[PyMOL] MacPyMOL Beta 2 Announce/Caveat
Mac Users, Development and testing on the MacPyMOL Incentive Product continues, but parallel development on the open-source foundation has interfered a bit. However, since I promised a public MacPyMOL announcement by late January, I am hereby announcing that MacPyMOL Beta 2 can now be downloaded from the following public URL: But first, a word of caution -- YOU MAY WISH TO WAIT for a later release. Why? Because MacPyMOL Beta 2 is VERY BUGGY and largely UNTESTED. In addition to Mac-specific Aqua GUI, image copy & paste, and QuickTime export, it contains a whole bunch of brand new cross-platform user interface code that will soon be in the open-source release as well. The idea behind these changes is to improve overall PyMOL usability, but the job isn't nearly done. Current new stuff includes: scroll wheel support, double-click actions, multi-atom picking, cascading menus, preset renditions, viewer pop-up menus, a new file icon, and a cleaner looking internal_gui. So to summarize: only download this early MacPyMOL release if you are prepared to test and report on flaky software: http://www.delsci.com/macpymol is the URL. Have fun, be carfule, and set your MacPyMOL expectations low -- this code will get better soon. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020
RE: [PyMOL] SGI Crystal Eyes Problem
Chris, PyMOL only support one kind stereo of stereo: OpenGL quad-buffered-stereo. It's unclear to me from your message that your Octane can support QBS. Sybyl, I believe, can run using top/bottom stereo, so I am not sure that is a reliable indicator... PyMOL usually autodetects QBS on X11-based hardware, if it is available. If "stereo quadbuffer" doesn't work then you may be out of luck on that system. (FYI: On the Indigo2's, if you had a lower-end graphics option, it was necessary to change the video mode to a lower resolution in order to get QBS...perhaps the same is true of your system?) Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of Christian Rummey > Sent: Wednesday, January 28, 2004 4:42 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] SGI Crystal Eyes Problem > > > Dear all, > > I'd like to use pymol with our sgi shutter glasses, which are standard > ones > on an sgi octane R12000, working fine e.g. with Tripos SYBYL. > > when I try to use them with pymol, the default stereo setting isn't > quad-buffer (which means it is not available?), and if I manually set the > stereo mode > to 1 (= quad buffer) I can see the correct picture (objects are drawn > 'twice'), but the display doesn't enter stereo mode and the transmitter > accordingly > do not work. > > Is there something I miss? - that needs to be configured before quad > buffer > works on an sgi? > > any hints ary highly appreciated! > > thanks, > christian > > -- > Christian Rummey > > -- > +++ GMX - die erste Adresse für Mail, Message, More +++ > Bis 31.1.: TopMail + Digicam für nur 29 EUR http://www.gmx.net/topmail > > > > --- > The SF.Net email is sponsored by EclipseCon 2004 > Premiere Conference on Open Tools Development and Integration > See the breadth of Eclipse activity. February 3-5 in Anaheim, CA. > http://www.eclipsecon.org/osdn > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] nmr ensemble alignment
Doug, As far as I know there isn't any resource online, so I'll try to answer your questions here: PyMOL does not automatically align structures. intra_fit is presumably the command you're looking for to do this, since you're placing models are in one object. intra_fit name ca, 1 would for example align all of the models to the first model using alpha-carbon coordinates. intra_fit resi 10-15, 1 would align all models to the coordinates of atoms in residues 10-15. As far as RMS statistics go, PyMOL may be the best tool for this yet, since it doesn't current have the ability to generate statistics for the ensemble. What statistics in particular would you like it to provide? Also note that if you have you ensemble in a multiple-model pdb file (with MODEL and ENDMDL records), you can just load it in one command load ens.pdb Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of Douglas Kojetin > Sent: Monday, January 26, 2004 11:22 AM > To: pymol > Subject: [PyMOL] nmr ensemble alignment > > Hi All- > > Will reading in a structural ensemble > > load pdb01.pdb, ens > load pdb02.pdb, ens > ... > > ... automagically align the structures? If not, do I need to run > another command, such as ' intra_fit (name ca) ' ? Or should I use > normal 'fit'? > > Also, what is the best method for determining the RMS of the ensemble? > There are a few commands in the reference manual (rms, rms_cur, > intra_rms, intra_rms_cur), and I'm confused as to which is best for > structural ensembles. > > Or, to save typing, is there a current web resource for using PyMOL > with NMR models (with hints, scripts, etc.)? One thing I /miss/ from > MOLMOL is the 'sausage' display -- has anyone implemented this in PyMOL > yet? > > Thanks, > Doug > > > > --- > The SF.Net email is sponsored by EclipseCon 2004 > Premiere Conference on Open Tools Development and Integration > See the breadth of Eclipse activity. February 3-5 in Anaheim, CA. > http://www.eclipsecon.org/osdn > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] RE: c-alpha traces
Michal, Unfortunately, beautiful backbones require N and C coordinates as well, because PYMOL uses AA geometry to determine orientation vectors. The best you can do with CA only is a tube. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: Michal Kurowski [mailto:mic...@genesilico.pl] > Sent: Thursday, January 22, 2004 3:19 PM > To: Warren L. DeLano > Cc: pymol-users@lists.sourceforge.net > Subject: Re: c-alpha traces > > Warren L. DeLano [war...@delanoscientific.com] wrote: > > Yes, > > > > PyMOL can visualize CA-only models, perform CA-based alignments on CA > > models, visualize all-atom models, perform CA-based alignments on all > > atom models, and perform all-atom alignments on all-atom models. > > Thats great ! > > To make sure we both speak of the same thing: > > I specifically meant visualization of pdb files with c-alpha > - only structure subsets from rcsb without *any* action on > already centered molecules. Moreover, showing beautiful > backbones ;-). > > Is it right ? > > Regards, > > -- > Michal Kurowski > > >
RE: [PyMOL] translucent proteins
Lesley, set cartoon_transparency, 0.6 should do the trick. Note that you may need to ray-trace the image to avoid transparency artifacts. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of Lesley Debono > Sent: Wednesday, January 21, 2004 10:56 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] translucent proteins > > I would like to be able to make the backbone protein in a structure > translucent so that the active site is clearly visible through the > protein. Any ideas on how to do this? > > Lesley > > > > --- > The SF.Net email is sponsored by EclipseCon 2004 > Premiere Conference on Open Tools Development and Integration > See the breadth of Eclipse activity. February 3-5 in Anaheim, CA. > http://www.eclipsecon.org/osdn > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Help for user-defined functions
Thanks for the suggestion, and the solution.
In Versions >= 0.95, cmd.extend will will adds new commands into the
help dictionary.
In the meantime
cmd.help_sc.append('func_name')
will work...
Cheers,
Warren
--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
> -Original Message-
> From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
> ad...@lists.sourceforge.net] On Behalf Of Michael George Lerner
> Sent: Thursday, January 22, 2004 1:51 PM
> To: Gareth Stockwell
> Cc: pymol-users
> Subject: Re: [PyMOL] Help for user-defined functions
>
>
> Hi,
>
> I haven't seen this documented anywhere, so I have no idea if it's the
> Right Way to do things, but I think all you need to do is add
>
> cmd.help_sc.append('some_func')
>
> after the cmd.extend('some_func',some_func) call. should this be
built in
> to cmd.extend()?
>
> -michael
>
> --
> This isn't a democracy;|_ |Michael Lerner
> it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan
> -Torrence, Bring It On| - against HTML email X | Biophysics
>| / \ | mler...@umich
>
> On Thu, 22 Jan 2004, Gareth Stockwell wrote:
>
> > Does anyone know if it is possible to add 'help' documentation to my
own
> > user-defined functions? What I want is to be able to define a new
PyMOL
> > command by executing the following script:
> >
> >
> > #--
> >
> > def some_func:
> >
> > '''
> > Some help docs here...
> >
> > '''
> >
> > # Python code here...
> >
> > cmd.extend("some_func", some_func)
> >
> > #--
> >
> > ... and then type 'help some_func'.
> >
> > Gareth
> >
> > --
> > Gareth Stockwell
> > European Bioinformatics Institute
> >
> >
> >
> > ---
> > The SF.Net email is sponsored by EclipseCon 2004
> > Premiere Conference on Open Tools Development and Integration
> > See the breadth of Eclipse activity. February 3-5 in Anaheim, CA.
> > http://www.eclipsecon.org/osdn
> > ___
> > PyMOL-users mailing list
> > PyMOL-users@lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >
>
>
> ---
> The SF.Net email is sponsored by EclipseCon 2004
> Premiere Conference on Open Tools Development and Integration
> See the breadth of Eclipse activity. February 3-5 in Anaheim, CA.
> http://www.eclipsecon.org/osdn
> ___
> PyMOL-users mailing list
> PyMOL-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] How to send pymol command to pymol by python interpreter
Takefumi, You only need to worry about this if you're using an external Python interpreter with a modular build of PyMOL. For example, after installing a late-model linux PyMOL RPM, you run python script.py Where script.py contains the following sequence: import pymol pymol.finish_launching() which is needed to insure that PyMOL's API in the parallel thread is defined ready to receive messages. The problem is that PyMOL can't launch until "import pymol" completes and returns and __main__.pymol is defined. However, that means that the next command in your script will need to be executed before PYMOL has had a chance to initialize itself. So the current approach is to launch the PyMOL thread, and then call a function which blocks until PyMOL is all ready to go... Cheers, Warren [PS If there's anyone out there with a more elegant alternative for launching the PyMOL thread from a standalone Python script, I'd sure like to hear it : )]. -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of Takefumi Sora > Sent: Wednesday, January 21, 2004 10:57 PM > To: pymol-users@lists.sourceforge.net > Subject: RE: [PyMOL] How to send pymol command to pymol by python > interpreter > > > Hi. > > I appreciate your answer, Warren. > Thank you. > > Please let me ask one more question. > > You said I need two lines first: > import pymol > pymol.finish_launching() > > As long as I use,I can't the role of > "pymol.finish_launching()" > if I don't call this, what troubles will happen ? > > Takefumi SORA > > > > --- > The SF.Net email is sponsored by EclipseCon 2004 > Premiere Conference on Open Tools Development and Integration > See the breadth of Eclipse activity. February 3-5 in Anaheim, CA. > http://www.eclipsecon.org/osdn > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] c-alpha traces
Yes, PyMOL can visualize CA-only models, perform CA-based alignments on CA models, visualize all-atom models, perform CA-based alignments on all atom models, and perform all-atom alignments on all-atom models. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of Michal Kurowski > Sent: Wednesday, January 21, 2004 5:37 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] c-alpha traces > > Hi, > > Some structure comparison software is only able to generate alignments > built of c-alpha atoms of both structures compared. > > Is Pymol able to visualize such alignment with (faked) backbone > shown ? > > If not what could possibly show it ? > > Regards, > > > -- > Michal Kurowski > > > > > > --- > The SF.Net email is sponsored by EclipseCon 2004 > Premiere Conference on Open Tools Development and Integration > See the breadth of Eclipse activity. February 3-5 in Anaheim, CA. > http://www.eclipsecon.org/osdn > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] How to send pymol command to pymol by python interpreter
Takefumi,
# If launching PyMOL from an external interpreter, then you need
# these two lines first:
import pymol
pymol.finish_launching()
# If using PyMOL directly, then start here...
from pymol import cmd
# A command like the following
cmd.do("show cartoon")
# is essentially equivalent to:
cmd.show("cartoon")
# end example script
Now, if you save the above in a script.py file, you can
python script.py
assuming that PyMOL has been installed as a Python module.
If using a standalone version of PyMOL, then for synchronous execution,
issue:
pymol script.py
(equivalent to "run script.py" from within PyMOL)
or for asynchronous execution, issue:
pymol -l script.py
(equivalent to "spawn script.py" from within PyMOL)
On Windows use "(pymol-install-path)\pymolwin.exe" instead of "pymol".
Hopefully that answers your question : ). Sorry for the complexity, but
that's the price of flexibility.
Cheers,
Warren
--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
> -Original Message-
> From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
> ad...@lists.sourceforge.net] On Behalf Of Takefumi Sora
> Sent: Wednesday, January 21, 2004 8:42 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] How to send pymol command to pymol by python
interpreter
>
>
> Dear Pymol users
>
> I launch Pymol in my python program.
> After that, I can't change objects in pymol in my
> python program. In short I do not know how to
> send pymol command (ex cmd.do("show cartoon")) to
> Pymol not by directly input in pymol external command line
> but by python interpreter.
>
> Does anybody know how to do this ?
>
> Thank you.
> Takefumi SORA
>
>
>
> ---
> The SF.Net email is sponsored by EclipseCon 2004
> Premiere Conference on Open Tools Development and Integration
> See the breadth of Eclipse activity. February 3-5 in Anaheim, CA.
> http://www.eclipsecon.org/osdn
> ___
> PyMOL-users mailing list
> PyMOL-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] Problems with PyMOL + XIG Summit2.2
PyMOL Users,
It appears that some PyMOL users are having trouble with Xi Graphics'
Summit line of OpenGL graphics drivers, version 2.2.
Atom picking (which uses glReadPixels with color-encoded pixel buffers)
fails with these drivers. It's unclear right now whether the problem is
due to the XiG OpenGL implementation or with the default keyboard
modifier event mapping.
If you are both a PyMOL and Summit user (any version), please help by
responding to me directly with information about:
What numeric version of Summit are you using?
What Summit series do you have (LX, DX, CX, WX, etc.)?
What operating system, distro, and version are you running?
Does atom picking and mouse selection work for you in PyMOL?
Does PyMOL work fine under XFree86 with the identical hardware setup?
Once we understand the extent of the problem, we'll try to set up our
own Summit install here and then track down the problem...
Cheers,
Warren
--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
> -Original Message-
> From: Dr. Daniel James White PhD [mailto:d...@chalkie.org.uk]
> Sent: Wednesday, January 21, 2004 1:20 AM
> To: t.gran...@ubs.u-bordeaux1.fr; Warren L. DeLano
> Subject: pymol, with summit2.2 Xserver on linux
>
> Hi,
>
> I get this problem also.
> I fear is the the summit Xserver niot handling mouse events properly
or
> something.
> My mouse is a ps2 logitech with a scroll wheel button.
> I can't do ctrl-click operations.
>
> Have you also noticed that your sound does not work with summit, but
> does with XFree86?
>
> cheers
>
> Dan
>
>
> Message: 1
> From: "Warren L. DeLano"
> To: "'Thierry Granier'" ,
>
> Subject: RE: [PyMOL] mouse
> Date: Fri, 16 Jan 2004 08:12:42 -0800
>
> Thierry,
>
> This behavior could be the symptom of either malfunctioning OpenGL, or
a
> screen with two few colors to support color-encoded picking (which is
> what PyMOL uses behind the scenes).
>
> Please confirm that your display is running in 24 or 32 bit color. If
> that is the case and picking still fails, then please try saving a png
> file of what you see on the screen ("png filename.png"). If that PNG
> file exhibits any distortion or artifacts, then that's the cause of
the
> problems. Otherwise, PyMOL may have a bug...
>
> Cheers,
> Warren
>
>
> --
> mailto:war...@delanoscientific.com
> Warren L. DeLano, Ph.D.
> Principal Scientist
> DeLano Scientific LLC
> Voice (650)-346-1154
> Fax (650)-593-4020
>
> > -Original Message-
> > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
> > ad...@lists.sourceforge.net] On Behalf Of Thierry Granier
> > Sent: Friday, January 16, 2004 12:52 AM
> > To: pymol-users@lists.sourceforge.net
> > Subject: [PyMOL] mouse
> >
> > Good morning,
> >
> > I am trying to use pymol on a PC linux RedHat 9.0 using
> > the software summit 2.2 of Xig, and I run into the following
> > problem:
> > after loading a molecule, when I try to click on an atom, for
> selection,
> > using
> > CTRL shif lb or CTRL shift lb, I get the message
> > "no atom found nearby"
> >
> > I have tried all the mouse settings from the gui with no success.
> >
> > Any help will be appreciated,
> > thank you
> >
> > Thierry Granier.
> >
> >
> >
> >
> > ---
> > The SF.Net email is sponsored by EclipseCon 2004
> > Premiere Conference on Open Tools Development and Integration
> > See the breadth of Eclipse activity. February 3-5 in Anaheim, CA.
> > http://www.eclipsecon.org/osdn
> > ___
> > PyMOL-users mailing list
> > PyMOL-users@lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>
>
>
> Dr. Daniel James White BSc. (Hons.) PhD
> Cell Biology
> Department of biological and environmental science
> PO Box 35
> University of Jyväskylä
> Jyväskylä FIN 40014
> Finland
> +358 (0)14 260 4183 (work)
> +358 (0)414740463 (mob)
>
> http://www.chalkie.org.uk
> d...@chalkie.org.uk
> wh...@cc.jyu.fi
RE: [PyMOL] Ray Tracing Crash
Morri, The RH9 Patch is described and published on: https://rhn.redhat.com/errata/RHBA-2003-136.html I would not expect Debian to suffer from the same crash. If it does, then we may be dealing with a genuine bug in PyMOL (assuming that you're not simply running out of RAM). With respect to Debian, in order to debug the problem, you might want to send me a PyMOL session file which crashes on your system when the next command issued is "ray". Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: Morri Feldman [mailto:morrifeld...@yahoo.com] > Sent: Tuesday, January 20, 2004 10:36 PM > To: Warren L. DeLano; 'Matt Franklin'; 'Morri Feldman' > Cc: 'pymol-users' > Subject: RE: [PyMOL] Ray Tracing Crash > > Warren and Matt, > > Thanks so much for your help. I must be using the > stock glibc because "set max_threads, 1" allows me to > ray trace without crashing. I will tell my system > administrator to patch glibc. Do you know where I > should look for the patch? > > My debian/testing system at home also has trouble ray > tracing especially sticks. When it fails I get a > segmentation fault. Is my problem at home also due to > an unpatched glibc? > > The error message is: > /usr/bin/pymol: line 7: 32460 Segmentation fault > python > /usr/lib/python2.3/site-packages/pymol/__init__.py $* > > Thanks for creating such a great program, > Morri > > --- "Warren L. DeLano" > wrote: > > Morri, > > > > (First, thanks Matt for the great diagnostic > > advice!) > > > > This sounds to me like a potential threading > > deadlock, possible > > due to the broken threading in RedHat 9. Are you > > using the stock > > version or have you patched glibc? > > > > If you haven't patched your RedHat 9, then one way > > to be sure > > this is the problem is to "set max_threads, 1" > > before issuing the ray > > command. If PyMOL doesn't hang, then you've found > > the culprit. > > > > If have already patched your RH9, then let's do > > some more work > > to determine what's going on... > > > > Cheers, > > Warren > > > > -- > > mailto:war...@delanoscientific.com > > Warren L. DeLano, Ph.D. > > Principal Scientist > > DeLano Scientific LLC > > Voice (650)-346-1154 > > Fax (650)-593-4020 > > > > > -Original Message- > > > From: pymol-users-ad...@lists.sourceforge.net > > [mailto:pymol-users- > > > ad...@lists.sourceforge.net] On Behalf Of Matt > > Franklin > > > Sent: Tuesday, January 20, 2004 6:25 PM > > > To: Morri Feldman > > > Cc: pymol-users > > > Subject: Re: [PyMOL] Ray Tracing Crash > > > > > > Morri Feldman wrote: > > > > I am running pymol .93. When I try to ray trace > > a scene, the gui > > shows > > > a > > > > white status bar that moves halfway across the > > screen and then > > freezes. > > > > After this the GUI is frozen and must be killed. > > No error messages > > are > > > > shown. The computer is running RedHat 9 and has > > 4 processors. Has > > > > anyone else experienced this problem? Do you > > have any solutions? > > > > > > > > This message may double post because I > > accidentally tried to post it > > > from > > > > my other email account. Sorry > > > > > > > > Thanks, Morri > > > > > > > > Morri Feldman > > > > > > > > > > Hi Morri - > > > > > > The progress bar for raytracing doesn't move > > linearly - the first half > > > of the bar is covered fairly quickly, then more > > slowly, then very > > > slowly, then the last fifth is usually covered in > > one jump. Are you > > > sure you just aren't being impatient? Try > > raytracing a very simple > > > scene, like a single amino acid in spheres mode, > > to see if it hangs > > > then. Also try raytracing parts of your scene in > > case some funny bit > > of > > > your molecule is causing this problem. Finally, > > try reducing the > > > complexity of your surfaces and/or spheres: "set > > surface_quality, -1" > > (0 > > > is the default). > > > > > > Feel free
RE: [PyMOL] Ray Tracing Crash
Morri, (First, thanks Matt for the great diagnostic advice!) This sounds to me like a potential threading deadlock, possible due to the broken threading in RedHat 9. Are you using the stock version or have you patched glibc? If you haven't patched your RedHat 9, then one way to be sure this is the problem is to "set max_threads, 1" before issuing the ray command. If PyMOL doesn't hang, then you've found the culprit. If have already patched your RH9, then let's do some more work to determine what's going on... Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of Matt Franklin > Sent: Tuesday, January 20, 2004 6:25 PM > To: Morri Feldman > Cc: pymol-users > Subject: Re: [PyMOL] Ray Tracing Crash > > Morri Feldman wrote: > > I am running pymol .93. When I try to ray trace a scene, the gui shows > a > > white status bar that moves halfway across the screen and then freezes. > > After this the GUI is frozen and must be killed. No error messages are > > shown. The computer is running RedHat 9 and has 4 processors. Has > > anyone else experienced this problem? Do you have any solutions? > > > > This message may double post because I accidentally tried to post it > from > > my other email account. Sorry > > > > Thanks, Morri > > > > Morri Feldman > > > > Hi Morri - > > The progress bar for raytracing doesn't move linearly - the first half > of the bar is covered fairly quickly, then more slowly, then very > slowly, then the last fifth is usually covered in one jump. Are you > sure you just aren't being impatient? Try raytracing a very simple > scene, like a single amino acid in spheres mode, to see if it hangs > then. Also try raytracing parts of your scene in case some funny bit of > your molecule is causing this problem. Finally, try reducing the > complexity of your surfaces and/or spheres: "set surface_quality, -1" (0 > is the default). > > Feel free to contact me directly - I'm local! (Although Warren will be > more helpful...) > > - Matt > > > -- > Matthew FranklinPhone:(650)225-4596 > Postdoctoral Researcher Fax:(650)225-3734 > Genentech, Inc. > 1 DNA Way, South San Francisco, CA 94080 > > > > --- > The SF.Net email is sponsored by EclipseCon 2004 > Premiere Conference on Open Tools Development and Integration > See the breadth of Eclipse activity. February 3-5 in Anaheim, CA. > http://www.eclipsecon.org/osdn > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Cartoon does not display properly
Dan, Thats what happens when there is no secondary structure information defined. PyMOL's dss command will solve this, but note that dss will not give identical results to DSSP (the closest thing to a standard for secondary structure assignment). Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Daniel Moriarty Sent: Tuesday, January 20, 2004 10:41 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Cartoon does not display properly Hello everyone, I have a generated PDB file which gives very thick ribbons when I try to do the cartoon display. Apart from that, it seems fine. I remember seeing this problem once before with a file I downloaded from the PDB, and I couldnt resolve the problem then. Any ideas on what to do? Thanks, Dan
RE: [PyMOL] working directory
Lesley,
If you always want PyMOL to start in a different directory, you
can create a ".pymolrc" file in you home directory with a command like
cd /users/lesley/scripts
Which will be executed every time you start PyMOL.
Cheers,
Warren
--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
> -Original Message-
> From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
> ad...@lists.sourceforge.net] On Behalf Of Lesley Debono
> Sent: Sunday, January 18, 2004 11:56 PM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] working directory
>
> i have pymol installed on an OSX machine. When I begin pymol i am in
> the root ("\") directory. My scripts are in a different directory. Is
> there a way I can begin in another directory when starting Pymol?
>
> cheers
> Lesley
>
>
>
> ---
> The SF.Net email is sponsored by EclipseCon 2004
> Premiere Conference on Open Tools Development and Integration
> See the breadth of Eclipse activity. February 3-5 in Anaheim, CA.
> http://www.eclipsecon.org/osdn
> ___
> PyMOL-users mailing list
> PyMOL-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] homologous alignments?
Camille, If I understand your question, you're looking for the setting which creates a discrete color transition at the edges of helices and strands, instead of blending. It is: set cartoon_discrete_colors, on For example color grey, name ca color yellow, ss s and name ca color red, ss h and name ca set cartoon_discrete_colors, on Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of cami...@mrc-lmb.cam.ac.uk > Sent: Monday, January 19, 2004 7:37 AM > To: Warren L. DeLano > Cc: 'Michael Bovee'; pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] homologous alignments? > > Hello, >I am unable to read the archive at the moment so can anyone tell > me the command that allows colouring of the edge of helices and strands > (usually grey). I think this was posted recently but I don't have it in > any of my saved scripts. > > Many thanks, > Camille > > Dr Camille Shammas > Medical Research Council Laboratory of Molecular Biology Hills Road, > Cambridge CB2 2QH, UK. > Tel: +44 (0)1223 402407 > Mobile: 07812035842 > E-mail: cami...@mrc-lmb.cam.ac.uk > > > > --- > The SF.Net email is sponsored by EclipseCon 2004 > Premiere Conference on Open Tools Development and Integration See the > breadth of Eclipse activity. February 3-5 in Anaheim, CA. > http://www.eclipsecon.org/osdn > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] mouse
Thierry,
This behavior could be the symptom of either malfunctioning OpenGL, or a
screen with two few colors to support color-encoded picking (which is
what PyMOL uses behind the scenes).
Please confirm that your display is running in 24 or 32 bit color. If
that is the case and picking still fails, then please try saving a png
file of what you see on the screen ("png filename.png"). If that PNG
file exhibits any distortion or artifacts, then that's the cause of the
problems. Otherwise, PyMOL may have a bug...
Cheers,
Warren
--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
> -Original Message-
> From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
> ad...@lists.sourceforge.net] On Behalf Of Thierry Granier
> Sent: Friday, January 16, 2004 12:52 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] mouse
>
> Good morning,
>
> I am trying to use pymol on a PC linux RedHat 9.0 using
> the software summit 2.2 of Xig, and I run into the following
> problem:
> after loading a molecule, when I try to click on an atom, for
selection,
> using
> CTRL shif lb or CTRL shift lb, I get the message
> "no atom found nearby"
>
> I have tried all the mouse settings from the gui with no success.
>
> Any help will be appreciated,
> thank you
>
> Thierry Granier.
>
>
>
>
> ---
> The SF.Net email is sponsored by EclipseCon 2004
> Premiere Conference on Open Tools Development and Integration
> See the breadth of Eclipse activity. February 3-5 in Anaheim, CA.
> http://www.eclipsecon.org/osdn
> ___
> PyMOL-users mailing list
> PyMOL-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Restrict surface transparency to limited region
Tsjerk, It would be nice if it was that easy, but in reality, transparent elements need to be rendered out of sequence and Z-sorted (as much as possible). Starting from scratch, one could preprocess the rendering stream and lift transparent regions out prior to rendering anything, but PyMOL wasn't written that way, and if it was, performance would be noticeably worse. Nevertheless, as PyMOL evolves, it may be possible to add this kind of behavior -- it is something that has been asked for enough times that I do hope to find a solution : ). Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of Tsjerk Wassenaar > Sent: Thursday, January 15, 2004 4:29 AM > To: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] Restrict surface transparency to limited region > > > Hi Warren, > > Wouldn't it be possible to change the [r,g,b] representation in Pymol to > [r,g,b,t]. Then it would be trivial to have gradual transparencies in > surfaces or other things. Since transparency is supported... > > Cheers, > > Tsjerk > > Warren L. DeLano wrote: > > >Roger, > > > > This isn't possible right now. The only way to do it is to > >create two objects, surfacing different atoms in each object, and then > >enabling transparency in just one of the two objects. > > > >Cheers, > >Warren > > > > > >-- > >mailto:war...@delanoscientific.com > >Warren L. DeLano, Ph.D. > >Principal Scientist > >DeLano Scientific LLC > >Voice (650)-346-1154 > >Fax (650)-593-4020 > >-Original Message- > >From: pymol-users-ad...@lists.sourceforge.net > >[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Roger Dodd > >Sent: Wednesday, January 14, 2004 4:49 AM > >To: pymol-users@lists.sourceforge.net > >Subject: [PyMOL] Restrict surface transparency to limited region > > > >Dear PyMOL users/devs, > > > >I am trying to produce a figure with a molecular surface and would like > >to make this surface transparent only covering certain residues. I have > >tried creating a separate surface for these residues and the rest of the > >protein and setting transparency for the object covering only those > >residues, but this gives a very discontinuous looking surface > >representation. Is it possible to just enable transparency on a limited > >region of a surface? > > > >Thanks > > > >Roger > > > >-- > >Roger Dodd > >CIMR > >University of Cambridge > >Wellcome Trust / MRC Building > >Addenbrooke's Hospital > >Hills Road > >Cambridge > >CB2 2XY > > > > > > > >--- > >This SF.net email is sponsored by: Perforce Software. > >Perforce is the Fast Software Configuration Management System offering > >advanced branching capabilities and atomic changes on 50+ platforms. > >Free Eval! http://www.perforce.com/perforce/loadprog.html > >___ > >PyMOL-users mailing list > >PyMOL-users@lists.sourceforge.net > >https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > -- > ~ > -- :) > -- :) Tsjerk A. Wassenaar, M.Sc. > -- :) Molecular Dynamics Group > -- :) Dept. of Biophysical Chemistry > -- :) University of Groningen > -- :) Nijenborgh 4 > -- :) 9747 AG Groningen > -- :) The Netherlands > -- :) > ~ > -- :) > -- :) Hi! I'm a .signature virus! > -- :) Copy me into your ~/.signature to help me spread! > -- :) > ~ > > > > > > --- > The SF.Net email is sponsored by EclipseCon 2004 > Premiere Conference on Open Tools Development and Integration > See the breadth of Eclipse activity. February 3-5 in Anaheim, CA. > http://www.eclipsecon.org/osdn > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Restrict surface transparency to limited region
Roger, This isnt possible right now. The only way to do it is to create two objects, surfacing different atoms in each object, and then enabling transparency in just one of the two objects. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Roger Dodd Sent: Wednesday, January 14, 2004 4:49 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Restrict surface transparency to limited region Dear PyMOL users/devs, I am trying to produce a figure with a molecular surface and would like to make this surface transparent only covering certain residues. I have tried creating a separate surface for these residues and the rest of the protein and setting transparency for the object covering only those residues, but this gives a very discontinuous looking surface representation. Is it possible to just enable transparency on a limited region of a surface? Thanks Roger -- Roger Dodd CIMR University of Cambridge Wellcome Trust / MRC Building Addenbrooke's Hospital Hills Road Cambridge CB2 2XY
RE: [PyMOL] build instructions
Steve, Although static building isn't supported by us, and although we make no guarantees that the static launch process won't change drastically without warning and at any time, you may wish to consult setup/Rules.linux-semistat-py22 for an example. The trick with static builds is that PyMOL needs to do a bunch of magic to get the environment right before the Python interpreter gets going and Tkinter starts up. Also note that you need to provide static builds of all of the external dependencies in order to generate a truly portable static build. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of Steven F. Killen > Sent: Tuesday, January 13, 2004 12:37 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] build instructions > > Greetings, > > I'm trying to build pymol statically (instead of as a Python module) and > the documentation doesn't seem to have the options listed for the > variables in the Makefile. Is there somewhere I may not be looking? > > -- > Steve Killen > > > --- > This SF.net email is sponsored by: Perforce Software. > Perforce is the Fast Software Configuration Management System offering > advanced branching capabilities and atomic changes on 50+ platforms. > Free Eval! http://www.perforce.com/perforce/loadprog.html > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] DeLano Scientific Closed Until Jan 7, 2004.
PyMOL Users, This is the final reminder that I am now off-line and away from DeLano Scientific (which will be closed) until January 7th. Everyone please have a wonderful holiday and a Happy New Year! Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020
RE: [PyMOL] Question
Avram, set cartoon_highlight_color, red Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of slo...@mail.med.upenn.edu > Sent: Friday, December 19, 2003 11:38 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Question > > Hi, > > does anyone know how to color the inside of helices a different color > than the outsides? > > thanks > > Avram > -- > Avram M. Slovic > Biochemistry and Molecular Biophysics > University of Pennsylvania > 420 Curie Blvd. > 1010 Stellar Chance Bldg. > Philadelphia, PA 19104 > > L:215-898-3496 > > > --- > This SF.net email is sponsored by: IBM Linux Tutorials. > Become an expert in LINUX or just sharpen your skills. Sign up for IBM's > Free Linux Tutorials. Learn everything from the bash shell to sys admin. > Click now! http://ads.osdn.com/?ad_id=1278&alloc_id=3371&op=click > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] unsetting cartoon_colors
David, For settings such as cartoon_color, surface_color, mesh_color, the default value is -1. set cartoon_color, -1 or set cartoon_color, -1, object-name will restore the color. Thanks for pointing out that: set cartoon_color, default doesn't work! Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of David A. Horita Sent: Thursday, December 18, 2003 10:50 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] unsetting cartoon_colors Hi all, I have a collection of molecules and want to color a particular helix (in cartoon mode) a specific color different from other helices. Unfortunately, I had previously set cartoon_color from "default" to another color, so now specifying a color for that helix (or even "color red, ss h") has no impact. (it does change the color of the Calpha, but not the cartoon itself). So, the question is, how do I unset the cartoon_color variable (without wiping out my scene)? The variable setting comes with the .pse file, "set cartoon_color, default" gives an error about not knowing what color default is. Thanks, Dave Horita - David A. Horita, Ph.D. Department of Biochemistry Wake Forest University School of Medicine Winston-Salem, NC 27157-1016 Tel: 336 713-4194 Fax: 336 716-7671 email: dhor...@wfubmc.edu web: http://www.wfubmc.edu/biochem/faculty/Horita/
[PyMOL] RE: 3-button mice
Chris, I hereby nominate the Targus PAUM01U as the official 3-button mouse for PyMOL users on the go. http://www.targus.com/us/product_details.asp?sku=PAUM01U They might be too small for some, but they work great for me, at home and on the road! (plus, they color-coordinate with Ti PowerBooks) Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- Sent: Thursday, December 18, 2003 5:45 AM To: war...@delanoscientific.com Subject: pymol Hi, I plan to update the website (http://www.macinchem.fsnet.co.uk) over the Christmas Break and one question I'm often asked is which 3-button mouse should I use for PYMOL under MacOSX? Any suggestions? Thanks Chris
RE: [PyMOL] Display of electrostatic potential surfaces
Roger,
The problem with computing electrostatic maps in PyMOL
currently is that the Coulomb equation assumes a uniform dielectric and
thus doesn't give you correct potentials for macromolecules. It is much
better to use an external tool such as Grasp, MEAD, APBS, or Delphi,
which can apply a different dielectric constant to the inside of the
protein than to the surrounding solvent.
Yes, PyMOL can compute a Coulombic map using the approach
you've outlined if partial charges have been assigned - but there isn't
a good way to do that in PyMOL just yet.
Cheers,
Warren
--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Roger Dodd
Sent: Thursday, December 18, 2003 3:53 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Display of electrostatic potential surfaces
Dear PyMOL users,
I would like to generate a figure of my protein where the surface
electrostatic potential is displayed. PyMOL now comes with a demo
function for display of such a surface. However, when I apply the
commands used in this demo, i.e.
cmd.set("coulomb_dielectric",80.0)
cmd.map_new("e_pot","coulomb",1.0,"pept",5)
cmd.ramp_new("e_lvl","e_pot",[-3.6,-1.6,0.4])
cmd.set("surface_color","e_lvl","pept")
cmd.refresh()
to the model from my pdb file, I get a uniformly blue surface. I believe
this must be due to the lack of assignment of partial/formal charges to
the atoms in the pdb file. So, my questions are:
1. Is it possible to automatically assign the correct charges to atoms
within PyMOL
2. If not, is there a program that will do this and if so can the output
from this program be understood by PyMOL in some way.
Thanks for your help
Roger
--
Roger Dodd
CIMR
Addenbrooke's Hospital
Cambridge
RE: [PyMOL] electrostatic surface
Ruslan, PyMOL can't yet calculate the electrostatic surface, but it can display the potential as output by Grasp, Delphi, MEAD, or Zap. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of Sanishvili, Ruslan > Sent: Tuesday, December 16, 2003 8:29 AM > To: Warren L. DeLano; pymol-users@lists.sourceforge.net > Subject: [PyMOL] electrostatic surface > > Hi all, > Inexplicably, I haven't been following the PyMol news lately. Does it > now calculate and display the electrostatic fields/surfaces of proteins > (a la GRASP, or similar)? If it does, starting from which version? > Thanks, > Nukri > > > Ruslan Sanishvili (Nukri), Ph.D. > > GM/CA-CAT, Bld. 436, D007 > Biosciences Division, ANL > 9700 S. Cass Ave. > Argonne, IL 60439 > > Tel: (630)252-0665 > Fax: (630)252-0667 > rsanishv...@anl.gov > > > > > --- > This SF.net email is sponsored by: IBM Linux Tutorials. > Become an expert in LINUX or just sharpen your skills. Sign up for IBM's > Free Linux Tutorials. Learn everything from the bash shell to sys admin. > Click now! http://ads.osdn.com/?ad_id78&alloc_id371&op=ick > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] expand to molecule (by connectivity)
Michal, This capability is not in PyMOL yet as a selection operator, but if you issue "edit" on a single atom, then the resulting "pkchain" selection will contain that atom and all covalently attached atoms. edit 14/ca color red, pkchain unpick Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of Michal Bozon > Sent: Saturday, December 13, 2003 7:25 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] expand to molecule (by connectivity) > > Dear pymol experts, > > I wonder if there's a simple way how to select a molecule (or expand the > selection to molecule) by connectivity. > I mean the case there if there are more molecules in the object and I want > to select one of them and create a new object from it in order to change > it's properties. > 'Byres' and similar seleciton operators do not work. > > thanks, > > Michal Bozon > > > --- > This SF.net email is sponsored by: SF.net Giveback Program. > Does SourceForge.net help you be more productive? Does it > help you create better code? SHARE THE LOVE, and help us help > YOU! Click Here: http://sourceforge.net/donate/ > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] RE: Stereo on G4 Laptop?
Doug, Yes, I just confirmed that PyMOL on a Mac 17" G4 PowerBook can drive stereo using the StereoGraphics SVGA display adapter with an external monitor. I would expect any G4 PowerBook to be able to do this. The command line way to launch in stereo mode is given below. /Applications/PyMOL.app/Contents/MacOS/PyMOL -BGS Alternative, you could simply click on the "PyMOL Stereo" icon in the Demos folder. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > Sent: Monday, December 15, 2003 11:16 AM > To: war...@delanoscientific.com > Subject: Stereo on G4 Laptop? > > Dear Warren, > > I am a crystallographer from the university of oregon. I am > considering purchasing a G4 laptop and was wondering if you had used > the crystal eyes from Stereographics on a vga monitor plugged into one > of these laptops. > > Thanks, > Doug
RE: [PyMOL] About licensing
K.K. Liang, Thanks for your comments. Like a handful of other modern software companies, DeLano Scientific is pursuing a business model that can work to promote Open-Source software as well as business success. As far as I know, we are the only company with this goal in the molecular modeling and visualization field, but there are others in the scientific arena (e.g. Enthought, Inc.). Just to be clear, sponsorship is an option, not a requirement. You can use the Open-Source versions of the code without cost. However, if you do sponsor the project through purchase of a perpetual license and a renewable one-year subscription, then you get the added benefits of support, upgrades, improving documentation, and access to Incentive Products such as MacPyMOL (Jan 2004), for the duration of the subscription. DeLano Scientific LLC will provide a receipt for your purchase that can be used for reimbursement, and which shows you the duration of your subscription. Or if you'd like, you can have your university directly purchase PyMOL from us using a purchase order on your behalf. Please direct any further business questions to me directly (war...@delanoscientific.com) since the user's list isn't really the right place for these discussions. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of Kuo-Kan Liang > Sent: Saturday, December 13, 2003 4:53 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] About licensing > > Dear Dr. DeLano and all PyMolers, > > In April I am moving to a group in Kyoto University working on a new MD > package. > I will be in charge of much of the design of the system. > In terms of visualization, my first pick is PyMol. > > I checked the PyMol webpage which I did not looked at carefully for a > long time. > (I was denied of protein researches in the past year) > I am very glad to see that we can now call PyMol from other Python > programs, > among other impressive improvements. > It is also important to find that now PyMol has a licensing system. > I really hope that this step will make PyMol a continually progressing > program, > in an even faster pace than before. That will bring us more wonders. > Therefore, I promise that in April I will ask the new lab to spend $500 > for PyMol. > (This new MD package is supposed to be distributed over research > institutes in Japan > in several years. I hope that PyMol will dominate Japan with us, too.) > > But what I did not find on the webpage is, whether DeLano company can > issue > formal receipt for the lab to get refund? > Maybe it's a stupid question. There must be one. > This is going to be the second year for me to stay in Japan. > I have not been dealing with refunding, not to mention refunding after > buying > something through network from a company in the US. > Please give me some ideas. > > Regards, > K.K.Liang > > > > > > --- > This SF.net email is sponsored by: SF.net Giveback Program. > Does SourceForge.net help you be more productive? Does it > help you create better code? SHARE THE LOVE, and help us help > YOU! Click Here: http://sourceforge.net/donate/ > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] assign secondary structure?
Michael, Unfortunately PYMOL/dss doesn't generate quite enough information to recreate PDB SHEET and HELIX records. PyMOL (like other programs) simplifies the secondary structure concept down to a per-residue property. There is no such thing as a sheet or helix in PYMOL, but merely sets of proximal residues with a secondary structure property (ss) of 'H' or 'S'. load object-name.pdb hide show cartoon dss object-name Should be sufficient to get you a secondary structure representation for any protein. States represent multiple conformations -- you shouldn't need to worry about them Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of Michael Bovee > Sent: Thursday, December 11, 2003 1:38 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] assign secondary structure? > > Hi, > I have a 'raw' pdb file of atom coordinates only, and I'm hoping to use > the dss command in pymol to get helix and strand designations that I > can paste back into the header space of the pdb so that I can model > fancy helices and strands and so forth to get a nice picture in pymol. > Then I can superpose features with homologous proteins for which this > header info is available. I just didnt want to modify or create this > header info 'by hand' if I didn't have to... > > But, I can't get dss to work in pymol (even the refman warns that this > algorithm has not been rigorously validated). The refman says USAGE is > dss selection, state > Does this mean I need to first make a selection that encompasses some > part (or whole) of the molecule, or should this work on the entire pdb? > I don't know what 'states' are so I just opted for '0' which is > supposed to mean 'all states'. > > Thanks, > --Michael Bovee > > > > --- > This SF.net email is sponsored by: SF.net Giveback Program. > Does SourceForge.net help you be more productive? Does it > help you create better code? SHARE THE LOVE, and help us help > YOU! Click Here: http://sourceforge.net/donate/ > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Trying to plug APBS into PyMOL for electrostatics (not working yet)
Michael, Impressive! I think you're one of the few people to delve into PyMOL's source like this. Obviously I'd be the best person to look at your code, but I'm crunched right now getting ready for this upcoming trip. Also, if the code is GPL-contaminated, then it can't be useful in the main version, but perhaps we can rewrite this cleanly later on. I can probably help you in January. What you've written sounds right... One thing I'd suggest for debugging in the meantime is that you use the isomesh or isosurface routines to explore what data is ending up in the Map, before trying to use the color ramps. There may also be some code in the chempy brick stuff which could serve as an example for populating the list. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020
[PyMOL] DeLano Scientific Downtime (Dec. 22-Jan 7)
PyMOL Sponsors and Users, Please be advised that due to vacations, travel, and participation in the CCP4 study weekend, DeLano Scientific LLC will be officially closed from December 21st through January 7th. Sporadic email communication may be possible before Dec. 24th and after Jan. 3rd, but essentially all other business functions (phone, fax, quotes, invoices, receipts, etc.) will remain unavailable until after the 7th. During the break, please direct all PyMOL questions to the mailing list where your peers may be able to assist you. Also, please be sure to have yourself a wonderful holiday season and a happy new year! If there are any budgets out there with "end of year" money that simply must be spent, DeLano Scientific would be glad to process your PyMOL purchases and support subscription renewals prior to the 19th of December. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020
RE: [PyMOL] electron density settings
Robert, If you're using version 0.93 or greater, set mesh_width, value will adjust the mesh thickness in units of pixels. Something in the range of 1.5-2.5 usually works best. set mesh_width,2.0 ray If you're using an older version, you'll need to set mesh_radius instead, which is in angstrom units. To display the density around a ligand, create a mesh using the "carve" option. load map.ccp4 load protein.pdb load ligand.pdb isomesh m1, map, 1.0, ligand, carve=2.1 Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of Robert > Sent: Wednesday, December 10, 2003 2:55 PM > To: 'Warren L. DeLano' > Cc: pymol-users@lists.sourceforge.net > Subject: [PyMOL] electron density settings > > Hi there, > > 1. How can I reduce the density-map line thickness in the ray-traced > image? > 2. Is there a way to just display the density around a ligand > > many thanks > robert > > Robert Schwarzenbacher, PhD > The Joint Center for Structural Genomics > phone: 858 822 3637 > > > > > > --- > This SF.net email is sponsored by: SF.net Giveback Program. > Does SourceForge.net help you be more productive? Does it > help you create better code? SHARE THE LOVE, and help us help > YOU! Click Here: http://sourceforge.net/donate/ > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Unable to read Gamess-US output
Jerome, Generally speaking, PyMOL doesnt read any GAMESS formats, although there is some code in the chempy modules which at one time could submit and retrieve output from a few simple GAMESS-US calculations. My advice would be to find another tool better suited for Quantum chemistry applications. But if you still want to use PyMOL, then you'll need to convert your files into something like .mol or .pdb... Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of Jerome Levesque > Sent: Friday, December 05, 2003 8:37 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Unable to read Gamess-US output > > Hello, > > I am using GAMESS-US (not PC-GAMESS) on Linux to model very small > molecules. When I try to load a GAMESS ".dat" file into PyMOL, it does > not complain at all, but does not show anything either. There isn't even > a new object appearing in the right part of the PyMOL visualization > window. > > I find this behaviour somewhat strange, since it seems to be specific to > my .dat files and do not even occur when I try to load silly files, such > as jpegs for example. Even in such silly cases, a new object will > appears in the list (but not for my GAMESS ".dat" files!) > > Thanks in advance for any help, > > Jérôme Levesque > > -- > Jérôme Levesque, Ph.D. student > > Femtosecond Research Program > National Research Council > 100 Sussex drive, room 2044 > Ottawa, ON > K1A 0R6 > Canada > > tel.: 613-998-9468 > fax.: 613-991-3437 > > > > > --- > This SF.net email is sponsored by: SF.net Giveback Program. > Does SourceForge.net help you be more productive? Does it > help you create better code? SHARE THE LOVE, and help us help > YOU! Click Here: http://sourceforge.net/donate/ > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] residues deviate from protein secondary catoon representation
(becoming an FAQ) For starters, set cartoon_smooth_loops, off set cartoon_flat_sheets, off If that doesn't meet your needs, then you'll need to split your object into separate objects to get the desired effect of mixing smoothed and non-smoothed cartoons. Thankfully, the next version will provide an easier workaround for this... Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of Yunfeng Hu > Sent: Tuesday, December 02, 2003 1:57 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] residues deviate from protein secondary catoon > representation > > Dear pymol users, > > I am trying to show some residues in sticks while the whole protein is in > cartton representation. However I find that some residues do not attach > to the cartoon at all. I understand that the secondary cartoon is an > approximation along the backbone. Is there a way that I can show at least > those residues are anchored in the cartoon? Thanks. > > Yunfeng > > > > > --- > This SF.net email is sponsored by: SF.net Giveback Program. > Does SourceForge.net help you be more productive? Does it > help you create better code? SHARE THE LOVE, and help us help > YOU! Click Here: http://sourceforge.net/donate/ > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Viewing homotetramers with PyMol
Rene, The problem is that each biological unit copy in the PDB is handled as a separate molecular state (i.e. a movie), which then become distinct states in PyMOL. Hit play to see what I mean. To solve this, the most recent versions of PyMOL can split multi-state objects into multiple single-state objects automatically: load 1f41_tetra.pdb split_states 1f41_tetra dele 1f41_tetra With older versions, you'll need to create the new objects manually load 1f41_tetra.pdb create 1f41_tetra_1, 1f41_tetra, source_state=1, target_state=1 create 1f41_tetra_2, 1f41_tetra, source_state=2, target_state=1 dele 1f41_tetra Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of René Wuttke > Sent: Tuesday, December 02, 2003 1:08 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Viewing homotetramers with PyMol > > Hi everyone, > > I am quite new to PyMol and structural biology as well, since I am > still a student. I installed PyMol via Fink on my iBook running Panther > 10.3.1. I want to view the homotetramer of the TTR-protein. I got it > from the PDB (PDB-id: 1f41). The asymmetric unit is a dimer. But the > assumed biological molecule is the tetramer. One can download the > coordinates of this molecule. But when I try to load it in Pymol, only > the dimer shows up. I am quite sure that this file should contain the > right coordinates, because the "origin of rotation" differs between the > tetramer file and the dimer file. How can display the other dimer? This > is necessary in particular, because i am supposed to examine the loops > which mediates the dimer-dimer-interaction. Do you want me to send the > coordinates file to the list? > > Thanks in advance and please apologize my bad english, > René Wuttke > > > --- > This SF.net email is sponsored by: SF.net Giveback Program. > Does SourceForge.net help you be more productive? Does it > help you create better code? SHARE THE LOVE, and help us help > YOU! Click Here: http://sourceforge.net/donate/ > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] Clarification on "A Few Good MacPyMOL OS X Beta Testers"
Open-Source PyMOL foundation, it will continue to evolve and improve in synchronization with the cross-platform open-source version. The beta test remains open through January for those who meet the six qualifications. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020
RE: [PyMOL] cannot 'fit' a particular pdb file
Michael, Try align... Fit only works when all of the atom identifiers match. Align matches atoms through a 1D alignment and then performs some optimization: align TtHisRSca, EcHRSadeca align SaHRSca, EcHRSadeca Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of Michael Bovee > Sent: Tuesday, December 02, 2003 11:17 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] cannot 'fit' a particular pdb file > > Hi, > I have loaded 3 pdb files of homologous forms of an enzyme. The 'fit' > command works for superimposing/aligning two of them, but the third > file always gives a No Atoms Selected error. Is there something in the > pdb file I can fix? As a general rule now, I Hide Everything at first > and then Show Lines as I begin with a new PyMOL session. I can see all > three molecules, just can't align the third one (EcHRSade) with the > first two (TtHisRS and SaHRS). > > PyMOL>fit TtHisRS, SaHRS > Executive: RMS =4.222 (718 to 718 atoms) > > PyMOL>fit TtHisRS, EcHRSade > ExecutiveRMS-Error: No atoms selected. > PyMOL>fit EcHRSade, TtHisRS > ExecutiveRMS-Error: No atoms selected. > PyMOL>fit EcHRSade, SaHRS > ExecutiveRMS-Error: No atoms selected. > > Thanks, > --Michael > > > > --- > This SF.net email is sponsored by: SF.net Giveback Program. > Does SourceForge.net help you be more productive? Does it > help you create better code? SHARE THE LOVE, and help us help > YOU! Click Here: http://sourceforge.net/donate/ > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
FW: [PyMOL] detecting the existence of a selection
(repost: the mailing list was down yesterday afternoon and this message
never made it onto the list)
-Original Message-
From: Warren L. DeLano [mailto:war...@delanoscientific.com]
Sent: Monday, December 01, 2003 3:21 PM
To: 'Tina Li'; 'pymol-users@lists.sourceforge.net'
Subject: RE: [PyMOL] detecting the existence of a selection
Tina,
Use the Python "in" operator
selection-name in cmd.get_names("selections")
PyMOL>print "foo" in cmd.get_names("selections")
False
PyMOL>select foo, all
Selector: selection "foo" defined with 1631 atoms.
PyMOL>print "foo" in cmd.get_names("selections")
True
Cheers,
Warren
--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
> -Original Message-
> From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
> ad...@lists.sourceforge.net] On Behalf Of Tina Li
> Sent: Monday, December 01, 2003 11:50 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] detecting the existence of a selection
>
> Hello,
>
> I wonder if there is a quick and simple way of detecting whether a
> selection
> exists without triggering any errors. e.g. to check if there are
currently
> any
> atoms picked (and collect the residue IDs if there is any), I do:
>
> cmd.iterate("(lb)","stored.list.append((resi))")
>
> if no atoms were picked, I would see the alarming error messages:
>
> Selector-Error: Unknown keyword or selection.
> Selector-Error: Malformed selection.
> ( ( lb<--
>
> Is it possible to suppress them and still get the result?
>
> Thanks in advance!
>
> Tina
>
>
>
>
> ---
> This SF.net email is sponsored by: SF.net Giveback Program.
> Does SourceForge.net help you be more productive? Does it
> help you create better code? SHARE THE LOVE, and help us help
> YOU! Click Here: http://sourceforge.net/donate/
> ___
> PyMOL-users mailing list
> PyMOL-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Object orientation matrices
Laurence, Sort of. Right now PyMOL doesn't fully support translations of individual objects by independent matrices, but you can translate their representations by a matrix for animation purposes using "translate" and "rotate" with the object argument. However, you can cleanly transform the atoms in an object. See print cmd.transform_selection.__doc__ for details on the matrix used for that. The object matrix system is just about due for an overhaul -- we need more flexibility than is currently provided... Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of Laurence Pearl > Sent: Tuesday, December 02, 2003 5:47 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Object orientation matrices > > Is there any way of accessing the matrices that define the orientation > and position of an individual object relative to the world in PyMol in > the same way that get_view and set_view do for the overall view matrix ? > > > -- >Laurence H. Pearl > >Section of Structural Biology, Institute of Cancer Research >Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK > >Phone +44-207-970 6045 : Secretary +44-207-970 6046 >FAX +44-207-970 6051 : E-Mail laurence.pe...@icr.ac.uk > > -- >" Live Simply and do Serious Things .. " - Dorothy Crowfoot Hodgkin > > -- > > > --- > This SF.net email is sponsored by: SF.net Giveback Program. > Does SourceForge.net help you be more productive? Does it > help you create better code? SHARE THE LOVE, and help us help > YOU! Click Here: http://sourceforge.net/donate/ > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] More on "A Few Good MacPyMOL OS X Beta Testers"
Because MacPyMOL is built on the Open-Source PyMOL foundation, it will continue to evolve and improve in synchronization with the cross-platform open-source version. The beta test remains open through January for those who meet the six qualifications. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020
RE: [PyMOL] detecting the existence of a selection
Tina,
Use the Python "in" operator
selection-name in cmd.get_names("selections")
PyMOL>print "foo" in cmd.get_names("selections")
False
PyMOL>select foo, all
Selector: selection "foo" defined with 1631 atoms.
PyMOL>print "foo" in cmd.get_names("selections")
True
Cheers,
Warren
--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
> -Original Message-
> From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
> ad...@lists.sourceforge.net] On Behalf Of Tina Li
> Sent: Monday, December 01, 2003 11:50 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] detecting the existence of a selection
>
> Hello,
>
> I wonder if there is a quick and simple way of detecting whether a
> selection
> exists without triggering any errors. e.g. to check if there are
currently
> any
> atoms picked (and collect the residue IDs if there is any), I do:
>
> cmd.iterate("(lb)","stored.list.append((resi))")
>
> if no atoms were picked, I would see the alarming error messages:
>
> Selector-Error: Unknown keyword or selection.
> Selector-Error: Malformed selection.
> ( ( lb<--
>
> Is it possible to suppress them and still get the result?
>
> Thanks in advance!
>
> Tina
>
>
>
>
> ---
> This SF.net email is sponsored by: SF.net Giveback Program.
> Does SourceForge.net help you be more productive? Does it
> help you create better code? SHARE THE LOVE, and help us help
> YOU! Click Here: http://sourceforge.net/donate/
> ___
> PyMOL-users mailing list
> PyMOL-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] A Few Good Mac PyMOL OS X Beta Testers
Mac Users: I have something new in the works for OS X/Aqua and need some beta testers for the next couple of months. Specifically, I am looking for users who: 1) have experience with full PyMOL (under Fink, X11, or Windows). 2) are current PyMOL sponsors/subscribers. 3) are running OS X 10.2.8 or 10.3. 4) have QuickTime 6.4 installed. 5) would value a Mac-enhanced PyMOL derivative. 6) don't mind closed-source software. If you meet all of these qualifications, please email me. If you don't, then please sit tight for now -- more information will be forthcoming in January. Thanks, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020
RE: [PyMOL] electron density settings
Igor is right. However, there is a new command in recent versions map_double map-name that will cut the map spacing in half by interpolating a new map via trilinear interpolation. This will generate a map with 2^3 = 8-fold more grid points (and require 8X more RAM!) load map1.ccp4 map_double map1 isomesh mesh1, map1, 1.0 will generate a mesh with half the spacing of the original map. Note that map_double can usually only be used once on a given map before averaging artifacts appear. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of Igor Pechersky > Sent: Tuesday, November 25, 2003 7:23 AM > To: mwilke > Cc: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] electron density settings > > mwilke : > > Does anyone know how to alter the isomesh settings? I'm trying to > prepare > > a figure with pretty electron density and would like to be able to > decrease > > the gap size of the mesh. I found the variables that seem to make sense > > like "mesh_quality" and "min_mesh_spacing", but changing these variables > > doesn't seem to do anything. "mesh_width" and "mesh_radius" only > control > > the thickness of the mesh lines. > > Mark, > you are correct, saying that "mesh_quality" and "min_mesh_spacing" have > nothing with > isomesh. They are used only for surface maps (RepMesh). For map-based > mesh, PyMOL uses > dimension from the density map itself, without "smoothing interpolations". > So, to > increase "visual toughness" of your isomesh, you should just load more > fine-grained > density map... > As a "visualization trick", one might try to play with the set of > isomeshes, based on > the same density map and slightly differentiated by level, like this: > > isomesh mesh1, map1, 1.0 > isomesh mesh2, map1, 1.25 > isomesh mesh3, map1, 1.50 > isomesh mesh4, map1, 1.75 > isomesh mesh5, map1, 2.0 > > and then color them differently. > > > BTW, even with RepMesh you can't decrease gap size (via min_mesh_spacing) > less than > some "hard lower threshold" - roughly, it is equivalent to 80 lines per > maximal > dimension of the surrounding box for the underlying object. > mesh_quality deals rather with the level of icosahedron approximations for > spheres... > > > > --- > This SF.net email is sponsored by: SF.net Giveback Program. > Does SourceForge.net help you be more productive? Does it > help you create better code? SHARE THE LOVE, and help us help > YOU! Click Here: http://sourceforge.net/donate/ > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] dss & ribbon representation
There is one other convenient format: ".pkl", that works like PDB, but
is a Pickled copy of the PyMOL Model Class. The main advantage this has
over .pdb is that it saves and restores extra properties such as
secondary structure code, atom types, van der waals radii, formal and
partial charges, etc.
load myprot.pdb
dss
show cartoon
alter 100-110/, ss='H'
alter 65-67,ss='L'
save myprot.pkl
... quit program, complete your PhD, take a vacation, and come back...
load myprot.pkl
show cartoon
will work.
".pkl" has the additional advantage of being a simple molecular object
useful in straight Python, outside of PyMOL. All you need to do is have
a copy of PyMOL's "chempy" module available in your PYTHONPATH
from chempy import io
model = io.pkl.fromFile("myprot.pkl")
for atom in model.atom:
print atom.name
Cheers,
Warren
--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
> -Original Message-
> From: pymol-users-ad...@lists.sourceforge.net
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
> Igor Pechersky
> Sent: Friday, November 14, 2003 3:07 AM
> To: andr...@biochem.utah.edu; Andreas Foerster
> Cc: pymol
> Subject: Re: [PyMOL] dss & ribbon representation
>
>
> Andreas Foerster :
>
> > - The dss algorithm is great, a very quick way to assign secondary
> > structure. Is there a way of conserving the information when saving
> > the pdb?
> There are at least 3 ways to store SS assignments from PyMOL.
> Depends on your needs:
>
> 1. Save PyMOL session (*.pse). Atom properties, including
> "ss", will be restorable by
> PyMOL.
>
> 2. Print SS in "PHD-like" format. So, assuming that unfamous
> 1tii.pdb is loaded
> PyMOL>import pymol
> PyMOL>stored.ss = []
> PyMOL>iterate 1tii//a//ca, stored.ss.append(string.ljust(ss,1))
> PyMOL>print string.join(stored.ss,"")
>
> will print single string like
> LSSLLLHHHLHHLLLSLL
> LLL
> LSSSHLLHHHLLHHHLSSSLLL
> LLLHHHLLLLL
> HLLHHHLL
>
> 3. Wait for Warren to vivify cSetting_save_pdb_ss :)
>
>
> > Sometimes it's nice to edit the assignment.
> I haven't understood your question. You might edit dss
> assignment just by
> PyMOL>alter pk1, ss='S'
>
> Is it sufficient?
>
> -igor
>
>
> ---
> This SF.Net email sponsored by: ApacheCon 2003,
> 16-19 November in Las Vegas. Learn firsthand the latest
> developments in Apache, PHP, Perl, XML, Java, MySQL, WebDAV,
> and more! http://www.apachecon.com/
> ___
> PyMOL-users mailing list
> PyMOL-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
RE: [PyMOL] Reference
http://pymol.sourceforge.net/faq.html#CITE -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Chris Sent: Tuesday, November 11, 2003 1:29 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Reference Hi Warren Could you tell me how I should reference Pymol in papers etc? I've tried finding it one the web and i've not seen it Ta Chris
[PyMOL] RE: Stereo parameters, again
> I still do not understand your stereo parameters: the > stereo_angle should > define the rotation (around the y-axis) between the pictures > for the left and > right eye, whereas the stereo_shift should define whether the > origin or > midpoint of the picture is within the plane of the screen or > in front of or > behind it. However, changing the settings of these parameters lead to > completely unexpected results: setting the stereo_shift to > "0" and the > stereo_angle to "3.0" results in a mono picture with no > separation at all, > whereas setting the stereo_shift to "3.0" and the > stereo_angle to "0" leads > also to a mono picture shifted to the back. So, could you > please check this > and maybe explain it again to me? After looking back at the code, I realize that these parameters are perhaps misnamed. These are not the rotations of the objective, but rather parameters input into the stereo equations. stereo_shift is the separation between the two cameras observing the image, expressed as a % of the distance from the objective. stereo_angle is a scaling factor applied to the natural angular difference which would occur between two eyes at that distance, both looking at the objective. Generally speaking stereo_shift is the main depth control parameter, and stereo_angle should remain close to 2 in order to generate "correct" stereo geometry. However, adjusting stereo_angle can reduce ghosting and change the apparent Z location of the objective. Detting stereo_shift to zero makes you a Cyclops (you're basically telling PyMOL that your eyes are superimposed). The defaults are: PyMOL>get stereo_shift, get: stereo_shift = 2.0 PyMOL>get stereo_angle, get: stereo_angle = 2.1 which are tuned to minimize CrystalEyes "ghosting" in the foreground. The actual translation(+/-) and rotation(+/-) of the camera at "distance" are: translation = distance * (stereo_shift/100) rotation = (stereo_angle/2) * (arctan(stereo_shift/100)) (default = +/- 1.2 deg) If you want a stronger stereo effect, set stereo_shift to 3, 4, or 5 (resulting in rotations of 1.8, 2.4, and 3.0 degrees, respectively). Cheers, Warren
RE: [PyMOL] surface area calculation
Close, but it depends on whether you want the surface area of the
residues alone, or in the context of the molecule.
load protein.pdb
get_area resn arg
will be less than
create arg_object, resn arg
get_area arg_object
This is because the first example will give you only the exposed area of
the arginines in the presence of the other atoms, whereas the second
gives the area of the arginines in isolation.
Cheers,
Warren
--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Kaushik
Raha
Sent: Wednesday, November 12, 2003 2:50 PM
To: Harp, Joel M
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] surface area calculation
To calculate surface area for a defined object from the PyMOL command
line type:
print cmd.get_area("obj")
where obj is the name of your object.
for arginines:
create ARG, resn ARG
print cmd.get_area("ARG")
Kaushik.
On Wednesday, November 12, 2003, at 05:10 PM, Harp, Joel M wrote:
Is it possible to get pymol to calculate surface area for a defined
object? For instance, can it calculate surface area occupied by
arginines.
Thanks,
Joel
Joel M. Harp
Vanderbilt University
RE: [PyMOL] surface area calculation
Joel, Yes, PyMOL does have this capability, but it is immature and not routinely validated. The basic concepts are: 1) "get_area selection" command will return the effective surface area of the dots that you would see from "show dots, selection". This is a discrete approximation -- not an exact calculation. 2) you can use the "dot_solvent" setting to control whether you get solvent surface area or a molecular surface area. 1=solvent, 0=molecular 3) the accuracy of the measurement depends on the density of dots, which is controlled by the "dot_density" setting (1-4). 4) the solvent radius is controlled by the "solvent_radius" setting (default 1.4). For example: PyMOL> load $TUT/1hpv.pdb PyMOL> show dots, resn arg PyMOL> get_area resn arg cmd.get_area: 1147.956 Angstroms^2. PyMOL>set dot_solvent, on PyMOL>get_area resn arg cmd.get_area: 673.084 Angstroms^2. PyMOL>set dot_density, 3 PyMOL>get_area resn arg cmd.get_area: 674.157 Angstroms^2. PyMOL>set dot_density, 4 PyMOL>get_area resn arg cmd.get_area: 672.056 Angstroms^2. PyMOL>get_area all cmd.get_area: 13837.804 Angstroms^2. This code has not been recently validated (though I did check it a couple years back), so I would suggest that people perform some kind of independent check on their system before trusting the results. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Harp, Joel M Sent: Wednesday, November 12, 2003 2:10 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] surface area calculation Is it possible to get pymol to calculate surface area for a defined object? For instance, can it calculate surface area occupied by arginines. Thanks, Joel Joel M. Harp Vanderbilt University
RE: [PyMOL] Re:labeling atoms in GUI
Eric,
PyMOL will source startup files in your home directory -- just
put your commands in there:
On Mac/Unix:
$HOME/.pymolrc (for PyMOL commands)
$HOME/.pymolrc.py (for Python code)
On Windows:
%HOMEPATH%\pymolrc(for PyMOL commands)
%HOMEPATH%\pymorc.py (for Python code)
To show distances, use the distance wizard:
wizard distance
then ctrl-middle-clock on two atoms in succession.
Cheers,
Warren
--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
> -Original Message-
> From: pymol-users-ad...@lists.sourceforge.net
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Eric Hu
> Sent: Wednesday, November 12, 2003 11:22 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] Re:labeling atoms in GUI
>
>
> Warren, I want to be able to use those useful
> definations every time I load pymol. I wonder how to
> edit the general startup script pymol in order to do
> that? By the way, I also want pymol to show distance
> when I click two atoms. Thank you.
>
> Eric
>
>
> > Quoting "Warren L. DeLano"
> > :
> >
> > > Richard,
> > >
> > > It's not GUI, but you could simply bind a function
> > key such as F1 to
> > > that command:
> > >
> > > cmd.set_key('F1',lambda :cmd.label("(lb)",'"%s %s
> > > %s"%(name,resn,resi)'))
> > >
> > > You might then want to bind 'F2' to something
> > which hides all labels.
> > >
> > > cmd.set_key('F2',cmd.label)
> > >
> > > Cheers,
> > > Warren
> > >
> > > --
> > > mailto:war...@delanoscientific.com
> > > Warren L. DeLano, Ph.D.
> > > Principal Scientist
> > > DeLano Scientific LLC
> > > Voice (650)-346-1154
> > > Fax (650)-593-4020
> > >
> > > > -Original Message-
> > > > From: pymol-users-ad...@lists.sourceforge.net
> > > > [mailto:pymol-users-ad...@lists.sourceforge.net]
> > On Behalf Of
> > > > rbax...@uchicago.edu
> > > > Sent: Wednesday, October 29, 2003 5:14 PM
> > > > To: pymol-users@lists.sourceforge.net
> > > > Subject: [PyMOL] labeling atoms in GUI
> > > >
> > > >
> > > > Dear All,
> > > >
> > > > I want to look at my structure in PyMOL and,
> > having centered
> > > > on something defined by my selection script,
> > pick atoms
> > > > nearby and see what residues they belong to.
> > That is, I want
> > > > to pick select an atom with the mouse and have
> > its name,
> > > > residue name and residue number appear on
> > screen, like it does in O.
> > > >
> > > > I figured out that [Ctrl] + Left-Mouse-Button
> > selects the
> > > > atom as "lb", and that the command 'label
> > (lb),"%s %s %s" %
> > > > (name,resn,resi)' gives me the label I want. Now
> > how could I
> > > > get something like that to appear as a menu
> > function in the
> > > > GUI so I don't have type it in all the time? Can
> > it be a
> > > > command executed as part of my startup script?
> > > >
> > > > Maybe some function like this already exists,
> > otherwise I
> > > > think it is a very useful thing.
> > > >
> > > > regards,
> > > >
> > > > Richard Baxter
> >
> >
>
>
> __
> Do you Yahoo!?
> Protect your identity with Yahoo! Mail AddressGuard
> http://antispam.yahoo.com/whatsnewfree
>
>
>
> ---
> This SF.Net email sponsored by: ApacheCon 2003,
> 16-19 November in Las Vegas. Learn firsthand the latest
> developments in Apache, PHP, Perl, XML, Java, MySQL, WebDAV,
> and more! http://www.apachecon.com/
> ___
> PyMOL-users mailing list
> PyMOL-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/p> ymol-users
>
RE: [PyMOL] homologous alignments?
Michael, Welcome to PyMOL! I don't think PyMOL is a replacement for SPDV -- the feature sets are distinct, and you should be able to use both together. Yes, I think "align" is what you want. After... load x.pdb load y.pdb This would do an all-matched-atoms alignment: align x, y And this would do a CA-only alignment: align xca, yca To see which atoms are aligned, add and object name: align xca, yca, object=alignment Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Michael Bovee Sent: Friday, November 07, 2003 3:31 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] homologous alignments? Hi there, I'm switching to pymol from swiss pdb viewer because I simply needed better quality final images, but one of the coolest features of spdbv was the 'magic fit' where a single mouse click would superpose overall alignment of, say, the same protein from two different bacterial organisms (obviously high homology situation) opened in two different 'layers'. In pymol, it looks like the 'align' command is what I want (don't know if pymol uses the layers analogy), but I'm having difficulty understanding if I am to use parentheses and brackets as shown in the refman.pdf, and the use of this punctuation style doesnt seem to be defined in the pdf. USAGE align (source), (target) [,cutoff [,cycles [,gap [,extend \ [,skip [,object [,matrix [, quiet (This style of outlining command formats is probably old hat to programmers, but that's not me.) So, is this the right command for superposition alignments in pymol, after loading pdb files x and y, for instance? Sorry for such a basic question; its getting late and I'm floundering :0) Thank you, --Michael
[PyMOL] RE: X11 1.0 instability
Jack, I posted some instructions onto the list a while back, but it's pretty simple: # load the PHI map and model load phimap.phi load prot.pdb # show a surface show surface, prot # create a color ramp based on the potential ramp_new ramp, phimap # now apply that color_ramp to the protein surface set surface_color, ramp, prot Now you can ctrl-middle click and drag on the ramp to change the range. You can also specify the red,white, & blue points precisely: ramp_new ramp, phimap, [-10.0, 0.0, 10.0] Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > > Warren, >Thanks for the information. Oh, one other thing. We are > trying to use the new .phi map support in the MacOS X G4 > demo version of pymol and it isn't obvious at all how this > should be done. Are there any instructions or tutorial files > on how to display electrostatic surfaces generated by GRASP in pymol? > Jack
RE: [PyMOL] aa residues disconnected from 'fancy helices'?
Michael, That's because sheet's aren't flat -- cartoons aren't reality. set cartoon_flat_sheets, off set cartoon_smooth_loops, off In order to force the cartoons to follow the true CA trace. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Michael Bovee > Sent: Friday, November 07, 2003 8:50 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] aa residues disconnected from 'fancy helices'? > > > Hi all, > I'm just starting to try out PyMOL (fink package 0.90-2, running > through Apple's X11beta2, on a Lombard G3PB, MacOS 10.2.4). > Its much easier to learn that I thought it would be! Well > done Warren, > and codevelopers! One puzzling thing I've noticed: when I build a > model of my protein of interest using 'set > cartoon_fancy_helices,1' and > then show sidechains for several key catalytic residues, I find that > the amino acids that reside along beta sheet or alpha helix regions > appear properly connected to the alpha carbon backbone > representation, > but sidechains of amino acids that reside on 'strand' regions appear > to float in midair and do not connect to the strand backbone. Anyone > else seen this behaviour? > > Thanks! > --Michael Bovee > University of Vermont > > > > --- > This SF.net email is sponsored by: SF.net Giveback Program. > Does SourceForge.net help you be more productive? Does it > help you create better code? SHARE THE LOVE, and help us help > YOU! Click Here: http://sourceforge.net/donate/ > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/p> ymol-users >
RE: [PyMOL] DSSP
Ben, Great response! Indeed, the PDB's limited capacity for secondary structure does indeed represent this as one single helix, not two. > +/- 15 degrees is pretty difficult to see - so I think that DSSPs > +assignment > in this case, while liberal, is certainly acceptable. I hardly think it acceptable that one residue with 3-10 PHI/PSI constitutes a helix when you have so many other telltale characteristics of a Type II' beta turn, including a Glycine in position i+1 and all deviations within 22 deg. of ideal turn, as well as four planer CA atoms (actually five, C-alphas 98-102 are all nearly planer). Some turns do look like helices, but not this one -- not even close. > Great example of where DSSP fails, but perhaps a bit contrived. I don't think this example is contrived. One of the many tests I put PYMOL through regularly is to render the entire PDB over several hours, so I literally see thousands of structures on a routine basis. Such "objective but bogus" assignments are far more common than one would like to think. It is a real problem. > The reason that consistency is of paramount importance in assigning secondary structure > is so that different scientists can talk about the same protein in context. > If everyone uses the same definition of secondary structure - "helix 1" is always "helix 1". Good point, but I disagree. In acknowledging the subjective and relative nature of assignments, I think it is more reasonable to ask scientists to define their terms rather than to perpetuate broken conventions. Given how evolution, crystallization, and protein processing work, even with DSSP, Helix 3 can easily be Helix 2 or 4 in another structure of the identical or a related protein, so the savings in confusion is slight. Also, keep in mind that all numbering is relative and increasingly problematic as more and more homologous structures are solved, and explicit conceptual labels are far more general than numeric ones. But finally, do understand that I would provide DSSP as an option if it were possible to do so, but frankly, it's not. The paper does not enable an exact reimplementation, and the owners of DSSP, instead of making DSSP source code usable and redistributable as an open standard, have decided to use the software for revenue generation (presumed modest at best). It is exatly this kind of short-sighted restrictiveness that PyMOL was created to combat. We must end this dismal pattern of scientists developing research software that is so drastically and artificially limited by licensing terms that it has little or no ability to enable future scientific advances. Computer-dependent scientific fields like structural biology and computational chemistry will be handicapped until we can all effectively access and improve upon existing software systems. That will not happen until research scientists and academic institutions stop viewing such software programs as potentially lucrative intellectual properties and start viewing them as the critical building blocks that will enable future breakthroughs if and when they become widely shared. Imagine... What would happen if all scientists stopped publishing their discoveries and kept all information within one lab or institution? Scientific progress would come to a halt. That's basically what has occurred with so much scientific software over the last 20 years. Don't get me wrong -- some great code has been written -- and some of that code has been shared without cost to some or for a low fee to others. However, most of that code has almost never been shared in such a way as to enable extension, modification, and redistribution. As a result, we are not making much cumulative progress. Software programs resemble ideas: they must be shared, questioned, altered, and refined in order for lasting progress to occur. Otherwise they stagnate just like old ways of thinking. DSSP (circa 1983) is a great example of how many computer-dependent sciences remain trapped in the 1980s. Whether it works better than PyMOL or not is almost beside the point. It is simply not an appropriate standard for us to be using today in this age of open standards, open source, and composite systems. We can and should do better than this. My hope is that if PyMOL and enough similar projects are successful, that governments, companies, and funding agencies will begin to back these kinds of efforts wholeheartedly with money and policies, and thus drive rapid progress and widespread benefits throughout the sciences. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: Ben Hitz [mailto:bh...@exelixis.com] > Sent: Monday, November 03, 2003 11:0
RE: [PyMOL] DSSP
Ben, Granted -- and there are certain times when it makes sense for everyone to be "wrong" in order to be consistent. But is this one such case? I think not. If DSSP "helices" aren't actually helices, then of what use is the standard? Neither the resulting statistics nor the cartoon figures will be correct. I've put up one particularly egregious DSSP example on the web at http://www.pymol.org/not_helix for inspection. If you are comfortable with obvious turn regions (such as this one) being assigned as helix, then by all means, go right ahead and continue using DSSP via rTools or the PDB. But for me, I am not going to lose sleep over deviating from an existing standard in PyMOL. As I said before, the DSSP paper wasn't even written in such a way as to enable exact reproduction of their research other than by running their proprietary (1000 EURO) software program or by analyzing their source code. PyMOL's new "dss" algorithm is nowhere near validated enough to become a standard, but I do think that if we are going to agree upon a standard for secondary structure assignment, that the standard should reflect common notions of secondary structure, be exactly described, be reproducible, and be available in an open-source reference implementation. Does DSSP meet these criteria? No, but STRIDE might (if one could find it), and "dss" probably could in time. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Ben Hitz > Sent: Monday, November 03, 2003 8:28 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] DSSP > > > Warren - > The advantage of using DSSP over another heuristic method, is > that it is a standard. A DSSP helix is a DSSP helix > everywhere, even if a crystallographer might extend the end a bit. > > Ben > -- > Ben HitzExelixis > Computational Biology and Informatics > bh...@exelixis.com 650-837-8137 > > > > --- > This SF.net email is sponsored by: SF.net Giveback Program. > Does SourceForge.net help you be more productive? Does it > help you create better code? SHARE THE LOVE, and help us help > YOU! Click Here: http://sourceforge.net/donate/ > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/p> ymol-users >
RE: [PyMOL] a couple of newbie questions
> > Hello all. > I am relatively new to pymol, so please excuse me if > these questions > are too simple for the list as a whole. I am running 0.90 on a Linux > system by way of introduction. > > 1) What is the easiest way to select one molecule out of > several on the > screen and translate it independently from everything else? I try > selecting it. but moving the mouse while holding the mov button still > translates everything. Select "3 Button Editing Mode" from the mouse menu (or click on the mouse matrix, or simply type "edit_mode"). Ctrl-middle click on one atom in the molecule you wish to translate. A white ball should appear on that atom. Then shift-middle-click on that same atom to translate the molecule, or shift-left-click to rotate it. (If you click on other atoms in the molecule, only that fragment, relative to the ball will be translated) When done, click the Unpick button, or type "unpick", or ctrl-middle click away from any atoms to clear the picked selection. > 2) Is there an easy way to superimpose many molecules > independently? I > know that I can do individual pairwise alignments, but that > seems like a > good way to let more errors creep into the process. Not really. "fit" and "align" give you pairwise alignments -- there isn't any multiple-sequence-alignment capability in PyMOL yet. > 3) Is there an automated way to take HET groups in a > structure read from a > PDB file and make independent molecules out of them? The following commands will move the heteroatoms into a separate object: create hetobj, hetatm remove hetatm and not hetobj Cheers, Warren
[PyMOL] PyMOL 0.93 Released
Well, juat a week after 0.92, I'm releasing version 0.93 in order to address various problems with v0.92. First, O/BRIX map reading really does work in 0.93, but note that your O maps need to be in platform-independent BRIX/DSN6 format, and not in the older platform-dependent DSN6 format. (I'll gladly add support for the older DSN6 format if provided with a few test cases). Second, for users with old session files, there was a bug with some 0.86 sessions which has been fixed. Third, I've tweaked the Z-axis behavior of the roving_origin so that one can move a clipping plane in or out without having such a dramatic impact on the origin of rotation. Fourth, on the Mac, I've changed the default PNG save location to insure that files don't by default get written to a "hidden" location inside the application bundle. Fifth, Thanks to everyone who provided such quick feedback on 0.92! Sixth, Thanks to PyMOL users for understanding that software releases aren't always perfect. http://pymol.sourceforge.net/ Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020
RE: [PyMOL] labeling atoms in GUI
Richard,
It's not GUI, but you could simply bind a function key such as F1 to
that command:
cmd.set_key('F1',lambda :cmd.label("(lb)",'"%s %s
%s"%(name,resn,resi)'))
You might then want to bind 'F2' to something which hides all labels.
cmd.set_key('F2',cmd.label)
Cheers,
Warren
--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
> -Original Message-
> From: pymol-users-ad...@lists.sourceforge.net
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
> rbax...@uchicago.edu
> Sent: Wednesday, October 29, 2003 5:14 PM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] labeling atoms in GUI
>
>
> Dear All,
>
> I want to look at my structure in PyMOL and, having centered
> on something defined by my selection script, pick atoms
> nearby and see what residues they belong to. That is, I want
> to pick select an atom with the mouse and have its name,
> residue name and residue number appear on screen, like it does in O.
>
> I figured out that [Ctrl] + Left-Mouse-Button selects the
> atom as "lb", and that the command 'label (lb),"%s %s %s" %
> (name,resn,resi)' gives me the label I want. Now how could I
> get something like that to appear as a menu function in the
> GUI so I don't have type it in all the time? Can it be a
> command executed as part of my startup script?
>
> Maybe some function like this already exists, otherwise I
> think it is a very useful thing.
>
> regards,
>
> Richard Baxter
>
>
> ---
> This SF.net email is sponsored by: SF.net Giveback Program.
> Does SourceForge.net help you be more productive? Does it
> help you create better code? SHARE THE LOVE, and help us help
> YOU! Click Here: http://sourceforge.net/donate/
> ___
> PyMOL-users mailing list
> PyMOL-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/p> ymol-users
>
RE: [PyMOL] secondary structure assignment and surface potential calc/mapping
> 1) Is the secondary structure assignment function in 0.92 > more reliable? Or does the "WARNING: it will make mistakes, > so don't publish anything based on this algorithm!" statement > still apply? Good question! I added that warning message to "util.ss" back when I believed that there was such as thing as "correct" secondary structure assignment and because util.ss had a very primitive H-bonding definition -- distance only. "dss" is something completely new. In creating the new "dss", I took some time to go through the 1983 DSSP paper (Kabsch & Sander) and discovered much to my surprise that the H-bond criterion used by DSSP has very little to do with what crystallographers today think about hydrogen bonds. Did you know that DSSP H-bonds can be as long as 5.2 Angstroms between heavy atoms (Fig 1)? Plus, there is no simple analytic form of their criterion provided which could be implemented by something like PyMOL. Furthermor, and more disturbing, I discovered that DSSP doesn't take backbone torsion geometry into account at all, which finally explained to me why so many DSSP-assigned PDB structures have obviously non-helical regions assigned as HELIX. It's just a naive algorithm, and as far as I'm concerned, H-bonds just aren't the whole story when it comes to secondary structure. Thus, I had to admit that DSSP itself wasn't correct with repect to my personal interpretation of secondary structure. In looking at RasMOL's code it suffers from some of the same problems, and I don't think it actually implements DSSP -- just an approximation to it. So I decided to create my own best-attempt at a secondary structure assignment algorithm based on the spirit of DSSP, but which also takes into account backbone geometry as well as hydrogen-bonding . Like DSSP, PyMOL's hydrogen-bonding criteria is angle-dependent, but the default range is more contemporary (within 3.2 A at 63 deg, 3.6 A at 0 deg). After validating the algorithm manually on ten structures, I sat down and visually compared PDB (DSSP) assignments to PyMOL's "dss" over several hundreds proteins. In general, both programs find the same set of helices and large sheets. However, they differ on the exact start and stop points of these elements. On small sheets or helices, one program may miss something that the other finds. However, divergent regions seemed to involve borderline cases for the most part. "dss" and DSSP seem to do equally well on cut-and-dry idealized systems. So "dss" is reasonably validated, in my view, but I am looking for feedback and specific problem cases when they're found. But speaking as an artist rather than as a scientist, I think "dss" has better aesthetics than DSSP when it comes to cartoon diagrams -- there are simply fewer goofy-looking assignments. Whether it is more scientifically correct or not is an open question. Cartoons themselves are pretty misleading...one might add. By the way, there are a some new settings in PyMOL 0.92 which cover h-bond detection and secondary structure assignment. Here are the most important ones: h_bond_max_angle, 63.0 h_bond_cutoff_center, 3.6 h_bond_cutoff_edge, 3.2 ss_helix_psi_target, -48.0 ss_helix_phi_target, -57.0 ss_strand_psi_target, 124.0 ss_strand_phi_target, -129.0 Basically, if helix or sheet hydrogen bonds are present, and backbone geometries are close to the target values, PyMOL will assign residues as helix or sheet. Otherwise, they're considered loops. The allowable Phi/Psi inclusion/exclusion boxes are adjustable with settings too. For the curious, my algorithm is about 1,000 lines of code and consists of the SelectorAssignSS function found in layer3/Selector.c around line 500. > 2) Is there a 0.92 function to calculate and map surface > potential? This would be useful beyond compare. I wish. Your choices for this are Grasp, MEAD, Delphi, or Zap. Only MEAD is freely available. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Neiditch, Matthew > Sent: Friday, October 31, 2003 12:46 PM > To: 'pymol-users@lists.sourceforge.net' > Subject: [PyMOL] secondary structure assignment and surface > potential calc/mapping > > > Dear List, > > > > Regards, > > Matthew Neiditch > > Postdoc > Hughson Lab > Princeton University > neidi...@molbio.princeton.edu > > > --- > This SF.net email is sponsored by: SF.net Giveback Program. > Does SourceForge.net help you be mo
RE: [PyMOL] secondary structure and movie
Alan,
Unfortunately, secondary structure is currently defined as an
atom rather than a coordinate property. Thus, in order to "animate"
secondary structure, you'll need to run dss automatically for each
state. For example:
mset 1 -5
mdo 1, dss state=1
mdo 2, dss state=2
mdo 3, dss state=3
mdo 4, dss state=4
mdo 5, dss state=5
Of course, Python can automate this:
from pymol import cmd
cmd.mset("1 -%d"%cmd.count_states())
for a in range(1,cmd.count_states()+1): \
cmd.mdo(a,"dss state=%d"%a)
After which...
PyMOL>mdump
Movie: General Purpose Commands:
1: dss state=1
2: dss state=2
3: dss state=3
etc.
Cheers,
Warren
--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
> -Original Message-
> From: pymol-users-ad...@lists.sourceforge.net
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
> Alan Wilter Sousa da Silva
> Sent: Friday, October 31, 2003 3:48 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] secondary structure and movie
>
>
> Hi List!
>
> I did a polyalanine in helix ss.
> I tested:
> 1: dss (ok)
> 2: run stride_ss.py, stride2pymol (ok)
> 3: dssp (from rtools) (???)
>
> Case (1) differs a little bit from (2) in N term.
>
> Case (3) seems not to work. Or, maybe, I do not know how to
> use it. Tried via menu and via command dssp. Got the same
> thing: two new objects
> (helix and sheet) that show nothing!
>
> In a crystallographic protein (HIV protease), (1) gave-me a
> better (and
> faster) result than (2). (3) still gave-me nothing (except
> the ref to
> Dssp, which is properly installed in my box).
> I really want to see dssp working.
>
> Anyway, all that said, what I want to do is loading a
> multi-pdb file and see dss calculating different ss for each
> frame. How could I do it?
>
> Cheers,
> -
> --
> Alan Wilter Sousa da Silva
> --
> B.Sc. - Dep. Física - UFPA
> M.Sc. - Dep. Física - PUC/RJ
> D.Sc. - IBCCF/UFRJ
> Bolsista Pesquisador LAC-INPE
> São José dos Campos (SP), Brasil
> www.lac.inpe.br/~alan
>
>
> ---
> This SF.net email is sponsored by: SF.net Giveback Program.
> Does SourceForge.net help you be more productive? Does it
> help you create better code? SHARE THE LOVE, and help us help
> YOU! Click Here: http://sourceforge.net/donate/
> ___
> PyMOL-users mailing list
> PyMOL-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/p> ymol-users
>
[PyMOL] Bugs in 0.92 (WARNING)
Warning. Several bugs have emerged in the 0.92 release which will cause me to issue a rapid 0.93 update in the next day or so. Thus, if you haven't upgraded yet, you might want to wait a few days for 0.93. The bugs are: 1) problems reading O maps (high frequency) 2) problems saving PNG files (frequecy unknown). 3) problems with version 0.86 session files containing CGO's (rare). Bugs 1 and 3 have been fixed, but bug 2 is still outstanding, and I have been utterly unable to reproduce this problem on any of my test machines. Thus, I would like to get a handle on how widespread the problem is. If you get this email on October 30th (today), and if you have downloaded 0.92, can you take a minute to your ability to save "PNG" files, and let me know what the result is? Please respond only to me mailto:war...@delanoscientific.com in order to avoid flooding the mailing list. Note on the Mac, if you are saving PNG files, you will need to direct them to a suitable location. For example: cd ~ png example.png or png ~/example.png will save the PNG file in your home directory. Otherwise, the files may end up in PyMOL.app/Contents/Resources, which may be practically invisible to you. By the way, if you notice any other serious bugs with the new version, please report them ASAP -- I'd like to fix them in 0.93 if possible. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020
RE: [PyMOL] movies and secondary structure
> I would like to make a movie from a trajectory of 50 frames
> with varying sec structure. Following Warren's advice in a
> previous thread (see below) I load every pdb file into a
> different object *and* state using
> file_list1 = glob("*_first.pdb")
> for file in file_list1:
> cmd.load(file,file,file[:1])
>
> { files are named 1_first.pdb, 2_first.pdb ...}
> However, the object loaded to the first frame also appears in
> the following ones.
Honest -- that's a feature, not a bug : )
set static_singletons, 0
to get the behavior you want...
> dssp calculation with rtools just gives
> the sec structure of the object in the first frame. As a
> workaround I tried to start loading into the 2nd frame and
> not to load anything into the first one. But then the command
> "dssp (2_first.pdb)" gives an error "no atoms selected"
> instead of any calculation.
This is an rtool's specific issue. If you're running version 0.92, you
might try
dss state=2
The results won't be identical to DSSP, but they are usually no worse...
Cheers,
Warren
RE: [PyMOL] How to load O/BRIX map
Huiying, PyMOL will recognize the following extensions for O maps: .o .omap .brix The following will render the entire brick at 1 sigma: load map.o isomesh m1, map, 1 Or if you have a pdb load model.pdb isomesh m1, map, 1, 100/, 8 will give you an 8 A brick around residue 100, etc. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Huiying Li > Sent: Wednesday, October 29, 2003 3:52 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] How to load O/BRIX map > > > > I am wondering how to load the O/BRIX maps into Pymol using > version 0.92. Is there a default file extension, say *.dsn6, > for O map, or need to define the map format with a keyword? > > Thanks for any help. > > -- > Huiying Li, Ph. D > Department of Molecular Biology and Biochemistry > Natural Sciences I, Rm 2443 > University of California at Irvine > Irvine, CA 92697, USA > Tel: 949-824-4322(or -1953); Fax: 949-824-3280 > email: h...@bragg.bio.uci.edu > -- > > > > > --- > This SF.net email is sponsored by: SF.net Giveback Program. > Does SourceForge.net help you be more productive? Does it > help you create better code? SHARE THE LOVE, and help us help > YOU! Click Here: http://sourceforge.net/donate/ > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/p> ymol-users >
RE: [PyMOL] Ray tracing dashed lines
Einat, with version 0.92: set dash_gap,0 set dash_length,1 seems to do the trick for me, raytraced or not. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Einat Sitbon > Sent: Thursday, October 30, 2003 4:29 AM > To: PyMOL-users@lists.sourceforge.net > Subject: [PyMOL] Ray tracing dashed lines > > > > Hello Pymolers, > > I'm using pymol 0.92. I changes some of the dash parameters - > I want the > distance lines to look continuous. This works fine, until I > ray trace the > protein. Then the dash returns to it's default settings... > Any suggestions? > thanks, Einat. > > Einat Sitbon > Department of Molecular Genetics > Weizmann Institute of Science > > _ > The new MSN 8: smart spam protection and 2 months FREE* > http://join.msn.com/?page=features/junkmail > > > > --- > This SF.net email is sponsored by: SF.net Giveback Program. > Does SourceForge.net help you be more productive? Does it > help you create better code? SHARE THE LOVE, and help us help > YOU! Click Here: http://sourceforge.net/donate/ > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/p> ymol-users >
[PyMOL] RE: Writing info to files
> Currently, i
> work on a complexe proteinic which includes two proteins.
> I calculate distances (in a cut-off of 10 Angström in order
> to obtain atoms
> which are within the interface of both molecules) between
> these proteins. Now, i would like to know what atoms belong
> to my selection and write them
> in a file. Could you help me please ?
iterate selection, python-code
For example:
load $PYMOL_DATA/demo/pept.pdb
output= open("output.txt",'w')
iterate (name ca), output.write("%s %s %s %s\n"%(resn,chain,resi,name))
output.close()
Would create "output.txt" containing:
ASP E 1 CA
CYS E 2 CA
ALA E 3 CA
TRP E 4 CA
HIS E 5 CA
LEU E 6 CA
GLY E 7 CA
GLU E 8 CA
LEU E 9 CA
VAL E 10 CA
TRP E 11 CA
CYS E 12 CA
THR E 13 CA
Notice how you can freely intersperse Python and PyMOL commands in PyMOL
command scripts in order to accomplish tasks such as this.
Cheers,
Warren
--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
[PyMOL] PyMOL 0.92 Released
PyMOL version 0.92 can be obtained from http://pymol.sf.net at your convenience. Though this is mostly an "under the hood" improvements release, there are some developments worth noting: Significant changes - New "dss" command assigns secondary structure quickly. - PyMOL can now read O/BRIX maps and some Biosym GRiDs maps. - Improved ray tracing quality and speed. - Long lists of residues in selections are now allowed. Other changes - New "import pymol" support for RPM & Win32 builds that use system Python. [Don't forget to call pymol.finish_launching() afterwards though!] - Improved alpha-channel support for transparent surfaces and backgrounds. - API's "cmd.do" can now take multi-line strings and lists. - New "split_states" command for separating NMR ensembles. - New "cartoon_transparency" setting. - Can display bond valences while in stick mode. - New "stick_ball", "stick_ball_ratio" settings for ball & stick models. - Gaussian map generation from model coordinates. - Can preserve original PDB atom IDs (pdb_retain_ids) & order (retain_order). - Much much faster loading of multi-model PDB files and trajectories. - Deuterium and Calcium handling improved. - New "set_symmetry" & "get_symmetry" commands. - Mutagenesis wizard preserves cartoons. - New "get_pdbstr" API function. - New "movie_loop" setting can disable looping. - Sculpting engine now aware of simple sp3-sp3 torsions. - Finer Z-scaling/movement control. - Upgrade facility for secure enterprises running Windows. PyMOL 0.92 also includes various bugs fixes with cartoons, rendering, CGOs, sessions, endianness, multithreading, raytracing, OS X, and isosurfaces. As always, upgrade with caution. Don't update right before an important presentation, and be sure to test your existing session files. Please report any trouble. Probably the most problematic aspect of the new version will be the increased WYSIWYG behavior of the ray-tracer with respect to line widths. If the bonds in your figure just got thinner, that's the culprit. You can manually adjust the various *_width or *_radius settings to achieve the desired results. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020
RE: [PyMOL] solvent accesible surface
Marcelo, PyMOL doesn't currently do a very good job with a solid solvent accessible surfaced because they aren't smooth like the Connolly surface. But here's what you can do: show spheres set sphere_solvent,1 or hide spheres show mesh set solvent_mesh,1 now add in show surface for a nice combination of the solvent and molecular surfaces. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Marcelo Castilho > Sent: Sunday, October 26, 2003 4:04 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] solvent accesible surface > > > Dear all, > > I am new to pymol and appologyze if his is an "easy > question", anyway here it goes; > > Is it possible to change the surface radius in pymol so that > I can represent the solvente accesible surface ? > > By the way, I am running pymol 0.90 under windows XP > > Thanks, > > Marcelo Castilho > > = > Marcelo Santos Castilho > tel 016 273 98 68 > R; Américo J. Canhoto 223 Apto 23 Bl 2 > São Carlos CEP 13564-350 > e-mail alternativo: casti...@if.sc.usp.br > > __ > Do you Yahoo!? > Exclusive Video Premiere - Britney Spears > http://launch.yahoo.com/promos/britneyspears/ > > > > --- > This SF.net email is sponsored by: The SF.net Donation > Program. Do you like what SourceForge.net is doing for the > Open Source Community? Make a contribution, and help us add > new features and functionality. Click here: > http://sourceforge.net/donate/ > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/p> ymol-users >
RE: [PyMOL] Save session on Mac OSX latest version?
Douglas, Simply: save filename.pse ie save today.pse Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Douglas Freymann > Sent: Sunday, October 26, 2003 2:26 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Save session on Mac OSX latest version? > > > I'm having a hard time finding how to save my session running on a G4 > Powerbook, using PyMOL v0.91. The command, File::Save, is grayed > out, and there's no command File::Save Session as described in the > Users Manual. Is there a trick, or a command line statement? > By the way, is there a way to set a default working directory when > PyMOL starts? > Sorry if these are FAQ's but I didn't find the answers > anywhere. Thanks, Doug > > -- > > Douglas M. Freymann freym...@northwestern.edu > > Molecular Pharmacology & Biological Chemistry > Ward 7-247, Northwestern University > 303 E. Chicago Ave., Chicago, IL 60611 > > (312) 503-1877fax: (312) 503-5349 > > > --- > This SF.net email is sponsored by: The SF.net Donation > Program. Do you like what SourceForge.net is doing for the > Open Source Community? Make a contribution, and help us add > new features and functionality. Click here: > http://sourceforge.net/donate/ > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/p> ymol-users >
[PyMOL] Release in progress...
(in a whisper) I'm still in the process of building binaries, but pioneers are welcome to start downloading 0.92, if your platform is represented. It has been a long time since our last release, so proceed with caution! http://sourceforge.net/project/showfiles.php?group_id=4546 Please bring any problems to my attention ASAP, before the Monday deluge. Warren
RE: [PyMOL] pymol 0.90 on redhat 9.0 - no Tk window
Florian, The main trick is to use an X11/Fink build of PyMOL. Under 10.3, I'm hoping OpenGL performance under X11 will be more that of the native version -- any early returns on this yet? For proficient developers with X11 installed, there another trick you can try: Link source-built PyMOL against native GLUT/OpenGL frameworks while simultaneously linking against X11-based Python/Tkinter/Tcl/Tk. This is what I call the "hybrid" build, which gives native-like OpenGL performance and X11-like user interface compatibility. Stability was a problem with this config though, which is why I've never tried to distribute such a build. Finally, there is a native Tcl/Tk Aqua port which doesn't require X11, and which in theory at least would enable a native-like GUI without having to write Aqua code directly. However I've heard that there are stability problems with this Tcl/Tk, and I'm not sure Python's Tkinter can even work with it. Does anyone out there have experience using Tkinter on OSX without X11? Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of Florian Nachon > Sent: Thursday, October 23, 2003 5:53 AM > To: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] pymol 0.90 on redhat 9.0 - no Tk window > > > On Oct 22, 2003, at 8:42 PM, pymol-users-requ...@lists.sourceforge.net > wrote: > > > Tkinter is a separate Python module that's an interface to the Tcl Tk > > library. It's probably just not installed on your system, but it is > > included in the RH 9 distribution (tkinter-2.2.2-26.i386.rpm) so it > > should > > be easy to find and install. > > By the way, isn't there a trick to get the Tk menu in the native MacOS > X version of Pymol? > > > > --- > This SF.net email is sponsored by: The SF.net Donation Program. > Do you like what SourceForge.net is doing for the Open > Source Community? Make a contribution, and help us add new > features and functionality. Click here: http://sourceforge.net/donate/ > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Using PyMol as a library - no GUI
Truls, That looks to me like a crash where the PyMOL API was somehow called before PyMOL was initialized...how and why this could happen is a mystery to me though -- that's what pymol.finish_launching() is supposed to prevent -- but there may be some flaw in the logic. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: Debian Chooser [mailto:ker...@herocamp.org] On Behalf Of Truls A. > Tangstad > Sent: Friday, October 17, 2003 3:18 PM > To: Warren L. DeLano > Cc: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] Using PyMol as a library - no GUI > > On Fri, Oct 17, 2003 at 09:41:24AM -0700, Warren L. DeLano wrote: > > > Truls A. Tangstad wrote: > > > I'm very interested in using alot of the functionality that PyMol > > > offers programmatically from Python, i.e. without using a GUI at > > > all. The chempy package seems to cover alot of my needs, loading > > > different file formats etc. even though it doesn't seem to be > > > documented. > > > > > > Is it also possible to use the rest of the functionality in PyMol from > > > other Python scripts? Right now, just importing the pymol package > > > seems to force the GUI to open. > > > If you've got PyMOL configured to open on > > > > import pymol > > pymol.finish_launching() > > > > You can suppress the GUI feature and suppress startup output by > > providing command line arguments as follows. Before importing PyMOL, > > set a "pymol_argv" list in the __main__ namespace. PyMOL will interpret > > this as a sys.argv styled list of command line arguments. > > > > import __main__ > > __main__.pymol_argv['pymol','-qc'] > > > > import pymol > > pymol.finish_launching() > > Thanks, seems to work like a charm in scripts after adding the > assignment operator: > __main__.pymol_argv = ['pymol', '-qc'] # adding miss > > Somehow it segfaults when trying the same thing in an interactive > python interpreter though, right after importing pymol. This might be > due to a shoddy install on my part, but I'm including a gdb backtrace: > > #0 0x41d7b21a in SettingGetGlobal_f () from /usr/lib/python2.3/site- > packages/pymol/_cmd.so > #1 0x41d7c683 in SettingGet () from /usr/lib/python2.3/site- > packages/pymol/_cmd.so > #2 0x41d6296d in OrthoAddOutput () from /usr/lib/python2.3/site- > packages/pymol/_cmd.so > #3 0x41d679a5 in PCatchInit () from /usr/lib/python2.3/site- > packages/pymol/_cmd.so > #4 0x4006d74d in PyCFunction_Call () from /usr/lib/libpython2.3.so.1.0 > #5 0x40045e37 in PyObject_Call () from /usr/lib/libpython2.3.so.1.0 > #6 0x400a2a4a in PyEval_CallObjectWithKeywords () from > /usr/lib/libpython2.3.so.1.0 > #7 0x4000 in PyFile_WriteObject () from /usr/lib/libpython2.3.so.1.0 > #8 0x400556e6 in PyFile_WriteString () from /usr/lib/libpython2.3.so.1.0 > #9 0x400d56b6 in PySys_WriteStderr () from /usr/lib/libpython2.3.so.1.0 > #10 0x400d4b2c in PySys_WriteStderr () from /usr/lib/libpython2.3.so.1.0 > #11 0x400d2c74 in Py_AtExit () from /usr/lib/libpython2.3.so.1.0 > #12 0x40101043 in _PyUnicode_TypeRecords () from > /usr/lib/libpython2.3.so.1.0 > > Any idea why it shouldn't work interactively? > > I'm using PyMol 0.90 and Python 2.3.2 on Debian unstable. > > -- > Truls - kerfue+pymol-us...@herocamp.org
RE: [PyMOL] pymol 0.90 on redhat 9.0 - no Tk window
Fred, The tkinter dependency is missing. RPM is supposed to check that, but I forget to add it to the list. Look for the tkinter RPM on your RH9.0 CDROM (or on the net). Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of fr...@mit.edu > Sent: Wednesday, October 22, 2003 3:33 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] pymol 0.90 on redhat 9.0 - no Tk window > > Hi PyMOLers, > > Can someone tell me why I don't get the Tk window with all of the menus > when I > start PyMOL under redhat 9.0? I installed the RPM file > pymol-0.90-1.rh90.py22.i386.rpm and got no errors during installation. > > Here's the content of the shell window after starting PyMOL: > > > Xlib: extension "XFree86-DRI" missing on display ":0.0". > > PyMOL(TM) Molecular Graphics System, Version 0.90. > Copyright (C) 1998-2003 by DeLano Scientific LLC. > All Rights Reserved. > > Created by Warren L. DeLano, Ph.D. > > Other Major Authors and Contributors: > >Ralf W. Grosse-Kunstleve, Ph.D. > > PyMOL is user-supported open-source software. Although most versions > are freely available, PyMOL is not in the public domain. > > If PyMOL is helpful in your work or study, then please volunteer > support for our ongoing campaign to create open and affordable > software > for molecular research. > > Updates and other information can be found at "http://www.pymol.org";. > > Please cite PyMOL in publications and presentations: > >Warren L. DeLano "The PyMOL Molecular Graphics System." >DeLano Scientific LLC, San Carlos, CA, USA. http://www.pymol.org > > Enter "help" for a list of commands. > Enter "help " for information on a specific command. > > Hit ESC anytime to toggle between text and graphics. > > OpenGL based graphics front end: > GL_VENDOR: Mesa project: www.mesa3d.org > GL_RENDERER: Mesa GLX Indirect > GL_VERSION: 1.3 Mesa 4.0.4 > Traceback (most recent call last): > File "modules/pymol/__init__.py", line 177, in exec_str > exec s in globals(),globals() > File "", line 1, in ? > File "modules/pymol/__init__.py", line 292, in launch_gui > __import__(invocation.options.gui) > File "modules/pmg_tk/__init__.py", line 22, in ? > # as /usr/lib/python2.1/site-packages > File "modules/pmg_tk/PMGApp.py", line 15, in ? > ImportError: No module named Tkinter > > > Thanks everyone. > > > > > --- > This SF.net email is sponsored by OSDN developer relations > Here's your chance to show off your extensive product knowledge > We want to know what you know. Tell us and you have a chance to win $100 > http://www.zoomerang.com/survey.zgi?HRPT1X3RYQNC5V4MLNSV3E54 > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] atom sphere radius
Robert, alter selection, vdw=number for example: alter elem fe, vdw=1.0 rebuild Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: Robert Schwarzenbacher [mailto:robe...@sdsc.edu] > Sent: Wednesday, October 22, 2003 1:43 PM > To: Warren L. DeLano > Cc: pymol-users@lists.sourceforge.net > Subject: [PyMOL] atom sphere radius > > Hi there, > > I would like to show an active site metal but the sphere radius is too > big. Is there a way to change the sphere radius for an atom or display > it otherwise with a radius of say 1A. > > > thanks, > robert > > --- > Robert Schwarzenbacher, PhD > The Joint Center for Structural Genomics > phone: 858 822 3637
RE: [PyMOL] Off screen drawing bug on a nForce 2 computer
Paulo, As far as I know, what you're reporting is a platform-dependent OpenGL bug (or feature). Many graphics cards don't support rendering to display context that is not visible. Ray-tracing doesn't have this limitation of course, but in theory we could teach PyMOL how to use auxillary buffers to enable off-screen OpenGL rendering as well. Unfortunately there isn't any way to color bonds independent of atoms in PyMOL. The closest thing you can do is create a new object consisting of just those to bonds and to color that object separately. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of Paulo Lai > Sent: Tuesday, October 21, 2003 7:55 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Off screen drawing bug on a nForce 2 computer > > Hi, > > I have added a very limited SOAP interface to PyMol and I've found that > when the viewer window is covered there are errors in the png files it > generates. For example if I load a structure and rotate it, it will save > the image of the structure in its new orientation overlaid on top of its > original position. It works fine on my laptop which uses the ATI > Mobility Radeon 7500, and I can get it to work on my nForce 2 desktop, > if I use the minimal level of hardware acceleration (when using the > latest version of the NVIDIA drivers). The other issue I've had is PyMol > freezes if I have it open normally, and then I use remote desktop to > connect to that computer, neither of these are critical. > > If anyone is interested, the SOAP libraries for Python (SOAPpy and ZSI) > are still quite rough with many relatively simple things not functioning > correctly, I've resorted to passing lists around. > > Final thing, is there a way to colour a single bonds in sticks view > without affecting the colour of the other bonds the atom is connected to? > > Cheers, > Paulo > > > > --- > This SF.net email is sponsored by OSDN developer relations > Here's your chance to show off your extensive product knowledge > We want to know what you know. Tell us and you have a chance to win $100 > http://www.zoomerang.com/survey.zgi?HRPT1X3RYQNC5V4MLNSV3E54 > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Is it possible to tell if a loaded PDB file contains secondary structure records?
Tom,
This does exist in the upcoming 0.92 release with the new "dss" command:
dss preserve=1
will assign secondary structure (quickly!) if it does not already exist,
or if it does, it will use what is in the PDB file.
In the current release, you can probably do something like:
from pymol import cmd
if cmd.count_atoms("ss H or ss S or ss L")==0:
util.ss()
Cheers,
Warren
--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
> -Original Message-
> From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
> ad...@lists.sourceforge.net] On Behalf Of Tom Walsh
> Sent: Wednesday, October 22, 2003 2:50 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] Is it possible to tell if a loaded PDB file contains
> secondary structure records?
>
>
> I'm writing a script that writes a Python script that loads PDB
> files and displays them in cartoon representation. The problem
> is that, if the PDB file doesn't contain secondary structure
> records, you get a ribbon-like representation rather than a
> proper cartoon. The obvious way to fix this is to run util.ss
> but this can be slow if you have a lot of structures. Is there
> a way in the API to tell whether a PDB file you've loaded contains
> secondary structure records, so that you can avoid an unnecessary
> call to util.ss?
>
> Tom Walsh
>
>
>
>
> ---
> This SF.net email is sponsored by OSDN developer relations
> Here's your chance to show off your extensive product knowledge
> We want to know what you know. Tell us and you have a chance to win
$100
> http://www.zoomerang.com/survey.zgi?HRPT1X3RYQNC5V4MLNSV3E54
> ___
> PyMOL-users mailing list
> PyMOL-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] 2004 PyMOL Budget Reminder
PyMOL Users, For all of you fortunate enough to have recurring annual software budgets, this is a gentle reminder and request for you to consider leaving room in your 2004 budget plans for a PyMOL support subscription (& license for new sponsors). We have been functioning as an independent open-source software company for a little over six months, and I am thrilled to be able to now state with confidence that as long as present trends continue, DeLano Scientific LLC will endure to support PyMOL and pursue its development indefinitely. We have reached a minimal "break even" point where our current (albeit low) costs are met by current revenue. PyMOL is now officially a sustainable long-term project with a bright future! However, we are not yet running as efficiently as possible because current sponsorship can just barely support one full-time equivalent, meaning that my time is split between support, development, system administration, management of contractors, and (unavoidable) paperwork. This achievement of minimal sustainability is an important milestone, but we are not yet able to tap into the significant gains in productivity that can be had through effective divisions of labor. Of course, I will multi-task for as long as is needed to insure the project's vitality -- that goes almost without saying. However, the greatest benefits to you, our users, will accrue when we can afford separate dedicated people, each focusing on one area: support (training, documentation, site-visits, etc.), development (new features, bug-fixes, customization), or general administration (including preparation of SBIR grant applications to cover aggressive new development projects). My hope is that with gradually increasing sponsorship, we will reach that level within the next year or so. However, control over our growth rate and the rate of PyMOL improvement ultimately lies in your hands. What would you like to see happen with the project? Do you share our vision for accessible and ubiquitous molecular graphics software? Are you willing and able to help bring it about sooner or later? If you have a budget, then please make room for a PyMOL subscription in it. Alternatively, if you are preparing a new grant, then please consider adding a line item for PyMOL along with any new hardware or software purchases. We can provide quotes to help with this kind of advanced planning upon request ( http://www.pymol.org/funding.html ). Thanks to all of you who have already sponsored the effort -- you are making this all possible. Thank you especially for your trust, your patience, and your continued belief in the value of our mission ( http://www.delanoscientific.com/about.html ). Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020
RE: [PyMOL] new error
Tom, Yes you're right: MGL's stuff messes with PYTHONPATH and possibly PYTHONHOME. These need to be undefined for PyMOL to work correctly. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Tom Thompson Sent: Friday, October 17, 2003 11:42 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] new error I just started to get this error mac-osx 10.2.6. Could it be correlated with a recent installation of the python-based molecular visualization programs from the MGL at Scripps. I have reinstalled the program and I get the same error. Traceback (most recent call last): File "/Applications/PyMOL/Darwin/modules/pymol/__init__.py", line 58, in ? import threading File "/Applications/PyMOL/Darwin/ext/lib/python2.2/threading.py", line 4, in ? import time ImportError: No module named time Thanks, -Tom -- __ Tom Thompson, Ph.D.PH 847-467-4049 Northwestern University 2205 Tech Drive Evanston IL 60208-0001
RE: [PyMOL] recommendations for G5
Wataru, I would tend to go with the 9800 if cost is not an issue -- it is a faster card than the 9600. Both work great with flat panels (though you'll need a CRT for stereo). Also, I've found that the 9600 does not support antialiased lines on the G5, much to my disappointment. I do now know whether or not the 9800 suffers this same limitation. Perhaps others can comment? There were some glitches with Stereo on the ATI series of cards, but these may have been fixed by now. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of wkag...@jota.gsc.riken.go.jp > Sent: Friday, October 17, 2003 12:50 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] recommendations for G5 > > Dear staff (and pymol users): > > I am looking for some suggestions on the power mac G5 hardware to run > pymol and other 3D applications without problems. > Between the two graphic cards offered by Apple (ATI Radeon 9600 pro or > 9800 pro), which do you recommend? Is it too risky to buy the 9800 pro > because of compatibility problems? How well does the Apple's flat > panel display work with those graphic cards? What are other flat panel > displays that work with those graphic cards? > > I'm sorry these questions are not directly related to pymol, but I > appreciate any suggestions. > > Wataru Kagawa > > > > --- > This SF.net email sponsored by: Enterprise Linux Forum Conference & Expo > The Event For Linux Datacenter Solutions & Strategies in The Enterprise > Linux in the Boardroom; in the Front Office; & in the Server Room > http://www.enterpriselinuxforum.com > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Using PyMol as a library - no GUI
If you've got PyMOL configured to open on import pymol pymol.finish_launching() You can suppress the GUI feature and suppress startup output by providing command line arguments as follows. Before importing PyMOL, set a "pymol_argv" list in the __main__ namespace. PyMOL will interpret this as a sys.argv styled list of command line arguments. import __main__ __main__.pymol_argv['pymol','-qc'] import pymol pymol.finish_launching() Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of Truls A. Tangstad > Sent: Friday, October 17, 2003 4:48 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Using PyMol as a library - no GUI > > I'm very interested in using alot of the functionality that PyMol > offers programmatically from Python, i.e. without using a GUI at > all. The chempy package seems to cover alot of my needs, loading > different file formats etc. even though it doesn't seem to be > documented. > > Is it also possible to use the rest of the functionality in PyMol from > other Python scripts? Right now, just importing the pymol package > seems to force the GUI to open. > > -- > Truls - kerfue+pymol-us...@herocamp.org > > > --- > This SF.net email is sponsored by: SF.net Giveback Program. > SourceForge.net hosts over 70,000 Open Source Projects. > See the people who have HELPED US provide better services: > Click here: http://sourceforge.net/supporters.php > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] transforming all atoms by a matrix
Tina,
> 1. I want to superpose object1 and object2 on top of each other, and
have
> derived a rotation matrix to transform object2 by. How do I apply this
> matrix
> to all its atoms? Either I parse its PDB coordinates, multiply them by
the
> matrix, and load the object (which can be really slow), or, I specify
the
> (axis, angle) data via PyMOL's "rotate" command, which needs me to
solve
> for
> three angles from the matrix, and it's messy. Is there a better way to
> specify
> a matrix to be multiplied to the atom coordinates?
I recently posted some information on transform selection which should
help with this...
See "RE: [PyMOL] Applying a rotation matrix to coordinates"
> 2. I have a series of commands in a python script to highlight
secondary
> structures:
>
> cmd.do(" util.ss")
> cmd.do(" color red, ss h")
> cmd.do(" color yellow, ss s")
> cmd.do(" color blue, ss l+''")
>
> I found the "color" commands race ahead of util.ss and some odd color
> schemes
> show up. I tried "cmd.sync(timeout=5.0, poll=2)" with numerous
> combinations of
> timeout and poll after util.ss but it still happened. Now I'm using
> time.sleep(1.5), which does block the main thread till util.ss
finishes,
> but
> it isn't nice for the program to "freeze" for the 1.5 seconds. My
question
> is:
> why does the sync command not work as expected? This race condition
> doesn't
> occur if the commands are put in a PyMOL script or program (I guess
there
> is
> only one thread of execution in those cases?).
I'm having problems reproducing this problem with the development
version of PyMOL, so the problem may be fixed. However, problems with
synchronization of cmd.do have sometimes occur in multithreaded
environments. For this reason, I recommend calling API functions
directly (cmd.color, util.ss, etc.) instead of passing statements
through cmd.do.
Your code will run faster that way too, since you skip the complex PyMOL
parsing loop.
Cheers,
Warren
RE: [PyMOL] make a bond from two different molecule
Eric, PyMOL's "fuse" command will merge two distinct objects into a one while forming a bond. For example: fragment arg move y,8 fragment glu zoom fuse arg/n, glu/o delete arg zoom glu will create an arginine and a glutamine, and then copy the arginine into the glutamine object, while forming a bond from the amino nitrogen in ARG to the carbonyl carbon in GLU. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of Eric Hu > Sent: Friday, October 10, 2003 2:05 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] make a bond from two different molecule > > Hi, I am using the newest pymol windows version. I > need to make a bond between the protein and ligand > since they form a covalent complex. When I use 'bond' > command, pymol requires that two bonded atoms are in > the same molecule. I have to load two molecules > seperately in order to identify the interactions (e.g. > hydrogen bond) between them. I wonder if I can unite > them into one molecule afterwards to use 'bond' > command. Or there is a better way to do it. Thanks! > > Eric > > __ > Do you Yahoo!? > The New Yahoo! Shopping - with improved product search > http://shopping.yahoo.com > > > --- > This SF.net email is sponsored by: SF.net Giveback Program. > SourceForge.net hosts over 70,000 Open Source Projects. > See the people who have HELPED US provide better services: > Click here: http://sourceforge.net/supporters.php > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Command line equivalent available?
Nick, > There are a few commands that I've been using for which I can't seem to > find a command line equivalent: This actions can be performed using selections with standard atom identifiers: > show/hide mainchain atoms show lines, object-nameca+c+n+o+h hide lines, object-nameca+c+n+o+h where object-name is the name of your object > show/hide sidechain atoms show lines, object-name and ((not name c+n+o+h) or pro/n) hide lines, object-name and ((not name c+n+o+h) or pro/n) Of course, you can substitute sticks, sphere, etc. for lines in the above. > select atoms for 'dist' command (H-bond creation) dist dist-name, selection1, selection2 i.e. dist d1, prot//N/23/CA, lig//X/1/O dist d2, prot//O/24/CA, lig//X/2/N Cheers, Warren
RE: [PyMOL] atom (sub) selections
Wolfram, select m1cha, mole1 and chain a select m2cha, mole2 and chain a You can then perform operations such as: color cyan, m1cha color yellow, m2cha align m1cha, m2cha Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of Wolfram Tempel > Sent: Tuesday, October 14, 2003 5:27 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] atom (sub) selections > > Hi, > the documentation states that selections will span across multiple > objects. However, how do I accomplish this: > I load two (homologous, aligned) coordinate files mole1.pdb and > mole2.pdb both of witch have a chain A. Now I would like to create a > selection consisting of the A chain of mole1 but NOT mole2. Can it be > done without having to modify the coordinate files? > Thanks! > > > > --- > This SF.net email is sponsored by: SF.net Giveback Program. > SourceForge.net hosts over 70,000 Open Source Projects. > See the people who have HELPED US provide better services: > Click here: http://sourceforge.net/supporters.php > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Applying a rotation matrix to coordinates
Tom, Neither transform_object or transform_selection are documented yet, and that reflects the fact the that transformation code in PyMOL is still immature and likely to change. However, for your purposes I suggest transform_selection, but be warned that future changes may break your code at some point. transform_selection takes a selection name, a matrix, and a 1-based state index. Selection can be an object name. cmd.transform_selection(string selection, list-of-16-floats matrix, int state-number): Note that matrix is NOT a standard homogenous 4x4 transformation matrix. Instead it is something PyMOL-specific which consists of the following: 1) a 3x3 matrix containing the rotation in the upper-left quadrant 2) a 3x1 translation to be applied before rotation in the right-hand column (matrix[3],matrix[7],matrix[11]) 3) a 1x3 translation to be applied after rotation in the bottom row (matrix[12],matrix[13],matrix[14]). In other words, if the matrix is: [ m0 m1 m2 m3 m4 m5 m6 m7 m8 m9 m10 m11 m12 m13 m14 m15 ] Atoms will be transformed as follows Y = M X y0 = m0*(x0+m3) + m4*(x1+m7) + m8*(x2+m11) + m12 y1 = m1*(x0+m3) + m5*(x1+m7) + m9*(x2+m11) + m13 y2 = m2*(x0+m3) + m6*(x1+m7) + m10*(x2+m11) + m14 Which is completely non-standard and confusing -- my apologies for that. I call these things TTT matrices (translate, transform, translate) to distinguish them from conventional 4x4's. Note that the 3x3 transformation is backwards from what you might normally expect in C or Python. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of Tom Walsh > Sent: Monday, October 13, 2003 2:48 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Applying a rotation matrix to coordinates > > Hi, > > I want to superimpose two structures using a translation vector and > rotation > matrix. Is the transform_object() function the best way to do this? > > Thanks, > >Tom Walsh > > > > --- > This SF.net email is sponsored by: SF.net Giveback Program. > SourceForge.net hosts over 70,000 Open Source Projects. > See the people who have HELPED US provide better services: > Click here: http://sourceforge.net/supporters.php > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Underside of surface color
Jason, Not really -- it's either blackish or lit, just like the front. To see the backside of surfaces: set two_sided_lighting,1 set backface_cull,1 Also, sometimes it is helpful to get rid of shadows when doing this: set ray_shadows, 0 Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of Jason Thomas Maynes > Sent: Friday, October 10, 2003 3:11 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Underside of surface color > > Hello: > > Is there any way to change the color of the underside of a surface. Right > now it is a very dark version of the top color. I would like to be able > to look at the surface contour from underneath. > > Thanks in advance. > > Cheers, > JTM > > "We can be sure that if a detailed understanding of the molecular basis of > chemo-therapeutic activity were to be obtained, the advance of medicine > would be greatly accelerated." > > Linus Pauling, Nobel Laureate 1954 > > "...everything that living things do can be understood in terms of the > jigglings and wigglings of atoms." > > Richard Feynman > > * > Jason Thomas Maynes > PhD/MD Program > Department of Biochemistry > Faculty of Medicine > University of Alberta > ja...@biochem.ualberta.ca > * > > > > --- > This SF.net email is sponsored by: SF.net Giveback Program. > SourceForge.net hosts over 70,000 Open Source Projects. > See the people who have HELPED US provide better services: > Click here: http://sourceforge.net/supporters.php > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Creating stereo figures for pub
> I am having a small problem creating stereo figures, probably a syntax > problem. > Using this set of commands returns an image that looks great in stereo, > but is > only 640X480 (default window size) Currently you're ray tracing twice... > ray 2000,2000 > ray angle=-3 should be ray 2000,2000,angle-3 > png image_left.png > > ray 2000,2000 > ray angle=3 and ray 2000,2000,angle=3 > png image_right.png Cheers, Warren
RE: [PyMOL] Accessing PyMol's commands from outside (or without viewer)
> Two more questions:
> Does the 'pymol -qc' takes command line variables (os.argv in python)?
> For example, the first line of my script would be:
> cmd.do('load %s' %os.argv[1])
That's not possible. In order to get this behavior (for now) you need
to treat PyMOL as a module (see below).
> Second question might be off a little bit.
> Is it possible to wrap PyMol as a module of Python?
Yes, but to do this (in most cases), you'll have to recompile and
install PyMOL as a standard "distutils" module. If you're not familiar
with compilation, then this isn't for you...
python setup.py build install
python setup2.py install
Then from python
import pymol
pymol.finish_launching()
can work
> I know can be
> installed as a Python module, but that doesn't seem to be able to let
me
> do things like:
>
> # Sample Python script
> import PyMol
> PyMol.cmd.do('..')
> distance = PyMol.cmd.do('distance ..')
Close.
from pymol import cmd
distance = cmd.distance('tmp',sele1,sele2)
> Does it make any difference whether or not I installed PyMol
independant
> of Python?
> I am a bit confused with cmd.do vs cmd.select.
cmd.do places string command to the PYMOL parser input queue and returns
nothing.
cmd.functionName calls the PyMOL API and returns the result (if any).
> So, if I am writing a script for running in PyMol(using
@some_script.py),
> I should use:
> import PyMol
> cmd.select('...')
>
> If I am writing a script for running PyMol in command line,
> I should use:
> from PyMol import cmd
> cmd.do('...')
The only time you'd use cmd.do is for convenience...
cmd.do("select cas, name ca")
will always be substantially slower than
cmd.select("cas","name ca")
because an extra parsing step in involved.
Cheers,
Warren
> Kind of confused...
>
> -shuhsien
>
> >Shu-hsien
> >
> >Sure, instead of cmd.select, use
> >
> >cmd.do("select ligand, resn XYZ")
> >cmd.do("select protein, ! ligand ")
> >
> >etc.
> >
> >./pymol -qc select_box.py
> >
> >Is the command line mode of PyMOL. "pymol -qc" can be used like
> >"python" in most cases.
> >
> >Cheers,
> >Warren
> >
> >
>
>
>
> ---
> This SF.net email is sponsored by: SF.net Giveback Program.
> SourceForge.net hosts over 70,000 Open Source Projects.
> See the people who have HELPED US provide better services:
> Click here: http://sourceforge.net/supporters.php
> ___
> PyMOL-users mailing list
> PyMOL-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Accessing PyMol's commands from outside (or without viewer)
Shu-hsien
Sure, instead of cmd.select, use
cmd.do("select ligand, resn XYZ")
cmd.do("select protein, ! ligand ")
etc.
./pymol -qc select_box.py
Is the command line mode of PyMOL. "pymol -qc" can be used like
"python" in most cases.
Cheers,
Warren
--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
> -Original Message-
> From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
> ad...@lists.sourceforge.net] On Behalf Of Shu-Hsien Sheu
> Sent: Saturday, November 08, 2003 10:58 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] Accessing PyMol's commands from outside (or without
> viewer)
>
> Hi,
>
> This should be a trial question though I cannot find a way of doing
it.
> I have a simple script that looks like this:
> (the original commands, rather than cmd.select..)
> select ligand, resn XYZ
> select protein, ! ligand
> select box, protein within 8 of ligand
> select box, box or byres box
> save box as box.pdb
>
> I don't need the viewer at all and would be even more efficient if I
can
> call the PyMol API from the shell. Or, in a python script.
> For example, I would like to have something like:
> ./pymol select_box.py
>
> thanks!
>
>
>
> ---
> This SF.net email is sponsored by: SF.net Giveback Program.
> SourceForge.net hosts over 70,000 Open Source Projects.
> See the people who have HELPED US provide better services:
> Click here: http://sourceforge.net/supporters.php
> ___
> PyMOL-users mailing list
> PyMOL-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Alpha channel support gone?
Jean, Did you set ray_opaque_background, 0 ? Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of Cartailler, Jean-Philippe > Sent: Wednesday, October 08, 2003 7:46 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Alpha channel support gone? > > What has happened to alpha channel support in PNG output? I could have > sworn it used to be there. I'm now working in version 0.9. > > thanks > > Jean-Philippe Cartailler > > > Vanderbilt University Medical Center > S-3223 Medical Center North > 1161 21st Avenue South > Nashville, TN 37232-2372 > > Phone: 615.322.7729 > FAX: 615.343.7156 > email: jp.cartail...@vanderbilt.edu > www: http://www.cartailler.com > > > > --- > This SF.net email is sponsored by: SF.net Giveback Program. > SourceForge.net hosts over 70,000 Open Source Projects. > See the people who have HELPED US provide better services: > Click here: http://sourceforge.net/supporters.php > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] slow ray-tracing since updating to 10.2.8 (mac os x)
Wataru, Yes, Apple's 10.2.7 and 10.2.8 broke auto-detection of the second processor. To fix this, manually set max_threads, 2 before ray tracing. The next release will fix the problem... Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of wkag...@jota.gsc.riken.go.jp > Sent: Tuesday, October 07, 2003 9:44 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] slow ray-tracing since updating to 10.2.8 (mac os x) > > Dear all, > > I noticed that ray tracing in pymol (v0.90) is significantly slower > ever since upgrading mac os x from 10.2.6 to 10.2.8. Has anyone > experienced this? > > Wataru Kagawa, Ph. D. > Special Postdoctoral Researcher > Protein Research Group > RIKEN (Physical and Chemical Research Institute) > > W221, West Research Bldg. > 1-7-22 Suehiro-cho, Tsurumi-ku > Yokohama, Japan 230-0045 > > tel. 045-503-9206 > fax. 045-503-9201 > > > > --- > This sf.net email is sponsored by:ThinkGeek > Welcome to geek heaven. > http://thinkgeek.com/sf > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Pymol script screenplay
Nat, PyMOL's ray-tracer is pretty simple -- it just divides 3D space up into equally sized boxes, so that ray-intersection and identification calculation can be performed rapidly. The smaller the boxes, the fewer the number of partial geometries will be present in the box. Hash_max is a hint to the ray tracer about the maximum number of subdivisions it should allow on each axis. In principle, the amount of RAM used is a 3rd-order function of this value. However, the ray-tracer will often use less RAM than that for a variety of reasons. PyMOL usually ships with hash_max set to 100, since that is reasonable for a machine with 256 MB of RAM. 300 is about the highest I've tried, and you could easily require over a Gig of RAM for a situation like that. However, there is definitely a point of diminishing returns, which depends on scene complexity, total number of pixels, etc. Typically each ray-tracing scene will have a different optimum, but usually 140-180 gives the shortest overall rendering times. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of Nat Echols > Sent: Sunday, October 05, 2003 2:28 PM > To: pymol-users@lists.sourceforge.net > Subject: RE: [PyMOL] Pymol script screenplay > > > By the way, you can also use extra RAM to speed up ray-tracing > > by 2-3 fold if you set hash_max to 150-200. > > Wait, I'm curious - what does this command do, and what are the limits? > For a machine with 2GB of memory, what can I get away with? Will I have > problems if I run multiple invocations of PyMOL at once? > > -Nat > > > > --- > This sf.net email is sponsored by:ThinkGeek > Welcome to geek heaven. > http://thinkgeek.com/sf > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] why is PyMOL renaming my residues?
> >Also note that by some conventions, "2OA2" in a PDB file really means > >atom "OA22". > > > I didn't know that. What conventions are those? Well, PDB atom names are supposed to have the atomic symbol right justified in the first two columns followed by a remoteness indicator and then a branching number. However, that isn't a sufficient number of fields for all situations, such as when significant symmetry is present in a system, and so a third field is required. This numeric field occupies the first column when the atom symbol itself is only one character. With hydrogens, this first numeric field has the additional defined purpose of enumerating (NMR?) equivalent hydrogens, so you will see atoms like "2HD" and "3HD" in ARG for instance. However, in the Amber world, the atomic symbol always comes first. Thus a PDB hydrogen 2HH2 becomes HH22 in Amber. Going from PDB to Amber is easy, but the reverse is not trivial, since Amber "CD1" remains PDB "CD1", but Amber "HE2" becomes "2HE" and "HH22" becomes "2HH2". Ambiguity occurs when there is a four-letter atom name which is not a hydrogen. "OA22" in Amber would thus need to become "2OA2" in order to comply with the PDB convention of having the Atomic symbol right justified in the first two columns of the file. However, that convention is only explicitly enforced for amino acids, so in theory "OA22" would be legal for a non-amino acid, whereas "2OA2" is required if the residue is an amino acid. What a mess! Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > >Also note that by some conventions, "2OA2" in a PDB file really means > >atom "OA22". > > > I didn't know that. What conventions are those? > > >Furthermore, in your example, they [ATOM IDs] are not unique (a > mistake?). > > > yup, a mistake. > > >However, I am trying to bend PyMOL around to meet your needs a bit > >better. > > > >Towards this end, I've created a new setting "pdb_retain_ids" which > >preserves the original PDB serial numbers in the output file. > > > >In future PyMOL versions, so long as > > > >set retain_order, 1 > >set pdb_retain_ids, 1 > >set pdb_no_end_record, 1 > > > That's absolutely fantastic. Right now, I have to use PyMOL, MOE and > AMBER (sander and carnal are the real problems) on the same systems, and > anything that makes this less painful is great! I'll probably set > retain_order and pdb_retain_ids in my .pymolrc.py and upgrade to the CVS > version within the next couple of days. > > Thanks! > > -michael > -- > michael lerner > > > > --- > This sf.net email is sponsored by:ThinkGeek > Welcome to geek heaven. > http://thinkgeek.com/sf > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Pymol script screenplay
Alan, VMD is more memory efficient that PyMOL. Probably the main reason for this is that PyMOL pre-calculates and stores all of the geometries it is going to show down to the last vertex. You can reduce the amount of memory PyMOL needs for cartoons by setting: set cartoon_sampling, 3 But the real way to solve your problem is to get more RAM. If you're using PyMOL to visualize MD trajectories, I recommend buying as much RAM as you can afford (and your system can take). 1 GB is a reasonable minimum. 1.5-2 GB is definitely better. I don't know what prices are like in Brazil, but a GB of RAM can be purchased here in the states for $150-400. By the way, you can also use extra RAM to speed up ray-tracing by 2-3 fold if you set hash_max to 150-200. To answer to your second question: import os os.system"(mencoder \*.png -mf on:fps=30 -o mvc1ec2.avi -ovc lavc -lavcopts > vcodec=mpeg4:vbitrate=6000:vhq:keyint=30") Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of Alan Wilter Sousa da Silva > Sent: Thursday, October 02, 2003 5:32 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Pymol script screenplay > > > Hi List! > > I finally got a Pymol script which does what I want, but I still have > problems. I follows my actual script: > > - > del all > mclear > set cache_frames=0 > set cartoon_fancy_helices, 1 > load c1/forcedin.pdb,c1 > frame 1 > hide all > run Pymol/stride_ss.py > stride2pymol c1 > stride2pymol c2 > show sticks, (resi 199) > show cartoon, all > color red, c1 > color blue, c2 > set orthoscopic=1 > viewport 640,480 > run Pymol/eixos.py > translate [18,18,20],object=axes > run Pymol/cgotext.py > translate [18,55.5,40],object=txt > reset > zoom all,-55 > clip near,2 > mset 1 x10 1 x72 -28 28 x72 28 x10 > util.mroll(11,82,1) > util.mroll(111,182,1) > set antialias=1.0 > set ray_trace_frames=1 > mpng png2/mvc1e2 > --- > > It works for a 28 frames of MD. But a test. Extending it for a real MD > (~500 frames) I found out that Pymol crashes when command 'show cartoon, > all' is running (after done the half of frames, I believe). Problably > memory problems, right? However a similar operation works fine in VMD > (sorry for comparison). I use a P4 1.6 GHz with 256 Mb Ram. > > BTW, how could I insert in Pymol script (python language) such command > bellow: > > mencoder \*.png -mf on:fps=30 -o mvc1ec2.avi -ovc lavc -lavcopts > vcodec=mpeg4:vbitrate=6000:vhq:keyint=30 > > > Thanks in advance for any help. > > Cheers, > > -- > -- > Alan Wilter Sousa da Silva > -- > B.Sc. - Dep. Física - UFPA > M.Sc. - Dep. Física - PUC/RJ > D.Sc. - IBCCF/UFRJ > Bolsista Pesquisador LAC-INPE > São José dos Campos (SP), Brasil > www.lac.inpe.br/~alan > > > --- > This sf.net email is sponsored by:ThinkGeek > Welcome to geek heaven. > http://thinkgeek.com/sf > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] why is PyMOL renaming my residues?
Michael, PyMOL's PDB handling is an attempt to navigate a minefield of incompatible standards which exist in the conventions of various software packages. Amber in particular poses significant challenges, as its PDB files are unusual. Since version 0.90, PyMOL's behavior has changed. Nowadays, your input data: HETATM 1313 OA22 NAP 164 28.315 61.969 12.250 31.54 O HETATM 1314 OA23 NAP 164 26.554 62.174 14.275 21.05 O HETATM 1314 ABCD NAP 164 28.554 64.174 16.275 11.05 O HETATM 1314 XYZ NAP 164 30.554 66.174 18.2751.05 O HETATM 1314 LMN NAP 164 32.554 68.174 20.275 41.05 O Would be returned as: HETATM1 OA22 NAP 164 28.315 61.969 12.250 0.00 31.54 O HETATM2 OA23 NAP 164 26.554 62.174 14.275 0.00 21.05 O HETATM3 ABCD NAP 164 28.554 64.174 16.275 0.00 11.05 O HETATM4 LMN NAP 164 32.554 68.174 20.275 0.00 41.05 O HETATM5 XYZ NAP 164 30.554 66.174 18.275 0.00 1.05 O END ...which does preserve atom names, but not the order. Note that white-space in the atom names is not preserved (an inherent limitation in PyMOL -- significant white-space within identifier is hell on users and parsers). Conventionally, atom names of length 3 or less are placed in the second column, not the first -- so your "LMN " atom may cause trouble. Also note that by some conventions, "2OA2" in a PDB file really means atom "OA22". PyMOL used to work this way (up to 0.90). Nowadays (v0.91+), "2OA2" is treated as "20A2" unless pdb_literal_names is on, in which case the old behavior returns. Note that in PyMOL, the PDB ATOM IDs are treated more as a property of the PDB file than of the atoms themselves since TER records also have unique IDs in that sequence and repeated MODELs sometimes do as well. Furthermore, in your example, they are not unique (a mistake?). However, I am trying to bend PyMOL around to meet your needs a bit better. Towards this end, I've created a new setting "pdb_retain_ids" which preserves the original PDB serial numbers in the output file. In future PyMOL versions, so long as set retain_order, 1 set pdb_retain_ids, 1 set pdb_no_end_record, 1 The following behavior will be obtainable: Assuming input of: HETATM 1313 OA22 NAP 164 28.315 61.969 12.250 31.54 O HETATM 1314 OA23 NAP 164 26.554 62.174 14.275 21.05 O HETATM 1315 ABCD NAP 164 28.554 64.174 16.275 11.05 O HETATM 1316 XYZ NAP 164 30.554 66.174 18.2751.05 O HETATM 1317 LMN NAP 164 32.554 68.174 20.275 41.05 O You'll get an output of: HETATM 1313 OA22 NAP 164 28.315 61.969 12.250 0.00 31.54 O HETATM 1314 OA23 NAP 164 26.554 62.174 14.275 0.00 21.05 O HETATM 1315 ABCD NAP 164 28.554 64.174 16.275 0.00 11.05 O HETATM 1316 XYZ NAP 164 30.554 66.174 18.275 0.00 1.05 O HETATM 1317 LMN NAP 164 32.554 68.174 20.275 0.00 41.05 O Which is as close as I think PyMOL is going to get... Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of michael lerner > Sent: Friday, September 26, 2003 8:44 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] why is PyMOL renaming my residues? > > Hi, > > If I load up a PDB file that looks like this: > > HETATM 1313 OA22 NAP 164 28.315 61.969 12.250 > 31.54 O > HETATM 1314 OA23 NAP 164 26.554 62.174 14.275 > 21.05 O > HETATM 1314 ABCD NAP 164 28.554 64.174 16.275 > 11.05 O > HETATM 1314 XYZ NAP 164 30.554 66.174 18.275 > 1.05 O > HETATM 1314 LMN NAP 164 32.554 68.174 20.275 > 41.05 O > > and then save it from PyMOL, the resulting PDB file looks like this: > > HETATM1 2OA2 NAP 164 28.315 61.969 12.250 0.00 > 31.54 O > HETATM2 3OA2 NAP 164 26.554 62.174 14.275 0.00 > 21.05 O > HETATM3 DABC NAP 164 28.554 64.174 16.275 0.00 > 11.05 O > HETATM4 LMN NAP 164 32.554 68.174 20.275 0.00 > 41.05 O > HETATM5 XYZ NAP 164 30.554 66.174 18.275 0.00 > 1.05 O > END > > You'll note that OA22 has been renamed to 2OA2, OA23 has been renamed to > 3OA2 and ABCD has been renamed to DABC. It looks to me like residue > with a four-letter name is getting renamed. > > No .. wait .. it's a little stranger than that .. if I open up the > second file
RE: [PyMOL] drawing the surface correctly
Michael, Thanks for your question. flag ignore, atom-selection, set rebuild Will enable you to remove the surface from selected atoms. For example: show surface flag ignore, resn wat or resi 150, set rebuild Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of michael lerner > Sent: Wednesday, September 24, 2003 11:03 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] drawing the surface correctly > > Howdy, > > I have a pdb file that contains a protein, a ligand and two water > molecules. Everything in the protein is normal, and is listed with ATOM > cards. The ligand and waters are listed as HETATMs. When I show the > surface in PyMOL, I see the surface drawn around the protein only. This > is what I want. > > After I do some things to my protein in AMBER, I get a pdb file where > everything is listed as an ATOM (it's a pretty simple pdb file .. ATOM, > ATOM, ATOM, TER, ATOM, ATOM, TER, etc.). When I load this into PyMOL > and show the surface, the surface is drawn around the everything > (ligand, water, and protein), rather than just around the protein. > > If I open up the PDB file by hand and change all of the appropriate ATOM > cards into HETATM cards and then load it up in PyMOL, everything works > well (I see the surface drawn only around the protein). But I'd like to > be able to do this all within PyMOL. My ligand is named NAP, so I type > "alter resn NAP or resn WAT, type='HETATM'" followed by "sort" and > "rebuild" to fix things. Unfortunately, this doesn't work and I still > get the surface drawn around everything. The strange thing is that if I > alter the file, save it and reload it, PyMOL displays the surface > correctly. > > Can I get PyMOL to display the correct surface without saving and > reloading the file? > > If it helps, I'm running PyMOL 0.90 on a Mandrake 8.2 laptop with an > nVidia GeForce2Go graphics card. > > Thanks, > > -michael > > -- > michael lerner > > > > --- > This sf.net email is sponsored by:ThinkGeek > Welcome to geek heaven. > http://thinkgeek.com/sf > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] access space group and cell dimensions of stored molecules
Peter, The next version of PyMOL has a get_symmetry function which can be used to obtain the crystal symmetry of an object. As far as wizards go, both the name of the file and the name of the derived class should match. PyMOL expects the first letter of the class (only) to be capitalized, but the filename should be all lowercase. For example: pymol/modules/wizard/mywiz.py containing class Mywiz(Wizard): ... should work. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of Peter Haebel > Sent: Wednesday, September 24, 2003 5:31 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] access space group and cell dimensions of stored > molecules > > i have started working on a space group class that can display symmetry > operators, etc... and i got stuck trying to obtain the space group > information from pymol molecule objects. > > - how can i get the space group and unit cell dimensions of an object? > > secondly, i am trying to write a wizard to easily access the new > functions. > > - but i dont fully understand how wizards work. if i simply rename the > density wizard it is no longer accessible in pymol, ie. 'wizard newname' > does not bring up the control panel. how can i rename/copy a wizard and > modify it? simply modifying the source code density wizard without > renaming > it seems to work. > > > cheers, > > peter > > > __ > > Bestes Testergebnis: Stiftung Warentest Doppelsieg fur WEB.DE FreeMail > und WEB.DE Club. Nur fuer unsere Nutzer! http://f.web.de/?mc=021182 > > > > --- > This sf.net email is sponsored by:ThinkGeek > Welcome to geek heaven. > http://thinkgeek.com/sf > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] RE:
> One quick question... how do I tell PyMOL to draw a cylinder (or bond) > of a given radius between two positions X,Y,Z and X', Y',Z'? (From Python...) from pymol.cgo import * from pymol import cmd obj = [] obj.extend( [ CUSTOM_CYLINDER, 1.0, 2.0, 3.0, # XYZ 1 4.0, 5.0, 6.0, # XYZ 2 2.0,# Radius 1.0, 1.0, 1.0, # RGB Color 1 1.0, 1.0, 1.0, # RGB Color 2 1, 1, # End caps (0=none, 1=flat, 2=round) ] ) cmd.load_cgo(obj,'my_cgo') Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020
RE: [PyMOL] two_sided_lighting
Meitian, Sorry, this is not possible. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of M Wang > Sent: Monday, September 22, 2003 9:49 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] two_sided_lighting > > Hello everybody, > > For two_sided_lighting, is there a way to change the relative brightness > of the two lights? > > Thanks, > > Meitian Wang > > > > --- > This sf.net email is sponsored by:ThinkGeek > Welcome to geek heaven. > http://thinkgeek.com/sf > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] modifying atom coordinates
Edmund, No, this kind of technical information isn't documented... If I recall correctly, when PyMOL hooks fragments together, it replaces hydrogen with a bond along the existing vectors. In other words, one fragment is translated so as to fit onto another. Peptides are a special case because the phi-psi vectors are fairly well defined. Nevertheless, I wouldn't trust peptide geometries generated by PyMOL until they've passed through some external force-field, such as MMFF or Amber/OPLS. PyMOL is a reasonable builder for defining the covalent scaffold of peptides and arbitrary small molecules, but it knows nothing about forces and energies. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of Edmund Kump > Sent: Thursday, September 18, 2003 8:59 PM > To: pymol-users@lists.sourceforge.net > Subject: RE: [PyMOL] modifying atom coordinates > > Yes, but what happens when, for example, I take a lysine residue, and > connect a glutamine residue? Shouldn't all the atoms have different > coordinates from when they are stand alone, based on the forces from > nearby atoms? Does pymol account for this as residues are added, or is > there a command or wizard which accounts for nearby atomic forces that I > would execute after I build my chain? > > To give some background to what I'm trying to do, the end goal of my > project is to modify the forces involved in protien folding. I'm sorry if > I'm asking questions that are documented, but I haven't seen anything that > answers my question yet. > > Much Thanks, > Edmund > > > On Wed, 17 Sep 2003, Warren L. DeLano wrote: > > > Hi Edmund, > > > > Actually, PyMOL uses a set of stored coordinates for fragments > > and residues. They can be found in $PYMOL_PATH/data/chempy/fragments. > > The files have .pkl extensions, which stands for pickled chempy model. > > These files can be viewed directly in PyMOL, or can be introspected by > > unpickling them in a Python interpreter. > > > > Cheers, > > Warren > > > > -- > > mailto:war...@delanoscientific.com > > Warren L. DeLano, Ph.D. > > Principal Scientist > > DeLano Scientific LLC > > Voice (650)-346-1154 > > Fax (650)-593-4020 > > > > > -Original Message- > > > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > > > ad...@lists.sourceforge.net] On Behalf Of Edmund Kump > > > Sent: Wednesday, September 17, 2003 3:49 AM > > > To: pymol-users@lists.sourceforge.net > > > Subject: [PyMOL] modifying atom coordinates > > > > > > Greetings, > > > > > > I am interested in modifying how pymol generates the coordinates of > > > atoms in a peptide chain as you add residues to it. I am an > > > undergraduate math student, so my knowledge in this area is in the > > > range of "nothing". I would assume that this would be in the bonding > > > or editor modules, but so far I haven't found what I'm looking for. In > > > what Chempy or Pymol module(s) can I find the code that determines > > > these coordinates? > > > > > > Thanks, > > > Edmund Kump > > > ek...@mathlab.sunysb.edu > > > Applied Mathematics and Statistics > > > SUNY Stony Brook > > > > > > > > > > > > --- > > > This sf.net email is sponsored by:ThinkGeek > > > Welcome to geek heaven. > > > http://thinkgeek.com/sf > > > ___ > > > PyMOL-users mailing list > > > PyMOL-users@lists.sourceforge.net > > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > > > > --- > This sf.net email is sponsored by:ThinkGeek > Welcome to geek heaven. > http://thinkgeek.com/sf > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] bug in rpm?
Nat, Are you running stock RedHat 9.0? The threading library in RH90 is broke. You may need to apply the glibc patches released by RedHat in order to get a stable system. Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of Nat Echols > Sent: Friday, September 19, 2003 12:47 AM > To: PyMOL-users@lists.sourceforge.net > Subject: [PyMOL] bug in rpm? > > > I just got a shiny new Gateway laptop - essentially a ripoff of the 15" > Apple (but cheaper), with NVidia chipset. I installed RedHat 9.0, NVidia > drivers, and the PyMOL rpm for rh9, but I get segfaults when I try to run > 'pymol'. The tar.gz file works perfectly, so it's not a problem for me, > but I figured I should check and see if this was a known issue or if I'm > doing something dumb. > > -Nat > > > > --- > This sf.net email is sponsored by:ThinkGeek > Welcome to geek heaven. > http://thinkgeek.com/sf > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] getting color of a residue + selecting non-natural residues
Tina, > I have two operations that I want to perform, and am not aware of a simple > way > (if possible) of doing them. So here it goes: > > 1. how (if possible) to retrieve the color for a residue as identified in > an > expression, e.g. "resi 9"? Note that it's not a range so no multiple > answers > is possible. I guess the question could extend to other attributes like > representation, etc. The reason I need that is to be able to switch back > to a > residue's original color after highlighting it in another. The iterate command can do this... iterate all, print color import pymol pymol.color_list = [] iterate all, color_list.append(color) print pymol.color_list > 2. how to select all non-natural residues (anything that's not in the list > of > 20 standard AAs)? > > I'm going the brute-force way, i.e. > > naturals1='asp+glu+lys+arg+phe+tyr+cys+met+ser+thr' > naturals2='asn+gln+leu+val+ile+gly+ala+his+trp+pro' > select naturals1, resn naturals1 > select naturals2, resn naturals2 > select nonnaturals, !naturals1 & !naturals2 Does the above work? I wouldn't expect variables to function in PyMOL statements, but perhaps you're actually using cmd.select(...), which can access variables. However, you don't need to brake it up quite so much: select naturals, resn asp+glu+lys+arg+phe+tyr+cys+met+ser+thr \ or resn asn+gln+leu+val+ile+gly+ala+his+trp+pro select nonnaturals, !naturals Cheers, Warren
