Re: [ccp4bb] Strange Density

One of the great things about open-source code is that you simply have no idea how, where, and when people will apply it. Nevertheless, it is important for everyone to recognize that the following activities are *unsupported* uses of the PyMOL open-source software: 1. solid, isomesh, or dot rende

Re: [ccp4bb] Mac Pro questions

Mischa, Though the FX4500 is expensive, it is (unfortunately) the only option for hardware stereo 3D. And with that card, I can personally attest to the fact that it is possible to have a 30" LCD and a ~22" stereo-capable CRT running simultaneously off of a single Mac Pro system. Thus, you can

Re: [ccp4bb] The CCP4 license is ambiguous

> Behalf Of Ethan Merritt > > What you cannot do is mix GPL and non-GPL code within a single > program. This sounds clear until the lawyers start arguing > about what is or is not a single program [*]. At this point > opinions and arguments and legal precedents diverge. [*] "Ay, there's the rub

Re: [ccp4bb] Pymol - windows

ds still available on the internet, (2) compile source code and self-support, or (3) convince someone else to do the work involved in option (2) on their behalf. Thanks to everyone who has or is sponsoring PyMOL. And yes, by the way, a 1.0-release has at last been issued :). http://www.pymol.org

Re: [ccp4bb] PDB format survey?

Joe, I feel that atom serial numbers are particularly important, since they, combined with CONECT records, provide the only semi-standard convention I know of for reliably encoding bond valences information into a PDB file. single bond = bond listed once double bond = bond listed twice triple b

Re: [ccp4bb] PDB format survey?

ence Center, KSC 121 > Idle Hour Blvd, Oakdale, NY, 11769 > > +1-631-244-3035 > [EMAIL PROTECTED] > = > > On Fri, 10 Aug 2007, Warren DeLano wrote: > > > That's easy: Bac

Re: [ccp4bb] PDB format survey?

t;record" > (whatever it's called now) be as long as we wish? Instead of > compressing a lot on a PDB record line, can we lengthen it to > 130 columns? > > > Bernie Santarsiero > > > On Fri, August 10, 2007 10:10 am, Warren DeLano wrote: > > Corre

Re: [ccp4bb] PDB format survey?

Message- > From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On > Behalf Of Warren DeLano > Sent: Thursday, August 09, 2007 5:53 PM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] PDB format survey? > > Joe, > > I feel that atom serial numbers are pa

Re: [ccp4bb] How to obtain specific chain protein structures without ligand?

Sure -- PyMOL can be used as a command-line tool to do stuff like this. pymol -qc input.pdb -d 'remove not polymer;save prot_only.pdb' > -Original Message- > From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On > Behalf Of Hyunchul Kim > Sent: Thursday, August 30, 2007 7:25 AM > To: C

Re: [ccp4bb] display a map from a quantum chemical calculation

What? You actually want to compare theory and experiment? Blasphemy! PyMOL can supposedly read simple Gaussian cube files (.CUBE) where the axes are XYZ-aligned -- and from what I understand, QM programs can output those kinds of CUBE files. Cheers, Warren > -Original Message- > From

Re: [ccp4bb] Protein models in Blender

PyMOL can save both VRML2 (.wrl) and native PovRay versions of the current scene via the save command. Limited support for Maya .OBJ is present now as well (export bug fixed in current open-source code). VRML: save scene.wrl POVRAY: save scene.pov MAYA (triangles only, w/o coor) save

Re: [ccp4bb] Why wwPDB and members are doing a poor job.

Nevertheless, there is a huge problem with interoperability between software packages, and this core issue greatly frustrates everyone, not only Joe. Frankly, it is a disgrace that even in 2007, software users in structural biology and computational chemistry still cannot reliably exchange basic m

Re: [ccp4bb] Morphing with mutations

http://delsci.com/morph It's a start... -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Gerard DVD Kleywegt Sent: Wednesday, October 03, 2007 6:55 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Morphing with mutations >What about to do

Re: [ccp4bb] carving up maps (was re: pymol help)

> contour the real density, but only display the contours within > certain radius of selected atoms. That is exactly what PyMOL does. -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Edward Berry Sent: Monday, October 29, 2007 4:33 PM To: CCP4BB@JISCMAIL

Re: [ccp4bb] carving up maps (was re: pymol help)

Along those lines, one of the things you can do with PyMOL is color map density based on the color of the nearest atom (if any): Example image at: http://delsci.com/img/map_color.jpg Example script: load ref.pdb load map.xplor isomesh mesh, ref, 1.0 ramp_new ramp, ref, [0,1.5,2], [-1, -1, grey70

Re: [ccp4bb] Any programs other than GRASP have a surface scribing function?

> As far as I am aware, the plugin is not > compatible with the non-X-windows PyMOL on OS X. Actually, it is -- the trick is to rename the "MacPyMOL.app" executable "PyMOLX11Hybrid.app". However, people should note that current MacPyMOL builds are commercial products (not FREE) avialable from

Re: [ccp4bb] 3D Glasses - Vuzix HMD by eDimensional

Pedro, The DV920 works even with frame-sequential stereo, but with a native resolution of 640x480, they aren't useful for real work. Plus, they're not all that comfortable -- I returned them after a couple of week. According to the Vuzix rep I spoke to on the phone, we are still years away from

Re: [ccp4bb] Vista

I pretty much agree with Tassos, but he neglected to mention that on an Intel Mac you can also run Linux and Windows at native speeds, on the same machine, simultaneously. With Parallels software, you also get the added advantage of OpenGL 3D hardware acceleration, whereas with VMWare, you get 64

Re: [ccp4bb] Citations in supplementary information are invisible

That's okay, we forgive you. As penance, you shall establish a new unsocial networking site: "myreciprocalspace.com" with your slighted colleagues cited as key crystal contacts obscured in the published unit sell. > -Original Message- > From: CCP4 bulletin board [mailto:[EMAIL PROTECTED

Re: [ccp4bb] Citations in supplementary information are invisible

age- > From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of > Warren DeLano > Sent: Friday, February 22, 2008 8:46 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Citations in supplementary information are invisible > > That's okay, we forgive you. > &

Re: [ccp4bb] Need help for supperimpose 2 homologous molecules

Hongnan, Recent PyMOL versions can do a structure-based (sequence-independent) superposition as follows: load protein1.pdb load protein2.pdb super protein1CA, protein2CA The per-residue alignment can also be visualized in 1D and 3D as follows: super protein1CA, protei

Re: [ccp4bb] off topic: stereo

Hi Tassos, It'll take more than a cable: the signal voltage changes from 12V to 5V (or vice versa, I forget). I've never seen any info on building a step-down transformer or aomplifier to address the issue, but for ~$200 USD, it's probably easier just to buy a new emitter. Cheers, Warren >

Re: [ccp4bb] While on the subject of stereo

Hi David, This has already been done with PyMOL. There's a video at: http://molviz.cs.toronto.edu/molviz/ and the code is downloadable. The stereo effect isn't so great with both eyes open, but I do think there is potential for use of head or object tracking as a means of controlling rota

Re: [ccp4bb] Making a Poly ala model

Within PyMOL: remove polymer and not name N+CA+C+O+CB alter polymer, resn="ALA" save polyALA.pdb Cheers, Warren -- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Bottomley, Matthew Sent: Thursday, May 29, 2008 5:35 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Making a Poly al

Re: [ccp4bb] 3D model building without CRT monitor

For used-stereo-3D-capable-CRT seekers, our stereo 3D page may be of some use. A number of target monitors are listed. http://pymol.sourceforge.net/stereo3d.html -Original Message- From: CCP4 bulletin board on behalf of Krojer,Tobias Sent: Mon 6/2/2008 5:24 AM To: CCP4BB@JISCMAIL.AC.UK

Re: [ccp4bb] Reminder - still no 3D stereo under OS X 10.5

Hello All, Since I have long been such a big Mac stereo 3D proponent in the past, it is especially important that I go on the record with an updated perspective. Based on all of the accumulated evidence to date, a verdict can now be rendered: we have lost the case. For stereo 3D visualization

[ccp4bb] Progresss with Stereo 3D under Mac OS X Leopard

CCP4bb, Some graphics news: Full operating-system support for stereo 3D has at last been restored on Mac OS X Leopard, but NOT in Leopard's X11 just yet (the Xquartz open-source community will hopefully soon remedy this...). While today's fix is great for native Mac OpenGL applications like MacP

Re: [ccp4bb] Generate high resolution pirctures in pymol

Remember, there's a whole mailing list & wiki dedicated to PyMOL, so no need to clutter up CCP4bb with PyMOL-specific questions! https://lists.sourceforge.net/lists/listinfo/pymol-users http://pymolwiki.org More complete answer: # assuming that movie has already been defined in PyMOL # (su

Re: [ccp4bb] available Stereo 3D LCD monitors / Linux compatibility

Christian, I think it would be great to continue this discussion on CCP4bb, especially as we learn more about all the new stereo-capable display products now hitting the market. It would be even more wonderful if a few volunteers could monitor this discusson and then summarize their distille

Re: [ccp4bb] Facebook for Neerds

> Warren DeLano once suggested myreciprocalspace.com Yes, indeed. But I couldn't quite figure out how to make it work: Instead of each person having their own page, each person would need to have a little weensy bit of everyone else's page. That just sounded way too comp

Re: [ccp4bb] PyMol bulletin Board

Greetings Fred, Links to both the PyMOL bulletin board and source code can be found on the pymol home page: http://pymol.org Seek "Mailing List" and "Source Code". Please do note that Subversion is the sole means for accessing current PyMOL source code, given that our main intent in releasi

Re: [ccp4bb] buster-tnt on OSX ?

or weak documentation, complex installations, sporadic crashes, or lack of undo -- that stuff is all fair game. But calling us just "buck makers"? Now that's below the belt, even in jest! Cheers, Warren DeLano Scientific LLC [EMAIL PROTECTED] -Original Message- From: CCP4 bu

Re: [ccp4bb] pymol cartoon problem

Pramod, PyMOL is sensitive to residue numbering... set retain_order rebuild may help. Cheers, Warren P.S. The PyMOL mailing list can be found at: http://sourceforge.net/mail/?group_id=4546 From: CCP4 bulletin board [mailto:[EMAIL

Re: [ccp4bb] Crystallographic computing platform recommendations?

They're all great! - Linux offers limitless possibility with its concomitant complexity and chaos. - Mac OS X offers the design integrity, consistency, and efficiency of centralized control. - Windows guarantees lowest common denominator functionality for a rock bottom price. So why not buy

Re: [ccp4bb] Planar Systems monitor

Vaheh, No, unfortunately, that will not work. None of the announced 120Hz stereo-capable LCDs are yet available on the market*. For example: http://www.product-reviews.net/2008/08/26/viewsonic-120hz-vx2265wm-lcd-p rototype-revealed/ Although stereo 3D-capable DLP displays are on the market, th

Re: [ccp4bb] Mac pro

> I've heard anecdotal evidence that VMWare Fusion is better, > but I've only used the Linux version. As a heavy user of both products under Mac OS X on an eight-core Mac Pro, I find VMWare to be far more robust and feature rich than Parallels. Regardless, only Parallels supports 3D OpenGL accele

[ccp4bb] Caution - 120 Hz LCDs: Not CRT killers yet...

Stereo 3D Users: I tested out the Samsung Syncmaster 2233RZ / NVIDIA 3D Vision bundle today ($599 for a 120 Hz LCD display with one pair of glasses). Unfortunately, the 2233RZ display is clearly not yet a drop-in replacement for your stereo-3D-capable CRT: The display is very nice, and the stere

Re: [ccp4bb] Nvidia 3D

https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0901&L=CCP4BB&T=0&F=&S =&P=192056 > -Original Message- > From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of > Chris Waddling > Sent:

Re: [ccp4bb] OT: VectorNTI alternatives

> From: Darren Hart > After several years of offering the molecular biology software VectorNTI > free to the academic community (their "open access program") and building > up a huge user base, Invitrogen have suddenly announced that they will no > longer renew these free licences and the existing

Re: [ccp4bb] Caution - 120 Hz LCDs: Not CRT killers yet...

om: Yong Y Wang [mailto:wang_yon...@lilly.com] > Sent: Saturday, January 31, 2009 12:51 PM > To: Warren DeLano > Cc: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Caution - 120 Hz LCDs: Not CRT killers yet... > > Hi Warren, > > The Zalman 3D LCD was mentioned last year. Do you kno

Re: [ccp4bb] Caution - 120 Hz LCDs: Not CRT killers yet...

FYI: I spent some time evaluating the iZ3D today as well. Like the others, this LCD-based solution is dependent on DirectX/3D drivers. But even if it weren't, there is far too much cross-talk between the two stereo images for it to be usable with PyMOL, Coot, etc. While the iZ3D's stereo ghos

[ccp4bb] If you need a Stereo 3D-capable LCD today...

Attention Stereo 3D Users: If you must obtain a Stereo 3D-capable LCD for use with PyMOL *today*, then, in our view, the Zalman Trimon ZM-M220W 22" LCD is the display you should buy: http://www.zalman.co.kr/eng/product/Product_read.asp?Idx=219 (Google: http://www.google.com/products?q=ZM-M220W

Re: [ccp4bb] Question about stereo on LCD monitor

Rafal, Actually, things only really started to change last month... Please see http://pymol.org and scroll down most of the way to the February 13th entry regarding the $600 Zalman ZM-M220W stereo-capable LCD. In my opinion, that is the best option on the market until the "powers that be" star

Re: [ccp4bb] Question about stereo on LCD monitor

. Perhaps this is what will change in April? Given the date, waiting for news does seem like the sensible option at this point. Cheers, Warren > -Original Message- > From: Rafal Dolot [mailto:rdo...@bio.cbmm.lodz.pl] > Sent: Monday, March 30, 2009 5:03 AM > To: Warren DeLano

Re: [ccp4bb] New human genome policy - please read.

You know Kevin, April fools notwithstanding, you idea actually makes good sense in a tiny-url sort of way. There would of course be collisions, and thus, need for a global disambiguation registry, but society could do a whole lot worse than something like: http://prot.seq.db/3fc28e91d74b39ec/a6

Re: [ccp4bb] pymol crashes un ubuntu 8.10

Hey, can one of you guys email me one of these crash-inducing pqr files? PyMOL is not supposed to blow chunks! Thanks, Warren > -Original Message- > From: W. G. Scott [mailto:wgsco...@gmail.com] On Behalf Of William G. > Scott > Sent: Saturday, April 04, 2009 2:21 PM > To: Talavera > Cc:

Re: [ccp4bb] largest distance between atoms

Andreas, In PyMOL: print cmd.get_extent(selection) where selection is the name of the molecule you'd loaded. Note that the set of coordinates which define an XYZ extent do not necessarily correspond to only to atoms. To find the two atoms most distant from one another, you could iterate ove

Re: [ccp4bb] Computer hardware and OS "survey"

My advice: Embrace virtualization for all tasks except interactive 3D visualization. If you're not yet familiar with VMware, Parallels, or open-source work-alikes, then it is high time you joined the revolution --- the rest of us have been running Mac OS X, Linux, and Windows on the same ha

Re: [ccp4bb] Pymol

Hello Mariah, Please note that is the CCP4 mailing list. The PyMOL mailing list is at: http://sourceforge.net/mail/?group_id=4546 In answer to your question, you might first try: dss # If thats doesn't solve your problem, then you can use alter to explicitly assign secondary structure manual

Re: [ccp4bb] 3D LCD and glasses

Stuart, Robert, & Others, I believe Stuart is confusing the Samsumg 2233rz frame-sequential stereo 3D display with the Zalman M220W interlaced stereo 3D solution. Due to lack of driver support, as far as I know, the Samsung isn't yet supported by any OpenGL-based software, although nVidia has

Re: [ccp4bb] Best 3D stereo combination for Mac OS X today

Danny, Last I checked, Apple dropped the Quadro option from the Mac Pro, and a quick check on Apple.com seems to confirm that: http://store.apple.com/us_smb_78313/browse/home/shop_mac/family/mac_pro Lacking indications to the contrary, we can only conclude that OpenGL stereo 3D support has an un

Re: [ccp4bb] Best 3D stereo combination for Mac OS X today

From: Danny Smith [mailto:smi...@omrf.ouhsc.edu] Sent: Tue 6/30/2009 4:03 PM To: Warren DeLano Cc: Danny G Smith; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Best 3D stereo combination for Mac OS X today Warren, Thank you very much for the quick reply. I didn't see it directly with the mac, but thi

Re: [ccp4bb] Best 3D stereo combination for Linux

David J. Schuller >modern man in a post-modern world >MacCHESS, Cornell University >schul...@cornell.edu > > > > Original message > > >Date: Wed, 1 Jul 2009 01:

Re: [ccp4bb] Best 3D stereo combination

: http://www.nvidia.com/object/IO_11761.html combined with the CCP4 wiki's advice (that the card should say "stereo" under display connectors) imply that we need to spend at least $760 on the video card alone. Is that really true??? EEK!! thanks, Phoebe Original message

Re: [ccp4bb] Best 3D stereo combination

ay from the anaglyph "Creature from the Black Lagoon" but once the movie gets going, you almost forget about the 3D effect. Shucks! Cheers, Warren -Original Message- From: Ethan Merritt [mailto:merr...@u.washington.edu] Sent: Sat 7/11/2009 1:31 PM To: Warren DeLano Cc: CCP4BB@

[ccp4bb] OpenGL Stereo 3D on 120 Hz LCDs, at last!

FYI, for folks not subscribed to pymol-users: nVidia today released beta drivers which at last enable OpenGL-based stereo 3D visualization on 120 Hz LCDs using Quadro graphics cards. So long as you are willing to put up with Windows, you can finally abandon those old CRTs without spending a

Re: [ccp4bb] how to generate the figure of buried surface area

Jiamu, That is a question for pymol-users, not ccp4bb: http://sourceforge.net/mail/?group_id=4546 Cheers, Warren PS. here's one answer: # create the objects load $TUT/1hpv.pdb create side1, chain A create side2, chain B dele 1hpv # splay apart the interface show surface, side1 within 5

Re: [ccp4bb] DS Visualizer ActiveX Control in PowerPoint

Yong-Fu, Microsoft in its infinite wisdom decided to bury ActiveX functionality in Office 2007. To access Controls, you need to click on the big round button in the upper-left, select PowerPoint Options, choose then "Popular" tab and then check the "Show Developer tab in the Ribbon" option. T

Re: [ccp4bb] [PyMOL] Extracting Amino Acid Sequence from PDB File

Buz, # Yep, PyMOL 1.2: load $TUT/1hpv.pdb save 1hpv.fasta # or by selection save 1hpv_A.fasta, chain A # etc. Cheers Warren > -Original Message- > From: Buz Barstow [mailto:b...@mac.com] > Sent: Thursday, August 13, 2009 2:39 PM > To: pymol-us...@lists.sourceforge.net; CCP4BB@JISCM

Re: [ccp4bb] curved cylindrical helices in PyMOL?

Actually, PyMOL cannot bend cylindrical helices. The workaround is to break them manually: load $PYMOL_PATH/test/dat/1tii.pdb as cartoon set cartoon_cylindrical_helices # Insert a break into the longest helix (only slightly bent) cartoon skip, C/216/CA Cheers, Warren PS. This is the CCP4

Re: [ccp4bb] [PyMOL] Stereo flipping in coot and pymol

I agree with Dirk - this is likely a hardware problem. From within PyMOL ,it can be worked around via the menu Display->Stereo->Swap Sides or by typing "st sw" (stereo swap) at the command line. Cheers, Warren From: Dirk Kostrewa [mailto:kostr...@genzentr

Re: [ccp4bb] Unit of electrostatic potential in PyMol

Partha, Sorry, but PyMOL's built-in potential calculation is qualitative -- if you care about the actual units, then you should be using APBS instead. Cheers, Warren From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Parthasarathy Sa