RE: [PyMOL] picking atoms with latest version (0.95)
Ken's answer covers it...the following just provide a little more in-depth coverage: What has happened is that PyMOL now supports the picking of multiple atoms, so use of the lb and rb selections is less necessary. Picking and selecting are not the same thing in PyMOL. Selections are merely lists of atoms. Picked atoms utilize chemical and topological properties to provide you with a much richer set of options, including a family of automatically generated selections (such as pkresi). CTRL-middle-click has always been the "picking" action, and it still works to pick one or more atoms (first pk1, then pk2, pk3, and pk4). This can get confusing -- especially for new users. So, in the default viewing mode, ctrl-right-click can always be used to clear the current pick set and pick a new single atom. (In Editing mode, ctrl-right-click still picks and rotates bonds, as before). I believe that all of the PyMOL actions which used to require the lb and rb selections now use pk1 and pk2 instead. This probably impacts measuring of distances most significantly: The quickest way to measure distances in PyMOL 0.95 and beyond is this: In Viewing Mode: ctrl-right-click on the first atom ctrl-middle-click on the second atom type ctrl-X -or- use the "dist" command (with optional name) Anywhere else: first, make sure no atoms are picked (click or type unpick) ctrl-middle-click on the first atom ctrl-middle-click on the second atom type ctrl-X -or- use the "dist" command (with optional name) As you're discovered, double-right-click works just like ctrl-middle-click. This makes it easier to perform certain actions without constantly have to invoke the ctrl key. Cheers, Warren > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Carina Lobley > Sent: Tuesday, April 13, 2004 12:51 AM > To: Eksterowicz, John > Cc: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] picking atoms with latest version (0.95) > > Hi, > I had that problem this weekend too. I've found that ctrl > right click picks one atom and shift right double click picks > a second atom. That seems to work for the 'dist' and 'bond' > commands anyway! > > Regards, > Carina > > On Mon, 12 Apr 2004, Eksterowicz, John wrote: > > > > > I am using the latest version of Pymol and I cannot figure > out how to > > pick more than one atom. > > > > In the past, ctrl-shft lb, picked the first atom, and ctrl-shft rb > > would pick a second atom. But now, ctrl-shft rb brings up > a pop-up menu. > > > > Any help would be appreciated. > > > > Thanks, > > John > > > > John Eksterowicz > > Celera Genomics > > > > > > > --- > This SF.Net email is sponsored by: IBM Linux Tutorials Free > Linux tutorial presented by Daniel Robbins, President and CEO > of GenToo technologies. Learn everything from fundamentals to > system > administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
RE: [PyMOL] picking atoms with latest version (0.95)
The lb and rb selections have changed in version 0.95. Looks like the "new" way to do this is with pk1 and pk2. Use ctrl-middle-click, or double-right-click to pick each atom. The first atom you pick will be pk1, the second will be pk2, etc. (up to pk4). You can then use ctrl-x to get the distance between pk1 and pk2, or ctrl-t to create a bond (or use the 'dist' or 'bond' commands). Ken -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net]on Behalf Of Carina Lobley Sent: Tuesday, April 13, 2004 12:51 AM To: Eksterowicz, John Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] picking atoms with latest version (0.95) Hi, I had that problem this weekend too. I've found that ctrl right click picks one atom and shift right double click picks a second atom. That seems to work for the 'dist' and 'bond' commands anyway! Regards, Carina On Mon, 12 Apr 2004, Eksterowicz, John wrote: > > I am using the latest version of Pymol and I cannot figure out how to > pick more than one atom. > > In the past, ctrl-shft lb, picked the first atom, and ctrl-shft rb would > pick a second atom. But now, ctrl-shft rb brings up a pop-up menu. > > Any help would be appreciated. > > Thanks, > John > > John Eksterowicz > Celera Genomics > --- This SF.Net email is sponsored by: IBM Linux Tutorials Free Linux tutorial presented by Daniel Robbins, President and CEO of GenToo technologies. Learn everything from fundamentals to system administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] picking atoms with latest version (0.95)
Hi, I had that problem this weekend too. I've found that ctrl right click picks one atom and shift right double click picks a second atom. That seems to work for the 'dist' and 'bond' commands anyway! Regards, Carina On Mon, 12 Apr 2004, Eksterowicz, John wrote: > > I am using the latest version of Pymol and I cannot figure out how to > pick more than one atom. > > In the past, ctrl-shft lb, picked the first atom, and ctrl-shft rb would > pick a second atom. But now, ctrl-shft rb brings up a pop-up menu. > > Any help would be appreciated. > > Thanks, > John > > John Eksterowicz > Celera Genomics >
[PyMOL] picking atoms with latest version (0.95)
I am using the latest version of Pymol and I cannot figure out how to pick more than one atom. In the past, ctrl-shft lb, picked the first atom, and ctrl-shft rb would pick a second atom. But now, ctrl-shft rb brings up a pop-up menu. Any help would be appreciated. Thanks, John John Eksterowicz Celera Genomics
RE: [PyMOL] picking atoms on a Win 2000 machine
Thanks Warren, I can set my depth cue to 24-bit (I'm running Pymol on a sony vaio SR1K laptop) and this works fine. Great package! I'll be waiting for the minimiser so I can do RSR on my laptop! Flip -Original Message- From: DeLano, Warren [mailto:war...@sunesis.com] Sent: Friday, March 01, 2002 18:58 To: Flip Hoedemaeker; pymol-users@lists.sourceforge.net Subject: RE: [PyMOL] picking atoms on a Win 2000 machine Hi Flip, This can happen on some graphics cards if the color depth isn't high enough. If you're in 16-bit color, try switching to 32 bit color using the start->settings->control-panel->display->settings->colors, and then restart PyMOL. If this is still happening with 32-bit color, then you've found a genuine bug, so please let me know what your exact PyMOL version and hardware configuration is. Cheers, Warren -- mailto:war...@sunesis.com Warren L. DeLano, Ph.D. Informatics Manager Sunesis Pharmaceuticals, Inc. 341 Oyster Point Blvd. S. San Francisco, CA 94080 (650)-266-3606 FAX:(650)-266-3501 > -Original Message- > From: Flip Hoedemaeker [mailto:f...@keydp.com] > Sent: Friday, March 01, 2002 9:10 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] picking atoms on a Win 2000 machine > > > Hi, > > I seem to have a problem with picking atoms with the "ctrl > middle" mouse > option. When I click on a specific atom a different atom is actually > selected, usually far away in the structure. The same happens > with the "ctrl > left" option (+lb). Can somebody tell me what is going on? > > Flip > > > > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
RE: [PyMOL] picking atoms on a Win 2000 machine
Hi Flip, This can happen on some graphics cards if the color depth isn't high enough. If you're in 16-bit color, try switching to 32 bit color using the start->settings->control-panel->display->settings->colors, and then restart PyMOL. If this is still happening with 32-bit color, then you've found a genuine bug, so please let me know what your exact PyMOL version and hardware configuration is. Cheers, Warren -- mailto:war...@sunesis.com Warren L. DeLano, Ph.D. Informatics Manager Sunesis Pharmaceuticals, Inc. 341 Oyster Point Blvd. S. San Francisco, CA 94080 (650)-266-3606 FAX:(650)-266-3501 > -Original Message- > From: Flip Hoedemaeker [mailto:f...@keydp.com] > Sent: Friday, March 01, 2002 9:10 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] picking atoms on a Win 2000 machine > > > Hi, > > I seem to have a problem with picking atoms with the "ctrl > middle" mouse > option. When I click on a specific atom a different atom is actually > selected, usually far away in the structure. The same happens > with the "ctrl > left" option (+lb). Can somebody tell me what is going on? > > Flip > > > > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
[PyMOL] picking atoms on a Win 2000 machine
Hi, I seem to have a problem with picking atoms with the "ctrl middle" mouse option. When I click on a specific atom a different atom is actually selected, usually far away in the structure. The same happens with the "ctrl left" option (+lb). Can somebody tell me what is going on? Flip
RE: [PyMOL] picking atoms
> From: Vajdos, Felix [mailto:felix_vaj...@groton.pfizer.com] > Does anyone know of a quick and easy way of just listing the > atoms in a > selection (i.e. I figured out how to interactively add atoms > to a selection > with Ctrl-LB, but I would like a way of just writing out a > list of the atoms > so picked). Of course, I can label all the atoms and write > down what they > are, but I was hoping there was some way of just listing them > (or writing > out a list of them). iterate (lb),print chain,resi,resn,name - Warren
[PyMOL] picking atoms
Hello, Does anyone know of a quick and easy way of just listing the atoms in a selection (i.e. I figured out how to interactively add atoms to a selection with Ctrl-LB, but I would like a way of just writing out a list of the atoms so picked). Of course, I can label all the atoms and write down what they are, but I was hoping there was some way of just listing them (or writing out a list of them). Felix Felix F. Vajdos Pfizer Inc Eastern Point Road MS 4039 Groton, CT 06340 860-715-6504 LEGAL NOTICE Unless expressly stated otherwise, this message is confidential and may be privileged. It is intended for the addressee(s) only. Access to this E-mail by anyone else is unauthorized. If you are not an addressee, any disclosure or copying of the contents of this E-mail or any action taken (or not taken) in reliance on it is unauthorized and may be unlawful. If you are not an addressee, please inform the sender immediately.
