Re: [PyMOL] Pymol 1.4 OpenGL issue with openSuSE 11.3 / 11.4

This appears to be a common problem with 1.4 and Jason is aware of it. The same issue exists in Ubuntu 9.04 with Nvidia 180.xx drivers, 32 bit. The Win version works OK. Roger Rowlett On Mar 29, 2011 7:53 AM, "Schubert, Carsten [PRDUS]" wrote: > Joachim, > > I'm running

Re: [PyMOL] Visualizing protein-ligand complexes of metalloproteins

. See the pymol wiki for how to select atoms to link with the bond command. You will have to show sticks to see the bond. Waters are usually visualized as spheres, and you may want to modify their vdw radius to 0.5-1.0 A to make them small enough. Cheers, Roger Rowlett On Apr 18, 2011 5:48 PM

[PyMOL] PUI session at 2012 ACA meeting

Pymol-ers, I am writing to alert the Pymol community that I will be co-organizing (under the auspices of the Council on Undergraduate Research) a session at the 2012 American Crystallographic Association meeting (July 28-Aug 1) devoted to practical aspects

Re: [PyMOL] about Display CCP4 Maps

Lina, If you want to create an "omit" map for your ligand using CCP4i, you can find instructions here for both Fo-Fc and 2Fo-Fc maps: http://capsicum.colgate.edu/chwiki/tiki-index.php?page=Model+Building+and+Validation#Creating_Omit_Maps_for_Ligands_using_Refmac To display an omit map in Pym

Re: [PyMOL] Electron Density

I think the isomesh command will let you set whatever contour level you wish, e.g.: isomesh map, mymap.map, X.X, maparea Where map is the name of the mesh object, mymap.map is the map file name, X.X is the desired contour level, and maparea, is the

Re: [PyMOL] 3D projector for low cost 3D Protein Cave

I'm using an older DepthQ-WXGA system and Quadro FX3700(?) graphics card in a classroom setting and it seems to work fine. Stunning, really. It uses a VGA cable and the 3-pin mini-DIN on the graphics card. I mount the IR emitter on top of the projector and everyone in the room can sync with it

Re: [PyMOL] morphing 3-states

ImageMagick can easily append/adjoin animated gifs. Roger Rowlett On Nov 24, 2012 8:38 PM, "Jordan Willis" wrote: > Hi, > > I have 3 different conformations of the same structure and I was wondering > what is the easiest possible way to morph 3 conformations. > > M

Re: [PyMOL] CentOS installation help

Sounds like a permissions issue. Without more info, I'm not sure what your problem might be specifically, but this is how I install pymol on a central server that is shared via NFS as /usr/local/xtal: 1. copy pymol-1.5.0.x directory into desired shared location, e.g., /usr/local/xtal. I do t

[PyMOL] Pymol 1.6.0.0 setup.sh issue

n shared object file: No such file or directory The pymol 1.5.0.3 shell script and symlink works fine. Running Ubuntu 12.04 LTS. Any ideas? Cheers, ___ Roger Rowlett Gordon & Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamil

Re: [PyMOL] Select different set of atoms in different molecules

What about the following commands: select mystuff, resi 1-3 and m1 select otherstuff, resi 7-9 and m2 Cheers, ___ Roger S. Rowlett Gordon & Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245

Re: [PyMOL] PyMol graphics problem in Ubuntu 13.10, ATI Radeon HD 4650

You can try installing the ATI proprietary driver (fglrx, Catalyst) instead of using the open source driver that come with Ubuntu. Check to see if this driver is compatible with your card. I've had nothing but trouble and bad luck getting ATI graphics cards to work under linux. If building fro

Re: [PyMOL] how to set different dash colors for the distance measurements

How about, color measure01, red color measure02, yellow etc. Roger Rowlett On Dec 24, 2013 8:51 AM, "Li Xue" wrote: > Hello all, > > Is it possible that I could use *different* colors for the dashes for the > distance measurements? > > I know I can use "set das

Re: [PyMOL] animation showing conformational change

You can also do this locally on your own machine if you arrange to get the CNS morph_dist.inp script. (You need CNS to run it, of course.) The nice thing about this method is that it minimizes the structures of the intermediate morphs into something sensible. I don't know how sophisticated PyMo

Re: [PyMOL] help

Clarisa, Depending on what you want to do with the file, you may not need to save a new PDB at all. You could for example, * Issue the command symexp ,,(all),4.0 to generate nearby symmetry mates, then remove the objects you don't need to form the proper dimer. ( is your PD

[PyMOL] Pymol 1.8.0.0 requires ZLIB 1.2.3.5?

Pymol 1.8.0.0 (64 bit linux) is throwing an error about a ZLIB requirement (v 1.2.3.5). The latest Ubuntu 12.04 LTS version through apt-get is 1.2.3.4. Is there supposed to be a local version of zlib.1.so in the pymol install package? ___ Roger S. Rowlett Gor

[PyMOL] Pymol 1.0 graphics bug

In Pymol 1.0, the pymol viewer freezes during an mpng command in progress if the mouse pointer is moved. (Windows XP XP2 only, using Intel chips and motherboard, Nvidia graphics card and driver) PNG files are written out properly, and viewer window becomes live again after completion of the mpn

Re: [PyMOL] Doubts regarding command line argument in pymol

"bg_color white" should do it. Nagarajan wrote: Hello all, I am having some doubts in command line argument in pymol. Can anyone tell me the command to change the background to white using command line..! I can use it in a movie script. Thanking you Nagarajan.P

Re: [PyMOL] customized "sleek looking" isomesh

You can find documentation for displaying CCP4 maps in Pymol at http://www.pymolwiki.org/index.php/Display_CCP4_Maps. Cheers, -- Roger S. Rowlett Professor Colgate University Presidential Scholar Department of Chemistry Col

Re: [PyMOL] The A B Cs of Pymol movies

I kind of like using Slerpy (found on the Pymol Wiki) to assemble highly controlled movies of static structures. The resulting PNG frames can be assembled into an animated GIF using ImageMagick, and if the GIFs are too big (they are lousy in Powerpoint) they can be converted to smaller more eff

Re: [PyMOL] COVER image

Try the command "png filename.png, 1200, 1600, -1, 1" to create an output image 1200 pixels wide by 1600 pixels tall, raytraced. To disable raytracing, change the last argument to zero. Cheers, -- Roger S. Rowlett Profess

Re: [PyMOL] Spheres for metal ions

Gary Hunter wrote: I am displaying pdb files of metalloenzymes, and like to show the metal ions as spheres. I select the metal and use show>spheres Fine Somehow recently I must have done something to reset the vdw radius of manganese (MN in the pdb), as Mn atoms now display as small spheres (a

Re: [PyMOL] Graphics Workstation

Buz Barstow wrote: Dear All, I'm considering purchasing a new graphics workstation for molecular graphics and macromolecular refinement. I'm considering buying a machine with 2 quad core xeon processors, and a nVidia Quadro FX graphics card with 1.5 Gb of memory. Can the current generation of s

Re: [PyMOL] How to view electron densities from the PDB

Robert Campbell wrote: Hi, On Fri, 27 Jun 2008 13:25:02 -0400, Michael Lerner wrote: This is probably a fairly basic question, but I'm stumped. I want to visualize electron densities along with my PDB file. So, say I'm interested in 2DJX. I go to the PDB and download 2DJX.pdb and 2djx-sf.c

Re: [PyMOL] Saving figures for publication

nches, for example, you will need to provide an image of 1800 x 1800 pixels to achieve the required 600 dpi. Roger Rowlett Professor Colgate University Presidential Scholar Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315

[PyMOL] (Simple) unit cell construction

Is there a relatively simply way to get pymol to populate a unit cell with exactly the correct number of copies of the asymmetric unit, i.e., similar to the Uppsala software factory utility XPAND or the "Build Crystallographic Symmetry" command in SPDBV? Ideally, it would be helpful to perform

Re: [PyMOL] advice for the novice movie maker

It's not GUI-based, but the SLERPY plugin is another option, and works well. I've used it to make numerous movies for my classes and research presentations. Cheers, -- Roger S. Rowlett Professor Colgate University Presidential Scholar Department of Chemistry Colgate University 13 Oak Drive

[PyMOL] Disabling cartoon_highlight_color

How do you disable cartoon_highlight_color once it has been enabled? The command "set cartoon_highlight_color, off" does not work in 1.2b3, as suggested by the Pymol wiki. Pymol just reports that "off" is not a color. Cheers, -- Roger S. Rowlett Professor Department of Chemistry Colgate Un

[PyMOL] Caver 2.0.003 plugin

Has anyone got the Caver 2.0.003 plugin working in Ubuntu 9.04? I can install the plugin in pymol, load the example pdb (1MJ5) and open the dialog box, which seems to have the correct paths to the plugin .jar and lib directory. I can even select the correct starting point and have it displayed

[PyMOL] DepthQ configuration in a classroom setting

Has anyone on the board configured a DepthQ projector for classroom use, i.e. using a ceiling-mounted projector. Our IT department has recently installed a DepthQ projector in a classroom-type setting, and it displays stereo Pymol images for about 20 seconds, then loses sync. My configuration i

Re: [PyMOL] Saving high resolution images

For photographs, 180 dpi is often sufficient for large prints. For diagrams, which are less complex, you might even get by with less, maybe even 120 dpi. You could try rendering a portion of your image at that resolution (e.g. 540 x 540 for a 3" square) and see how it holds up at a normal viewi

Re: [PyMOL] New Feature Ideas

Two items come to mind: 1. A Powerpoint plugin for live Pymol viewing in presentations. 2. A simpler method of doing structure morphs in Pymol. Intelligent morphing is incredibly powerful for visualizing protein conformational changes based on "endpoint" protein structures, or just evaluating/

Re: [PyMOL] Calcium radius

FYI, the ionic radius of Ca(2+) is 1.14 A. A calcium atom is 1.80 A. After issuing the "alter elem ca, vdw=1.14" command, you may have to execute the "rebuild" command to change the previously displayed sphere radius. Cheers. On 3/16/2010 11:31 AM, Jason Vertrees wrote: Raluca, Here's how

Re: [PyMOL] pymol and freemol

can run apbs from the command line. To have pymol use this apbs binary, change the path to binary in the apbs plugin configuration dialog box. Alternatively, you could just copy the apbs binary into the freemol/bin/ directory of pymol as apbs.exe (I think). Cheers, Roger Rowlett On 4/15/2010 1:53 PM,

Re: [PyMOL] Updates

Could anyone comment on the demise of pymol 0.99 for download? or the education-only builds? I see if you dig enough there is an educational-only version of Pymol that requires registration. Do the downloaded educational-only executables expire, and how does it d

[PyMOL] Pymol Endnote references

Jason, Thanks for the Endnote reference! I corrected a small formatting error in the author field which prevents it from displaying as "Schrodinger, L." in the citation instead of "Schrodinger, LLC". The Author field should be [Schrodinger,, LLC] and not

Re: [PyMOL] cd in windows

David, Use double quotes or start typing and autocomplete with the key. Cheers. On 9/20/2010 11:20 AM, David A. Horita wrote: Hi, How does one change directories in Windows when the directory

[PyMOL] Pymol 1.4 OpenGL issue with Ubuntu 9.04

When Pymol 1.4 is started in Ubuntu 9.04 with the latest available Nvidia driver for this OS (version 180) I get the following startup error (and strange window rendering where bits of the pymol rendering window are transparent): "Detected OpenGL version p

[PyMOL] Ubuntu 10.04 and pymol 1.4

In pymol 1.4, I get a strange error in Ubuntu 10.04 (VM): "pymol.exe: error while loading shared libraries: libtk8.5.so: cannot open shared object file: No such file or directory" The file is there, and is readable. Any ideas? I have run ./set

[PyMOL] Pymol no longer fetches from pdb

Has anyone else noticed that Pymol (v 1.3 or 1.4) will no longer fetch data from the pdb server? If I issue 'set fetch_host, pdbe' I can fetch data OK, but if you 'set fetch_host, pdb' I'm getting a fetch error for any accession number. --

Re: [PyMOL] Pymol no longer fetches from pdb

Thanks, all. Looks like I'll have to investigate local issues with our institutional firewall. Sigh. Not the first time... Roger Rowlett On Mar 22, 2011 12:58 PM, "Jason Vertrees" wrote: > Great, thanks, David. Just ensuring the problems been isolated. > > Cheers, >

Re: [PyMOL] Getting rid of shadows

One option is to turn off shadows: set ray_shadow, off Will that work for you? ___ Roger S. Rowlett Gordon & Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (

Re: [PyMOL] distance wizard

You are using d = sqrt(dx^2 + dy^2 + dz^2), right? (Where dx = x2 - x1, etc.) ___ Roger S. Rowlett Gordon & Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-2

Re: [PyMOL] How to see a homotetramer

fetch 6h07, type=pdb1 Roger Rowlett Gordon & Dorothy Kline Professor, Emeritus Department of Chemistry Colgate University On Tue, Jan 14, 2020, 3:42 AM Clelia Canova wrote: > Hi! > > I’m studying the file *6H07. pdb *for a project, download for rcsb.com. > How can I se

Re: [PyMOL] CCP4 maps not aligning to my PDB file

-protocols/home/model-building-and-validation Roger Rowlett On Mon, Apr 12, 2021, 2:35 AM shubhashish chakraborty < cshubhash...@gmail.com> wrote: > Hello, > I am not able to align my pdb file with its respective electron density > map generated by CCP4i. Kindly let me know what

Re: [PyMOL] Student version

m has an Intel i3 CPU.) An Intel Chromebook might be an attractive option for undergrads for biochemistry classes and/or protein crystallography research projects. You can install Pymol in Windows with pip as well. Roger Rowlett Gordon & Dorothy Kline Professor, Emeritus Department of Chemistr