Re: [PyMOL] Re. Pymol Ray problem

Hi Changdev -  Try the following command, which will save a ray-traced PNG image with transparent background (which is what is represented by the checkerboard pattern):     png myfigure.png, ray=1 Alternatively, you can adjust the ray background setting:     set ray_opaque_background, 1 Hope

[PyMOL] Re. Pymol Ray problem

Hello there, When I do ray, it shows brown and white square in the background. I want to capture image directly from screen but squares also get copied. Is there any way to remove these squares and capture image directly from the screen. Regards, Changdev _

Re: [PyMOL] re： cartoon and line representation

Hi Yeping - Yes, I can. But there is one additional requirement: to save all the states, you must add a `state=0` keyword argument to the save command to include all states. Otherwise, the default is `state=-1`, which includes only the current state. http://www.pymolwiki.org/index.php/Save

[PyMOL] re： cartoon and line representation

Dear Jared,I am using  Open Source PyMOL 1.6.0.0. If you save the whole virus structure as a single pdb file, and reload it into pymol and then show it as cartoon, can you still display the whole structure? As for me, it can display only one chain shown as cartoon_loop.Best regards. Yeping Sun

Re: [PyMOL] RE： RE： what is the pymol representation in this figure?

t work. > > Best Regard. > > Yeping Sun > > Institute of Microbiology, Chinese Academy of Sciences > > > -- > 发件人：Gianluca Santoni > 发送时间：2014年7月11日(星期五) 14:59 > 收件人：孙业平 > 抄　送：pymol-users &

Re: [PyMOL] RE： what is the pymol representation in this figure?

Dear Yeping, you should check Jared's reponse to your message. I think he gave you all the hints you need. :) Gian On 7/11/14 8:27 AM, sunyeping wrote: > > 发送时间：2014年7月10日(星期四) 21:20 > 收件人：pymol-users > 主　题：Re: [PyMOL] what is the pymol representation in this figure? > > It should be a solid surf

[PyMOL] RE： what is the pymol representation in this figure?

发送时间：2014年7月10日(星期四) 21:20 收件人：pymol-users 主　题：Re: [PyMOL] what is the pymol representation in this figure? It should be a solid surface with transparency on, if I'm not getting it wrong.Dear Gianluca,Thank you for the response, but how to set the side chain of the selected residues as solid su

Re: [PyMOL] RE： gradually changed colors with b-factor colum

Hi Yeping - It doesn’t look like Spectrumbar supports additional labeling, but you could add labels at each end by using pseudoatoms at the positions where you want the labels to appear (see the second example at http://pymolwiki.org/index.php/Pseudoatom). For the 2D gradient box, you can crea

[PyMOL] RE： gradually changed colors with b-factor colum

Dear Jared,Thank you for the reply. But I still have a couple of questions:      As for the spectrumbar script, how could I assign a particular data value to a particular color?  By using the command:spectrumbar blue, white, redI can get a spectrumbar. If the range of my data is -0.3~2.3, maybe I

[PyMOL] RE : How to install Psico module for pymol with window 7

OK Thomas, Thank you for your comments, I will try to upgrade to a more recent version of pymol. A bientot, Cheers Stephane De : Thomas Holder [thomas.hol...@schrodinger.com] Date d'envoi : vendredi 10 mai 2013 20:48 À : ABEL Stephane 175950 Cc: pymol

[PyMOL] RE : Replicate a cubic unit cell in the x, y, z directions

Hi Jason It is exactly what I want !!! Merci beaucoup Cheers Stephane De : Jason Vertrees [jason.vertr...@schrodinger.com] Date d'envoi : vendredi 10 mai 2013 20:25 À : ABEL Stephane 175950 Objet : Re: [PyMOL] Replicate a cubic unit cell in the x, y, z

[PyMOL] RE : Pymol Scripts for Coarse grained for non-protein molecules

Hi Tsjerk, Many thanks for your help, once again ;0 It works and it gives what i want. cool !! Stephane De : Tsjerk Wassenaar [tsje...@gmail.com] Date d'envoi : vendredi 1 mars 2013 13:56 À : ABEL Stephane 175950 Cc: pymol-users@lists.sourceforge.net Obje

[PyMOL] RE : Write in a file the number of water at a distance from a protein surface

Thank you for your response, i will try your suggestion A bientot Stephane De : Thomas Holder [ad...@thomas-holder.de] de la part de Thomas Holder [spel...@users.sourceforge.net] Date d'envoi : jeudi 22 septembre 2011 11:14 À : ABEL Stephane 175950 Cc : p

[PyMOL] Re： about tcl/tk gui window

Yes,I tried to install pymol_0.99 on fc4, and fc7 (my own is fc6) on different machine .Only fc4 works . Is there any simple way to fix it not changing the linux distribution. Best 寄件人﹕ Warren DeLano 收件人 LIU Changdong ; PyMOL-users@lists.sourceforge.net 傳送日期﹕

Re: [PyMOL] [Re: Help for X.org-based Stereo 3D on Linux?]

lto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Dirk Kostrewa Sent: Thursday, September 07, 2006 8:54 AM To: PYMOLBB Subject: [PyMOL] [Re: Help for X.org-based Stereo 3D on Linux?] Dear Warren and PyMOL users, we have a current Scientific Linux 4 (a non-commercial Red Hat Enterprise Clone) with X.org i

[PyMOL] [Re: Help for X.org-based Stereo 3D on Linux?]

Dear Warren and PyMOL users, we have a current Scientific Linux 4 (a non-commercial Red Hat Enterprise Clone) with X.org installed at PSI, and stereo works fine with an Nvidia Quadro card with 3-pin mini-DIN connector by just adding a "Stereo 3" option in /etc/X11/xorg.conf (and I've added a mode

[PyMOL] Re: PyMOL-users digest, Vol 1 #1223 - 4 msgs

Subject: [PyMOL] Superimpoition problem Use first structure for reference and then align rest of them to first one. --- pymol-users-requ...@lists.sourceforge.net wrote: > Send PyMOL-users mailing list submissions to > pymol-users@lists.sourceforge.net > > To subscribe or unsubscribe via

Re: [PyMOL] RE: povray image mapping and default pigments

te lake lapping at the shores of a checkered > beach??? > > :) > > -Tom > > > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net on behalf of Seth Harris > Sent: Tue 4/18/2006 2:45 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] R

RE: [PyMOL] RE: povray image mapping and default pigments

kered beach??? :) -Tom -Original Message- From: pymol-users-ad...@lists.sourceforge.net on behalf of Seth Harris Sent: Tue 4/18/2006 2:45 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] RE: povray image mapping and default pigments To answer my own question...instead of ent

[PyMOL] RE: povray image mapping and default pigments

To answer my own question...instead of entirely taking out the pigment{blah blah blah} statements from the texture_lists in the povray input as used to work, I found that in this case replacing them with "pigment {}" statements was still a permissible syntax and also allowed a #default pigment decl

[PyMOL] RE: filter for edit settings window

Hi Michelle, In case no one's mentioned it yet, Zac Panepucci has contributed a grepset.py script which, after being run, allows you to type "grepset x" to see all settings (and their values) associated with whatever x is. It's not directly integrated into the pymol distribution but pretty

[PyMOL] Re: pqr file

I probably didn't make myself clear in my last email. What I meant is that there is an option in pymol APBS tool that allows one to use pymol to generate pqr file from pdb file, instead of loading an pqr file generated externally. I noticed that the electrostatic potential looks quite different fo

[PyMOL] RE: labels not displaying

Marilyn, We saw this between unix and PC and one user figured out that label_font_id's were different. Thus older versions didn't recognize as many fonts as newer ones. I'm thinking this matches your description if the binaries on the two machines are in fact different versions. Try: set label_fo

[PyMOL] Re: Ray-tracing inner surface backside

So, I tried rendering using transparency_mode = 1 or 0 and got this result: http://pwe.no-ip.org/other/Pymol2.png Is there a way to get rid of the transparency that darkens some parts of the surface where something lies behind? I also tried povray to render the surface and it gives me a tex

[PyMOL] Re: PyMOL-users digest, Vol 1 #1176 - 1 msg

;Seth Harris" To: pymol-users@lists.sourceforge.net Subject: [PyMOL] RE: Angstrom-squared values for solvent/protein contact surface per residue --=_Part_19793_7876172.1144104983332 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disp

Re: [PyMOL] RE: making a movie from saved scenes

Dear Warren, this little thread points nicely to the major problem that I have quite often with PyMol: it is a really powerful program, but the documentation is somewhere scattered between various incomplete sources (manual, reference list, wiki, bulletin board, user home pages, ...). This mak

[PyMOL] RE: Angstrom-squared values for solvent/protein contact surface per residue

Just to throw my 2 cents in following Warren's invitation, I think Mark Gerstein's programs work well for this (calcsurf.exe or something...they're on his web site) ccp4's areaimol does something similar, though I can't recall whether its output was atom by atom. In either case, you may have to add

[PyMOL] RE: making a movie from saved scenes

Hi Sun, Warren (and others?) has posted some text before about this. A simple template for it is as follows with the key being that mview interpolate command at the end. This works, but I haven't been through it recently to remind myself of the nuances of the animate=0 options and the view=0 optio

[PyMOL] RE: SF

> Did you change anything on SourceForge? I lost CVS access > somehow. Is this due to the switch to SVN? Did you import > PyMol into SVN? > No. It's not just you -- SourceForge has been experiencing a major CVS outage since early Thursday morning.

[PyMOL] Re: building peptides (gilleain torrance)

Thx Gilleain! Cheers, Alan > Message: 1 > Date: Wed, 15 Mar 2006 09:37:55 + > From: "gilleain torrance" > To: Pymol > Subject: [PyMOL] Re: building peptides > > Hi, > > The wiki has a page on this: > > http://www.pymolwiki.org/index.php/Peptide

[PyMOL] RE: [ccp4bb]: off-topic: labelling stereo with PyMOL

Isabel, There is a PyMOL-Users mailing list for such questions at As for making stereo labels, the latest PyMOL release 0.99rc6 has variable-size, stereo 3D labels that can be positioning using the mouse (whe

[PyMOL] Re: building peptides

Hi, The wiki has a page on this: http://www.pymolwiki.org/index.php/Peptide_Sequence except it doesn't mention the zwitterion details. There's a link to Robert Campbell's scripts to do this sort of thing, so maybe the answer is there. As for for loops, this is best in a full python script (run

[PyMOL] Re: OSX quad buffered stereo possible on older G5 with GeForce FX5200!

Dear All, after reading the post below, for a new quad buffered stereo plugin for OSIRIX, I though I would try it out on my older apple G5 with GeForce FX5200, just for a giggle, not expecting it to work on this older graphics card. OSX 10.4.5 As far as I am aware, the only card apple rec

[PyMOL] RE: selecting surface residues only

Jean, I have been playing around with the Caver plugin to map concave areas on the molecule. The program makes a mesh map of the "tunnel" that you can then use as an object to select nearby atoms that tend to be on or near the surface. If anyone knows an easier way, please let us know. Aaron Ne

[PyMOL] Re: wizard path option

On Tue, Feb 28, 2006 at 10:38:40AM -0800, Warren DeLano wrote: > Indraneel, > > At present, wizards need to be located in the > $PYMOL_PATH/modules/pymol/wizard directory -- changing this would be > nontrivial, since all wizards are assumed to reside in the > "pymol.wizard" namespace. So this mea

[PyMOL] RE: wizard path option

Indraneel, At present, wizards need to be located in the $PYMOL_PATH/modules/pymol/wizard directory -- changing this would be nontrivial, since all wizards are assumed to reside in the "pymol.wizard" namespace. FYI: module-name.__path__ has a different meaning than sys.path. Cheers, Warren --

[PyMOL] Re: PyMOL-users digest, Vol 1 #1143 - 3 msgs

Dear all, I made a PQR file by PDB2PQR, and then in PyMOL, I run apbs. I got an error. Help. PyMOL(TM) Incentive Product - Copyright (C) 2006 DeLano Scientific LLC. A current PyMOL Maintenance and/or Support Subscription may be required for legal use of this Build beyond a finite honor-s

[PyMOL] Re: invoking pymol the unix way on os x

You can call the executable inside an application and it will work in the normal unix way, eg /Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL You might want to make an alias or a function or a symbolic link like alias pymol=/Applications/Xtal/MacPyMOL.app/Contents/MacOS/MacPyMOL or pymol(

[PyMOL] Re: electrostatic potential of nucleic acids possible in pyMOL?

Yes. In fact I just added a description of how to do this in the PyMol Wiki. http://www.pymolwiki.org/index.php/APBS The apbs plugin will work , but you should use pdb2pqr to generate the nucleic acid pqr file externally, and then read it in. Then it works the same as for proteins. HTH, Bill

[PyMOL] Re: PymolX11Hybrid problems (Avram Slovic)

> > I am having a hard time getting PymolX11Hybrid properly installed on > my G4 powerbook. My goal is to make molecular surfaces with > elctrostatic potentials. What am I doing wrong? I installed the > newest version of MacPymol, duplicated it, renamed it > PymolX11Hybrid. Then I downloaded the

[PyMOL] Re: using 1 button mouse with MacPyMol

I too have had this problem. Even if you switch to 2-button selecting, I can't seem to zoom, no matter what finger-twisting combinations I try! I do have a usb mouse, but I wonder if this is now vital, or merely still convenient? gilleain torrance On 2/7/06, andr...@biochem.utah.edu wrote: > An

RE: [PyMOL] Re: [ccp4bb]: Mac Intel Benchmarks

to:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Ulrich Baumann > Sent: Monday, February 06, 2006 12:27 AM > To: Warren DeLano; pymol-users@lists.sourceforge.net > Subject: [PyMOL] Re: [ccp4bb]: Mac Intel Benchmarks > > Hi Warren, > > is this a stereo system? This

[PyMOL] Re: [ccp4bb]: Mac Intel Benchmarks

Hi Warren, is this a stereo system? This would be very cheap, a quadro card costst usually more. Cheers, Ulrich - Original Message - From: "Warren DeLano" To: ; "CCL Subscribers" ; "CCP4BB" ; Sent: Sunday, February 05, 2006 10:42 PM Subject: [ccp4bb]: Mac Intel Benchmarks ***

[PyMOL] Re: [o-info] RE: [ccp4bb]: Current Stereo 3D Display Info

these displays for a rainy day. I've just given up on stereo and switched to using higher-end LCD displays. Less energy, less heat, and less eye fatigue for me. Let me quote myself from a posting to o-info from September 1994: > Real men don't Use Stereo A few hours later, Eleanor replie

[PyMOL] Re: [ccp4bb]: Current Stereo 3D Display Info

Hi Stuart, Well, 20,000 £ (ex VAT) for a 20" UXGA is probably not something a lab can afford as easily as a CRT + graphic board... unless you would like to ship some free for advertisement (-; Best regards, Philippe Le 31 janv. 06, à 14:25, Stuart McKay a écrit : Anastassis,   Interesting

Re: [PyMOL] Re: [ccp4bb]: Current Stereo 3D Display Info

Hi there, Most modern monitors are very clever and tell the X server their preferred sync rates (which never exceed 85 Hz). You can override this functionality by adding Option"UseEdidFreqs""0" to the "Device" section of your Xorg (or XFree86) config file. You will also need to speci

[PyMOL] Re: [ccp4bb]: Current Stereo 3D Display Info

Hi all - While on the subject and after thanking Warren for providing the excellent resource ...: We have some nice 3D monitors and Nvidia cards in Linux PC's we do stereo with. Warren correctly points out that you need: 1280x960 @ 120 Hz requires H-sync of 123 kHz 1344

[PyMOL] RE: [ccp4bb]: Current Stereo 3D Display Info

I believe that even the large Phillips (22") that you list is no longer being made and that what is in stock at places is just old inventory (could be wrong though). It is hard to believe, but these monitors just aren't being made anymore. We literally have people in our modeling group hording th

[PyMOL] RE: Program or Script to Calculate Atom-Atom Distances in pdb files

Irida, > I am looking for a free program > or script that can calculate all sulfur-sulfur distances in > pdb files from the Protein Data Bank. This is the kind of problem you can solve in PyMOL with just a few lines of Python code. For example: from pymol import cmd from glob import glob for

[PyMOL] Re: PyMOL-users digest, Vol 1 #1103 - 3 msgs

Some options were posted along these lines but you have to know what to look for since they are under titles like EM-izing your structure. You can try: set surface_quality, -3 (I think that's as low as you can go, more negative doesn't get any blobbier). And a bit less simple but I think you'll p

[PyMOL] Re: New spectral color pallette

how can i get 300 dpi image or picture of higher resolution from pymol On 1/5/06, Robert Campbell wrote: > Alexander, > > * alexander.paut...@bc.boehringer-ingelheim.com wrote: > > > > > > I would like to color my protein according to B-factor with a > self-defined > > > spectral palette (In this

Re: [PyMOL] Re: New spectral color pallette

Alexander, * alexander.paut...@bc.boehringer-ingelheim.com wrote: > > > > I would like to color my protein according to B-factor with a self-defined > > spectral palette (In this case I have put sequence conservation into the > > Bfactor this column). I found that > > spectrum b, blue_whit

[PyMOL] Re: New spectral color pallette

This is more half an answer than the real deal, but when I had the same issue I opted for the quick work around of setting the range from -100 to 100 for the blue-white-red palette which effectively made 0-100 correspond to white to red only since there were no negative B factors/conservation score

[PyMOL] Re: PyMOL-users digest, Vol 1 #1088 - 1 msg

It worked for me just yesterday. You should download the new version of the plugin (http://www-personal.umich.edu/~mlerner/PyMOL/apbs_tools.py) and replace the old (it should be located in $PYMOL_PATH/modules/pmg_tk/startup/ but on my Debian sarge system it can be found in found at /usr/lib/python

Re: [PyMOL] Re: PyMOL-users digest, Vol 1 #1085 - 5 msgs

It's broken at the moment. I'm working on a new version. It should be out asap. -- www.umich.edu/~mlerner |_ |Michael Lerner This isn't a democracy;| ASCII ribbon campaign ( ) | Michigan it's a cheer-ocracy. | - against HTML email X | Biophysics -Torrence, Bri

[PyMOL] Re: PyMOL-users digest, Vol 1 #1085 - 5 msgs

Hello, Has anyone gotten the new apbs-0.4.0 to work with the apbs_tools.py plugin script? It doesn't seem to be working for me. My guess is that there are new parameters needed in the input file for 0.4.0 that are not created correctly by the plugin script. I have used the older version (0.3

[PyMOL] RE. how to color inner and outer surface of helix

try this: set cartoon_highlight_color=$COLOR where $COLOR is the color of choice Andrew Wollacott, PhD University of Washington On 12/11/05, pymol-users-requ...@lists.sourceforge.net wrote: > Send PyMOL-users mailing list submissions to > pymol-users@lists.sourceforge.net > > To subscr

[PyMOL] RE: ATI as a substitute to nVIDIA

John & Alain, I am not sure John really intended to cross-post that message, but now that the damage is done, I'll take it one step further: I believe the problem is our sacred open-source cow Linux, or rather that nasty amalgamation of diverse hardware, operating systems, and drivers collectivel

RE: [PyMOL] RE: EMizing an xray structure (Warren DeLano)

to:war...@delsci.com > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Sarina Bromberg > Sent: Thursday, December 01, 2005 9:45 AM > To: pymol-users@lists.sourceforge.net > Subje

[PyMOL] RE: EMizing an xray structure (Warren DeLano)

Warren, These commands (see below) go a long way toward solving the problem of producing low resolution simple structures for my textbook project. I have some questions: The first command elicits an error: PyMOL>alter all,b=3D10 Alter-Error: Aborting on error. Assignment may be incomplete.

[PyMOL] Re: Slowwwww ray

Stuart, Stuart Endo-Streeter Default view, white with black background (sticks): Ray: total time: 15.68 sec. = 229.5 frames/hour. (15.68 sec. accum.) Surface ray (white w/ black background): Ray: total time: 32.67 sec. = 110.2 frames/hour. (48.35 sec. accum.) thanks a lot for the test. I g

[PyMOL] RE: NOTICE: mail delivery status

Now this has got to be the funniest bounce I've received to date as administrator of the PyMOL users list: > -Original Message- > From: pymol-users-ow...@lists.sourceforge.net > [mailto:pymol-users-ow...@lists.sourceforge.net] On Behalf Of > postmas...@name-deleted-to-protect-the-innocen

[PyMOL] Re: transpose_selection

Of course within minutes of posting my question about transpose_selection, I have found the answer for myself. There are a couple of new flags added to the command, which is now: def transform_selection(selection,matrix,state=0,log=0,homogenous=0,transpose=0) When I call it with the flag tra

[PyMOL] Re: flicker Mac 10.4.3

Hi, I can confirm that updating the ATI drivers and using the antialiasing x2 option for MacPyMOL removes the flicker problem (at least on my G4 iBook). The lines look much coarser though i.e. not as nice as usual - seems you win some you lose some.. Brian On 4 Nov 2005, at 13:15,

Re: [PyMOL] Re: macpymol beta 21 bug in 10.4.3?

Dan -- Dr. Daniel Moriarty Siena College Chemistry and Biochemistry Dept. 515 Loudon Road Loudonville, NY 12211 (518) 783-2472 fax: (518) 276-4887 > From: Martin Montgomery > Date: Fri, 4 Nov 2005 13:05:10 + > To: pymol-users > Subject: Re: [PyMOL] Re: macpymol beta 21 bug in

Re: [PyMOL] Re: PyMOL-users digest, Vol 1 #1050 - 7 msgs

Thanks Jesper, That seems to work!!! MGM On 4 Nov 2005, at 13:06, Jesper Karlsen wrote: Hi Mac users, MGM wrote: "Having just read Jesper's email regarding getting drivers at ATI's website, I had a look and there are no mac drivers available as far as I can see. Only the ATI Display

[PyMOL] Re: macpymol update

of PyMOL, it embeds its own python interpreter. Maybe this will resolve your problem. --=20 S=E9bastien Moretti http://www.igs.cnrs-mrs.fr/ CNRS - IGS 31 chemin Joseph Aiguier 13402 Marseille cedex --__--__-- Message: 4 Date: Fri, 04 Nov 2005 11:55:27 +0100 From: Jesper Karlsen To: pymol-users@li

[PyMOL] Re: PyMOL-users digest, Vol 1 #1050 - 7 msgs

Hi Mac users, MGM wrote: "Having just read Jesper's email regarding getting drivers at ATI's website, I had a look and there are no mac drivers available as far as I can see. Only the ATI Displays software. After installing this on my machine, nothing has changed. The molecule loads fin

Re: [PyMOL] Re: macpymol beta 21 bug in 10.4.3?

Just for completeness, I've now checked a 20" G5 iMac with a 128MB ATI card and it is fine. Also, I can confirm that there is not a problem whilst using X11 pymol on a 64MB ATI card. Cheers MGM Flicker problem here on a PowerBook 1.5 G4 w/ 64 MB ATI card under 10.4.3 however, if I l

Re: [PyMOL] Re: macpymol beta 21 bug?

Flicker problem here on a PowerBook 1.5 G4 w/ 64 MB ATI card under 10.4.3 however, if I launch X11 and run PyMol under that - (version 0.97), then there's no problem Chris On Nov 4, 2005, at 7:26 AM, Martin Montgomery wrote: I've just tested a G5 imac with a GeForce FX5200 with 64MB RAM an

Re: [PyMOL] Re: macpymol beta 21 bug?

I've just tested a G5 imac with a GeForce FX5200 with 64MB RAM and macpymol 99beta21/25 and it works fine with 10.4.3. It seems the problem is limited to ATI graphics cards with less than 256 RAM. nVidea cards are not affected. Will try an ATI card with 128MB RAM if I can find one here.

Re: [PyMOL] Re: macpymol beta 21 bug?

On Nov 4, 2005, at 12:38, Martin Montgomery wrote: Tested 99beta21 and 99beta25 on a dual 2.5 with ATI 9800 XT (256 MB) with 10.4.2 and it works fine. After upgrading to 10.4.3 on that machine, everything is still fine. Also tried 99beta25 on my machine (ATI 9600 Pro - 64MB) and that sti

[PyMOL] Re: macpymol beta 21 bug?

Hi Warren, Tested 99beta21 and 99beta25 on a dual 2.5 with ATI 9800 XT (256 MB) with 10.4.2 and it works fine. After upgrading to 10.4.3 on that machine, everything is still fine. Also tried 99beta25 on my machine (ATI 9600 Pro - 64MB) and that still has a problem. I then booted into my

[PyMOL] Re: PyMOL-users digest, Vol 1 #1049 - 6 msgs

HI Mac users, Brian Goodfellow wrote: has anyone noticed an annoying flickering appearing when rotating a =20 molecule in PymolX11 and MacPyMOL under 10.4.3 that wasn't present =20 under 10.4.2? The problem appears on both my iBookG4 and iMacG5. If =20 the window is moved then the flickering di

[PyMOL] Re: new MacPyMOL on Tiger : _opengl

Hi, Using the callbacks on the newest macpymol on tiger doesn't work: run /Applications/MacPyMOL.app/pymol/examples/devel/gl01.py Traceback (most recent call last): File "/Users/delwarl/MacPyMOL/build/MacPyMOL.app/pymol/modules/ pymol/parser.py", line 273, in parse File "/Users/delwarl/Mac

RE: [PyMOL] Re: Apple's tk and pymol

Hi Warren: The display window is actually X so I assume it must be fink/X11 glut. Sorry I omitted that. Bill > > Are you using Framework GLUT or Fink/Xll GLUT? The latter might work >

RE: [PyMOL] Re: Apple's tk and pymol

> -Original Message- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > William Scott > Sent: Thursday, October 20, 2005 4:28 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Re: Apple'

[PyMOL] Re: Apple's tk and pymol

I just fired up pymol installed via fink using Python compiled against a Framework build of Python that in turn is build against the TCL TK framework. your either get interaction with the GLUT GUI, or the Tcl/Tk user interface, but not both : (. I can't reproduce the problem, i.e., both gu

[PyMOL] Re: PyMOL-users digest, Vol 1 #1032 - 3 msgs

Oliver, I know it'll sound crazy but -- "get". :-) For example, get two_sided_lighting or get bg_rgb I think this is covered on the Wiki somewhere, too. (http://www.pymolwiki.org/) HTH, -- Jason On Wed, 2005-10-19 at 20:24 -0700, pymol-users-requ...@lists.sourceforge.net wrote: > Message:

Re: [PyMOL] Re:

Kostas, This command: dist name, sel1, sel2, mode=3D2 doesn't work because the move value should be a whole number ie. 1,2,3 etc. Also unless you have some objects actually called sel1 and sel2 you won't get anything meaningful back. something like this: dist name, resn lys, resn glu, mode=

[PyMOL] Re:

On Tuesday 18 October 2005 16:36, pymol-users-requ...@lists.sourceforge.net wrote: Hi Warren It's been a long time since my last post. Anyway I tried the polar contacts identifier as written below > dist name, sel1, sel2, mode=3D2 and I get the following error Traceback (most recent call last):

[PyMOL] Re: New user needs help! (Michael Morbious)

Michael Morbious wrote: > Dear All, > I am a new pymol user. Does anyone know if it is > possible to merge four units (all units are same) of a > tetrameric assembly by using pymol? Each unit has the > same Id and when I load each of them, they overlap. > If you please help me, I will be really

RE: [PyMOL] Re: Need testers for new MacPyMOL on Tiger

273 Cell:(650)-346-1154 . mailto:war...@delsci.com > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Kevin Gardner > Sent: Saturday, October 15, 2005 5:01 AM > To: pymol-users@li

[PyMOL] Re: Need testers for new MacPyMOL on Tiger

Hi Warren: For cutting-edge Mac users, there is a new MacPyMOL for Tiger that integrates into a single window and links to the system Python instead of bringing its own copy (in part this is necessary preparation for Intel...). http://delsci.com/beta Works great here, too. My only request wo

Re: [PyMOL] Re: PyMOL-users digest, Vol 1 #996 - 2 msgs

On Tue, 13 Sep 2005, surendra negi wrote: check this link! http://www.csb.yale.edu/userguides/graphics/pymol/electro.html That page is actually quite out of date. I emailed them about it a few months ago, but didn't get a response. You don't need to go through any of that hassle to use t

[PyMOL] Re: PyMOL-users digest, Vol 1 #996 - 2 msgs

check this link! http://www.csb.yale.edu/userguides/graphics/pymol/electro.html Hope it wud help. best sn --- pymol-users-requ...@lists.sourceforge.net wrote: > Send PyMOL-users mailing list submissions to > pymol-users@lists.sourceforge.net > > To subscribe or unsubscribe via the World W

[PyMOL] RE: [PyMOL] Re： RE: [PyMOL] ques tion about _cmd.pyd

essage- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > wenming hu > Sent: Wednesday, August 24, 2005 6:29 PM > To: Warren DeLano; pymol-users@lists.sourceforge.net > Subject: [PyMOL] Re： RE: [PyMOL] question

[PyMOL] Re： RE: [PyMOL] question about _cmd.pyd

I see. thank you for your answer. and i'm wondering, how do u develop python modules like _cmd.pyd? only via setup.py, and type python setup.py build to compile it? how do u debug it on the procudure of development? for me, it's not easy to develop _cmd.pyd only via setup.py script, i think, the

RE: [PyMOL] Re: Using CMYK color space

On Mon, August 22, 2005 2:55 pm, Warren DeLano said: > > Hold on -- from the end-user's standpoint, the only thing that matters > is: "does the image I see on the screen match what comes out of the > printer". Who cares about the "printer's point of view"?! The printer (a person running the press

RE: [PyMOL] Re: Using CMYK color space

> > Hi Pymol'rs, > > > > I have search the Wiki and Mail-list archive to find a protocul for > > using the CMYK color space, but have only found > "color-safe" definitions. > > > > My Question(s): > > > > When do you define the color space during the creation of a > figure to > > ensure usage o

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

Hi Joe and other KVM users, Not to revive too old of a thread (see emails below), but I thought you or some others might like to know what final KVM solution I settled upon for a mixture of windows and linux boxes. I initially tried the common Belkin OmniView SOHO 4-port KVM switch (PS/2 con

[PyMOL] Re: Using CMYK color space

On [2005-Aug-19] Christopher Colbert wrote: > > Hi Pymol'rs, > > I have search the Wiki and Mail-list archive to find a protocul for using > the CMYK color space, but have only found "color-safe" definitions. > > My Question(s): > > When do you define the color space during the creation of a figu

[PyMOL] Re: PyMOL-users digest, Vol 1 #981 - 12 msgs

Nat, I'm working on a 'smart' alignment program, hence the rotation and translation part is a subset of the work. (The part that's written thus far is the Kabsch algorithm for optimal alignment of two sets of points of vectors). I've uploaded the complete script, but what you want is the part to

[PyMOL] RE: [ccp4bb]: SUMMARY - nVidia Quadro FX 1400, FX 3400 and FX 4400

>>>*** ABOUT RivaTuner (suggested by Wang Chern Hoe): *** I'll keep that trick for my personal record and use, but we don't want to use any dual boot solution in the lab (at least not yet). For a whole lab solution I will agree with Cameron (cm...@ucsd.edu) who suggests to opt for a real ha

[PyMOL] Re: PyMOL-users digest, Vol 1 #963 - 12 msgs

Sreekala, You want to 'split_states'. Load the biological unit into Pymol then run 'split_states'. Check out the PyMolWiki: http://www.pymolwiki.org/index.php/Split_States where it's described more fully. -- Jason On Mon, 2005-08-01 at 20:22 -0700, pymol-users-requ...@lists.sourceforge.net wr

[PyMOL] Re: vmd-l: FC4 stereo problems

Hi, I can't comment about how the NVidia stereo works with other packages but there are a few facts about the NVidia drivers that apply equally to all of us: - Unlike classic graphics workstations like SGI and Sun, with NVidia you can have _either_ stereo, or you can have multisample

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

I have been using a Tripp-Lite 2 port KVM switch now for about 3 years with a whole different combination of platforms and have yet to run into a problem. Len On Wed, 2005-07-27 at 08:48, D. Joe Anderson wrote: > On Fri, Jul 15, 2005 at 01:15:13PM -0700, Cameron Mura wrote: > > > there may be m

[PyMOL] Re: PyMOL-users digest, Vol 1 #958 - 3 msgs

Yes. You can do this with pymol easily.First open both PDB files in PYMOL. Now go to mounse menu option and click on 3 Button editing mode. Next step double click on any atom of the PDB file which you want to rotate or translate wrt first. Press shift and use left mouse button to rotate or press s

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

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 nice if the KVM, linux boxes, and USB mouse were all > >interoperable. Reason i point this out is that the logitec

[PyMOL] RE: [ccp4bb]: nVidia Quadro FX 1400, FX 3400 and FX 4400 performances

Hi Philippe, If you are using the Windows platform, I suggest you get a Geforce 6800Ultra, and use rivatuner from http://downloads.guru3d.com/download.php?det=163 to modify the driver to Quadro FX 4400 under Windows XP. Thereafter, substitute O with NOC from http://noc.ibp.ac.cn/ and you shoul

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