Re: [PyMOL] [cctbxbb] draw_symops <-- cctbx(/phenix) broken due to boost segfault handling ?

: to this: for smx in space_group_info.group().all_ops(): With best regards, Cam -- ------- Cameron Mura Assistant Professor University of Virginia Department of Chemistry McCormick Road, Box 400319 Charlottesville, VA 22904-4319 Email: cm...@virginia.edu We

Re: [PyMOL] [cctbxbb] draw_symops <-- cctbx(/phenix) broken due to boost segfault handling ?

part is always the Python startup, and anything after boost::python::handle_exception is just the code producing the tracebacks. The important clues are somewhere in the middle. Ralf *From:* Cameron Mura *To:* cctb...@p

[PyMOL] draw_symops <-- cctbx(/phenix) broken due to boost segfault handling ?

it. Before delving into Boost codebase, cctbx's exception-handling in C++/Python Boost, etc., I'm wondering if anyone else has seen anything like this...? or has advice on how best to proceed? Any tips or suggestions would be most greatly appreciated. Thanks, Cam -- ---

[PyMOL] senior-level position for crystallographer / biochemist

a.edu/chem/people/faculty/mura/#openings . With best regards, Cameron -- --- Cameron Mura University of Virginia Department of Chemistry McCormick Road, Box 400319 Charlottesville, VA 22904-4319 Email: cm...@virginia.edu Tel: 434.924.782

Re: [PyMOL] Re: [o-info] KVM purchasing advice

MiniView III switch for high res displays. Cam === D. Joe Anderson wrote (on 07/27/2005 08:48 AM): === On Fri, Jul 15, 2005 at 01:15:13PM -0700, Cameron Mura wrote: there may be many O and PyMOL users who use stereo with a monitor connected through a KVM switch? 3) would be

[PyMOL] FC4 stereo problems

Demetres & Roger, I've had the same problem w/ stereo on FC4 (tested only w/ an nVidia Quadro 700 XGL card), and have been meaning to mail the list. The problem occurs even after taking the typical steps to set-up the nVidia drivers on the system (as described by Roger), and also occurs w/ h

Re: [PyMOL] nVidia Quadro FX 1400, FX 3400 and FX 4400 performances

get up to speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id492&op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Cameron Mura UCSD

Re: [PyMOL] loop/coil thickness

Development Lifecycle Practices Agile & Plan-Driven Development * Managing Projects & Teams * Testing & QA Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.ne

[PyMOL] Re: putty/sausage NMR figure (Douglas Kojetin)

PM To: pymol Subject: [PyMOL] putty/sausage NMR figure Hello All- From what I've read, the 'cartoon putty' command uses the PDB B- factor value to determine the appearance of the sausage diagram. How can I use the 'cartoon putty' command with NMR structures in a way that represents the structure ensemble, similar to that as the MOLMOL sausage diagram? Thanks, Doug -- Cameron Mura UCSD

[PyMOL] antialiasing and povray

hi, Is there anything special I need to do/set to achieve antialiased images via pymol + POV-ray? To be more explicit, i'm using robert campbell's make_pov.py to have pymol dump the scene into a povray input file, and then ray-tracing w/ a minimalistic command-line (e.g., "povray +Iwhatever_pov

[PyMOL] KVM purchasing advice

hi, i apologize for the somewhat off-topic post to both lists, but I figured there may be many O and PyMOL users who use stereo with a monitor connected through a KVM switch? if so, please see the 2nd question in my email below... thanks, cameron === Cameron Mura wrote (on 07/15/2005 10

Re: [PyMOL] tube thickness

alexandra, i was just able to load a molecule into pymol and set its tube radius to XYZ by doing the following: hide everything cartoon tube, all show cartoon, all set cartoon_tube_radius, XYZ another thing which you can try if you want variable (residue-specific) tube thicknesses which are

[PyMOL] building pymol rpm

Hi, Anyone out there have a spec file (or srpm) for building a pymol v0.98 RPM on CentOS-4 or Fedora Core 3? I succeeded in building a monolithic pymol RPM (~11MB) on CentOS by basically wrapping the standalone pymol-0_98rc3-bin-linux-x86-glibc23.tgz, but this resulted in an executable that w

Re: [PyMOL] returning image to PyMol viewer

ular image. for example if i type help show and all the manual appears how do I then clear the manual from the screen? thx, Sebastien This message was sent using IMP, the Internet Messaging Program. -- Cameron Mura UCSD

Re: [PyMOL] surface representation showing mutations

Sarma, I am trying to create a surface representation of a protein with mutations that abolish activity in one color (say yellow) and the ones that don't change activity in another (say green). The rest of the residues colored gray. I can change the color of the surface to gray or a rainbow gr

[PyMOL] sidechains and mutagenesis wizard

Hi, I'm wondering if any of you who've delved into the PyMOL source know what the following line (and subsequent block of code) from the file "data/chempy/sidechains/generate1.py" refers to: for fyle in glob("source/*"): I assume it's something like a sidechain rotamer database, but isn't

Re: [PyMOL] How to generate a DNA structure with given sequence?

Hi Hyun-Chul, It's easy to use PyMOL to build protein fragments in standard geometries ("Build" menu in the Tcl/Tk GUI window), but I'm not sure about DNA. Three non-PyMOL methods that I'm aware of are: (1) The program "B" (aka "Biomer") from Dave Case's group at Scripps (http://www.scripps

[PyMOL] molecular editing in pymol

Hi, I should probably google about some more for an answer to this, but maybe someone who's reading this already knows -- is a detailed description of pymol's molecular editing functionality available anywhere online (e.g., ctrl-right-click to select a bond and ctrl-d to delete it, and so on..

[PyMOL] Re: Documentation / Wiki Brain Storming

Hi, Say, what do people think about the idea of creating a PyMOL Wiki to hold nuggets of information like this? Or is there a better alternative to Wiki now available? I (still) think it's a great idea, and bet it would serve as an indispensible resource to both novice and seasoned PyMOLer

[PyMOL] PyMOL on Fedora Core 3

on(Fedora Core3) of pymol. Compiling pymol on my linux for linux newbiee like me is really an unforgetable experience and I don't want to do it again. But , I really like pymol. -- Cameron Mura UCSD

[PyMOL] Re: List participation commentary

Ultimately the mailing list serves as a form of living manual to the program, so it would be nice to preserve as many of these insights as possible! Thomas' above sentence reminds me -- has anyone thought about a PyMOL wiki? :-) Given that one of the points of pymol is to provide a user-frien

[PyMOL] Re: ribbon view of c-alpha only coordinates

~lsbb * -- Cameron Mura UCSD

[PyMOL] Re: PyMOL-users digest, Vol 1 #735 - 1 msg

Hi PyMOL comunity, The answer to my question should be rather easy, I guess: Is there any document explaining which is the structure of the program? OK, thank you all Luciano -- Cameron Mura UCSD

[PyMOL] Re: PyMOL-users digest, Vol 1 #714 - 1 msg

ester Biophysics and Structural Biology 575 Elmwood Ave Rochester, NY 14642 585-273-4800 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Cameron Mura UCSD

[PyMOL] Re: sausage patch to v0.97

Oops, sorry -- first link below should have been "http://mccammon.ucsd.edu/~cmura/PyMOL/"; (no trailing "ScriptsPatchesEtc/"). Cam. === Cameron Mura wrote (on 09/15/2004 07:50 PM): === Hi Warren & others, I've written a patch to the v0.97 source that ena

[PyMOL] sausage patch to v0.97

oked from the PyMOL command line as, e.g., "cartoon saus, all"), and its basic operation is analogous to the "tube"-style cartoons -- i.e., there are 'cartoon_saus_quality' and 'cartoon_saus_radius' settings. Please let me know of any questions or problems with its usage. Best regards, Cam. -- Cameron Mura UCSD

Re: [PyMOL] hiding one chain in pymol

rket... Oracle 10g. Take an Oracle 10g class now, and we'll give you the exam FREE. http://ads.osdn.com/?ad_id=3149&alloc_id=8166&op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/list

[PyMOL] pymol/apbs plugin rpm

urceforge.net/lists/listinfo/pymol-users -- Cameron Mura UCSD

Re: [PyMOL] loading electrostatic maps generated with apbs

g Python packages: CHEMCCA35:NFkB[8] rpm -qa | egrep -i python python-2.2.2-26 python-optik-1.4-2 rpm-python-4.2-1 python-devel-2.2.2-26 gnome-python2-canvas-1.99.14-5 gnome-python2-gtkhtml2-1.99.14-5 gnome-python2-bonobo-1.99.14-5 python-numeric-devel-22.0-2mdk libxml2-python-2.5.4-3.rh9 gnome-python2-1.99.14-5 python-numeric-22.0-2mdk -- Cameron Mura UCSD

Re: [PyMOL] loading electrostatic maps generated with apbs

et Broadband Sign-up now for SourceForge Broadband and get the fastest 6.0/768 connection for only $19.95/mo for the first 3 months! http://ads.osdn.com/?ad_id=2562&alloc_id=6184&op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.

Re: [PyMOL] different colors for two sides of a surface

70&alloc_id=3638&op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Cameron Mura UCSD

Re: [PyMOL] creating objects from pdb w/out chain id

n.com/?ad_id=1470&alloc_id=3638&op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Cameron Mura UCSD

Re: [PyMOL] PyMOL 0.95 Released

/ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Cameron Mura UCSD

[PyMOL] how to search PyMOL-users archive?

hi, simple/stupid question -- is it possible to search the archives of this mailing list?? If so, how does one go about it? I tried looking at , but didn't see an obvious search mechanism... Thanks, Cameron

[PyMOL] extracting number of residues

Hello, I'm wondering what's the easiest way to extract the number of residues from a PyMOL molecular object?? I need to be able to do this in an automated way for a python script I'm writing. I guess a roundabout way would be to define a selection (say "X_ca") from an object ("X"), and then us

Re: [PyMOL] External GUI does not load - RedHat 9

Hi Najeeb, We had this problem once too. You need to have "Tkinter" (Tk interface) installed -- it's a graphical user interface for the Python language in which PyMOL is written. For example, on our system we use the "python-2.2.2-26" and "tkinter-2.2.2-26" packages with PyMOL 0.88. The Tkint

Re: [PyMOL] settings for Adobe Premiere

For lots of image conversion/movie-making on your Windows PC -- including direct import of PNG sequences -- another piece of software to consider is Logipole's "Konvertor" file convertor. I used this a while ago when I was trying to go backwards from what most people are describing here (i.e.,

[PyMOL] 2 questions about Summit drivers w/ Radeon8500 card for stereo...

Dear PyMOL and O list members, I just got stereo working on my machine (PC, Red Hat 9, Radeon8500 (64MB) video card) after installing Xi Graphic's Summit v2.2 DX-Platinum drivers to enable quad-buffered software stereo, but I noticed that 3D stereo rendering in 'PyMOL' and 'O' seems a lot slow

Re: [PyMOL] (no subject)

Hi Martin, Visit Robert Campbell's repository of PyMOL scripts (http://adelie.biochem.queensu.ca/~rlc/work/pymol/)...where you'll find Python scripts to import into PyMOL for drawing unit cell edges (draw_cell.py), symmetry axes (draw_symops.py), and lots of other stuff... Cameron mkie

[PyMOL] stereo on rh9 ?

appreciate hearin bout it! Cameron -- ------ Cameron Mura Urey Hall, Rm. 4234 Department of Chemistry & Biochemistry University of California, San Diego 9500 Gilman Dr. Dept. 0365 La Jolla, CA 92093-0365 Email: cm...@mccammon.ucsd.edu Phone: 858.534.0956 Fax: 858.534.7042 --

[PyMOL] PyMOL compatibility w/ NVidia card on rh9 system

lized by PyMOL? But I don't know enough to fix it Has anyone else seen (and fixed?) this problem?? Thanks a lot, Cameron PS. How does one search through the pymol users list mail archive at http://sourceforge.net/mailarchive/forum.php?? -- -

[PyMOL] color by B-factor?

Hello, If possible, how does one color a PDB representation in PyMOL by the B-factor field?? Thanks! Cameron -- -- Cameron Mura Urey Hall, Rm. 4234 Department of Chemistry & Biochemistry University of California, San Diego La Jolla, CA 92093-