴
pymol-users
|
From: Anastassis P. (N. <a.p...@nk...> - 2004-09-27 09:05:17
|
Dear Warren et al, A couple of questions about PyMol: When I open a multi-molecule PDB file, it nicely stores every 'instance' of the PDB in a frame. This file is coming from the 'Dynamite' server of Martin Noble and has only Ca's. I have two problems: 1. How do I make a cartoon passing through Ca's ? It refuses to do that with default values like for a 'full' PDB file ! 2. I want to include another single molecule and have frames where the second molecules 'stays the same' while the first one changes in each frame. Is that easy to do ? Anyone has a script ? Thanks in advance, Tassos |
|
From: Warren D. <wa...@de...> - 2004-09-27 14:30:44
|
Tassos, > 1. How do I make a cartoon passing through Ca's ? It refuses > to do that with default values like for a 'full' PDB file ! set cartoon_flat_sheets, off set cartoon_smooth_loops, off Also, the following command will reduce cartoon "jitter" during animations set cartoon_refine_normals, off > 2. I want to include another single molecule and have frames > where the second molecules 'stays the same' This is actually the default behavior if you load a second PDB file that contains only one state. If it has multiple states, then you'll need to specifically set a state for that object. For example: load animation1.pdb load animation2.pdb set state, 1, animation2 mplay would freeze animation2 at state 1, while playing through animation 2 To change the default freezing behavior for single-state object, set static_singletons, off Cheers, Warren -- mailto:wa...@de... Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -----Original Message----- > From: pym...@li... > [mailto:pym...@li...] On Behalf Of > Anastassis Perrakis (NKI) > Sent: Monday, September 27, 2004 2:05 AM > To: pym...@li... > Cc: wa...@de... > Subject: [PyMOL] Ca-only and multi-mol PDB > > Dear Warren et al, > > A couple of questions about PyMol: > > When I open a multi-molecule PDB file, it nicely stores every > 'instance' of the PDB in a frame. > This file is coming from the 'Dynamite' server of Martin > Noble and has only Ca's. > > I have two problems: > 1. How do I make a cartoon passing through Ca's ? It refuses > to do that with default values like for a 'full' PDB file ! > 2. I want to include another single molecule and have frames > where the second molecules 'stays the same' > while the first one changes in each frame. Is that easy to do > ? Anyone has a script ? > > Thanks in advance, > > Tassos > > > > ------------------------------------------------------- > This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one > of 170 Project Admins to receive an Apple iPod Mini FREE for > your judgement on who ports your project to Linux PPC the > best. Sponsored by IBM. > Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > |
|
From: Bronwyn C. <bro...@st...> - 2005-08-17 03:44:41
|
Hi, A couple of things: a) I've just installed the latest MacPymol (after having a major crash and having to re-install EVERYTHING), and my middle mouse button doesn't seem to work. I can't move things around on the screen. The other buttons work fine, and the middle one scrolls OK, so I can slab - but I want to move things!! I have played with the MouseWorks thing in System Prefs, and can change the middle button clicking to do what any of the other button clicks do, but there is no option for "middle button". Is there a key combination I can put in that will let it move things? b)I'm trying to make a surface and a cartoon of a CA-only structure. A search of my email archive tells me that by now Pymol should be able to create at least a ribbon from this sort of file, but I can't figure out how to do it. Can someone please instruct me? Ta Bronwyn Bronwyn Carlisle Biochemistry Department University of Otago PO Box 56 710 Cumberland St Dunedin email: bro...@st... tel: +64 (0)3 4797704 |
|
From: Tsjerk W. <ts...@gm...> - 2005-08-18 18:07:01
|
Hi Bronwyn, Don't know about MacPymol, but with regards to the second issue, a C-alpha trace, you can do it with: set cartoon_trace,1 show cartoon The surface will be tougher, you could play with setting the vanderwaals ra= dius: show surface alter (all),vdw=3D4 rebuild And you can repeat the last two commands for different values for the vdwr to suit your needs. You could also play with setting the radius for the solvent probe to determine the surface. Hope it helps, Tsjerk On 8/17/05, Bronwyn Carlisle <bro...@st...> wrote: > Hi, A couple of things: >=20 > a) I've just installed the latest MacPymol (after having a major > crash and having to re-install EVERYTHING), and my middle mouse > button doesn't seem to work. I can't move things around on the > screen. The other buttons work fine, and the middle one scrolls OK, > so I can slab - but I want to move things!! I have played with the > MouseWorks thing in System Prefs, and can change the middle button > clicking to do what any of the other button clicks do, but there is > no option for "middle button". Is there a key combination I can put > in that will let it move things? >=20 > b)I'm trying to make a surface and a cartoon of a CA-only structure. > A search of my email archive tells me that by now Pymol should be > able to create at least a ribbon from this sort of file, but I can't > figure out how to do it. Can someone please instruct me? >=20 > Ta >=20 > Bronwyn >=20 >=20 >=20 > Bronwyn Carlisle > Biochemistry Department > University of Otago > PO Box 56 > 710 Cumberland St > Dunedin >=20 > email: bro...@st... > tel: +64 (0)3 4797704 >=20 >=20 >=20 >=20 > ------------------------------------------------------- > SF.Net email is Sponsored by the Better Software Conference & EXPO > September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practic= es > Agile & Plan-Driven Development * Managing Projects & Teams * Testing & Q= A > Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > |
|
From: <li...@ul...> - 2005-08-18 18:28:47
|
On Wednesday 17 August 2005 05:44, Bronwyn Carlisle wrote: > b)I'm trying to make a surface and a cartoon of a CA-only structure. > A search of my email archive tells me that by now Pymol should be > able to create at least a ribbon from this sort of file, but I can't > figure out how to do it. Can someone please instruct me? For the ribbon representation: set ribbon_trace_atoms,1 I don't know about the surface representation, though. -- Lieven Buts Ultrastructure Laboratory Vrije Universiteit Brussel |
|
From: Xavier D. <Xav...@st...> - 2005-08-18 18:55:07
|
Hi Bronwyn, I had the same problem (using a Logitech MX310 under OS X 10.4.2). As somebody previously suggested, I just uninstalled the Logitech software, so the os treats the mouse as 'generic'. And now the middle button behaves as expected. hope this helps, Xavier Bronwyn Carlisle wrote: > Hi, A couple of things: > > a) I've just installed the latest MacPymol (after having a major > crash and having to re-install EVERYTHING), and my middle mouse > button doesn't seem to work. I can't move things around on the > screen. The other buttons work fine, and the middle one scrolls OK, > so I can slab - but I want to move things!! I have played with the > MouseWorks thing in System Prefs, and can change the middle button > clicking to do what any of the other button clicks do, but there is > no option for "middle button". Is there a key combination I can put > in that will let it move things? > > b)I'm trying to make a surface and a cartoon of a CA-only structure. > A search of my email archive tells me that by now Pymol should be > able to create at least a ribbon from this sort of file, but I can't > figure out how to do it. Can someone please instruct me? > > Ta > > Bronwyn > > > > Bronwyn Carlisle > Biochemistry Department > University of Otago > PO Box 56 > 710 Cumberland St > Dunedin > > email: bro...@st... > tel: +64 (0)3 4797704 > > > > > ------------------------------------------------------- > SF.Net email is Sponsored by the Better Software Conference & EXPO > September 19-22, 2005 * San Francisco, CA * Development Lifecycle > Practices > Agile & Plan-Driven Development * Managing Projects & Teams * Testing > & QA > Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > -- Xavier Deupi, Ph.D. Department of Molecular and Cellular Physiology Beckman Center for Molecular and Genetic Medicine (B161) 279 Campus Drive, Stanford University School of Medicine Stanford, CA 94305 (USA) E-mail: Xav...@st... Phone: +1 (650) 725-6497 Fax : +1 (650) 725-8021 |
|
From: Bronwyn C. <bro...@st...> - 2005-08-18 20:31:27
|
Thank-you, that worked beautifully. Before the crash the MouseWorks software can't have been working properly. Bronwyn On 18/08/2005, at 10:01 AM, Xavier Deupi wrote: > Hi Bronwyn, > > I had the same problem (using a Logitech MX310 under OS X 10.4.2). > As somebody previously suggested, I just uninstalled the Logitech > software, so the os treats the mouse as 'generic'. And now the > middle button behaves as expected. > > hope this helps, > > Xavier > > Bronwyn Carlisle wrote: > > >> Hi, A couple of things: >> >> a) I've just installed the latest MacPymol (after having a major >> crash and having to re-install EVERYTHING), and my middle mouse >> button doesn't seem to work. I can't move things around on the >> screen. The other buttons work fine, and the middle one scrolls >> OK, so I can slab - but I want to move things!! I have played >> with the MouseWorks thing in System Prefs, and can change the >> middle button clicking to do what any of the other button clicks >> do, but there is no option for "middle button". Is there a key >> combination I can put in that will let it move things? >> >> b)I'm trying to make a surface and a cartoon of a CA-only >> structure. A search of my email archive tells me that by now >> Pymol should be able to create at least a ribbon from this sort >> of file, but I can't figure out how to do it. Can someone please >> instruct me? >> >> Ta >> >> Bronwyn >> >> >> >> Bronwyn Carlisle >> Biochemistry Department >> University of Otago >> PO Box 56 >> 710 Cumberland St >> Dunedin >> >> email: bro...@st... >> tel: +64 (0)3 4797704 >> >> >> >> >> ------------------------------------------------------- >> SF.Net email is Sponsored by the Better Software Conference & EXPO >> September 19-22, 2005 * San Francisco, CA * Development Lifecycle >> Practices >> Agile & Plan-Driven Development * Managing Projects & Teams * >> Testing & QA >> Security * Process Improvement & Measurement * http://www.sqe.com/ >> bsce5sf >> _______________________________________________ >> PyMOL-users mailing list >> PyM...@li... >> https://lists.sourceforge.net/lists/listinfo/pymol-users >> >> > > -- > Xavier Deupi, Ph.D. > Department of Molecular and Cellular Physiology > Beckman Center for Molecular and Genetic Medicine (B161) > 279 Campus Drive, Stanford University School of Medicine > Stanford, CA 94305 (USA) > > E-mail: Xav...@st... > Phone: +1 (650) 725-6497 > Fax : +1 (650) 725-8021 > > Bronwyn Carlisle Biochemistry Department University of Otago PO Box 56 710 Cumberland St Dunedin email: bro...@st... tel: +64 (0)3 4797704 |
|
From: Bronwyn C. <bro...@st...> - 2005-08-18 18:55:16
|
Yes, I know the move command, but my mouse USED to translate things when you clicked the scroll wheel, it just doesn't since I had to re- install things. I like using it rather than the command line. Bronwyn On 18/08/2005, at 8:14 AM, Peter Adrian Meyer wrote: > Hi Bronwyn, > > >> a) I've just installed the latest MacPymol (after having a major >> crash and having to re-install EVERYTHING), and my middle mouse >> button doesn't seem to work. I can't move things around on the >> screen. The other buttons work fine, and the middle one scrolls OK, >> so I can slab - but I want to move things!! I have played with the >> MouseWorks thing in System Prefs, and can change the middle button >> clicking to do what any of the other button clicks do, but there is >> no option for "middle button". Is there a key combination I can put >> in that will let it move things? >> > > move x,5.0; should work as far as translating the model. With a > three-button mouse (no scroll wheel), middle mouse translates and > shift-right mouse moves the clipping planes (on unix, at least, but it > might be of use for getting the system preferences configured). > > >> >> b)I'm trying to make a surface and a cartoon of a CA-only structure. >> A search of my email archive tells me that by now Pymol should be >> able to create at least a ribbon from this sort of file, but I can't >> figure out how to do it. Can someone please instruct me? >> > > Can't help you here...I've been wondering about how to do a ca- > trace for a > while (not sure what use a surface from a CA model would be, > though...). > > Hope this helps, > > Pete > > >> >> Ta >> >> Bronwyn >> >> >> >> Bronwyn Carlisle >> Biochemistry Department >> University of Otago >> PO Box 56 >> 710 Cumberland St >> Dunedin >> >> email: bro...@st... >> tel: +64 (0)3 4797704 >> >> >> >> >> ------------------------------------------------------- >> SF.Net email is Sponsored by the Better Software Conference & EXPO >> September 19-22, 2005 * San Francisco, CA * Development Lifecycle >> Practices >> Agile & Plan-Driven Development * Managing Projects & Teams * >> Testing & QA >> Security * Process Improvement & Measurement * http://www.sqe.com/ >> bsce5sf >> _______________________________________________ >> PyMOL-users mailing list >> PyM...@li... >> https://lists.sourceforge.net/lists/listinfo/pymol-users >> >> > > > Pete Meyer > Fu Lab > BMCB grad student > Cornell University > > Bronwyn Carlisle Biochemistry Department University of Otago PO Box 56 710 Cumberland St Dunedin email: bro...@st... tel: +64 (0)3 4797704 |
×
Want the latest updates on software, tech news, and AI?
Get latest updates about software, tech news, and AI from SourceForge directly in your inbox once a month.
Thanks for helping keep SourceForge clean.
X