Re: [PyMOL] save format for molecule files

Thomas, Joel, yes, writing to mol2 works. Thanks for the suggestion! Xavier Missatge de Thomas Holder del dia dj., 18 de maig 2023 a les 5:38: > Hi Xavier, > > The best option to transfer bond orders from PyMOL to Maestro might be > with .mol2 (or .sdf) format. These forma

[PyMOL] save format for molecule files

ommand and managed to get double bonds right, but the aromatic ones are ignored. Does anyone know how to write files that can be read properly by maestro? Alternatively, is there a way to convert aromatic bonds into alternating single/double bonds, as I think this would be easier to output based on

Re: [PyMOL] get_area algorithm and dot_density accuracy

lculations? DSSP > is likely to be using the rolling ball method. > > Regards. > > On Thu, Apr 27, 2017 at 1:35 PM, Emilio Xavier Esposito > wrote: >> Hi >> The accuracy of the calculation depends on the dot_density value (the >> amount of sampling done) with 1 be

Re: [PyMOL] get_area algorithm and dot_density accuracy

Hi The accuracy of the calculation depends on the dot_density value (the amount of sampling done) with 1 being the lowest quality and 4 being the best quality. A dot_density value of 1 uses less computational resources (time) than a dot_density of 4 because of the amount of sampling performed to ca

Re: [PyMOL] Transparent Background in Educational Version

Hi Cris Please include the ray=1 option in your png test.png, dpi=300 command or use the set opaque_background, off instead of the set ray_opaque_background, off command. Commands to create a PNG file with a transparent background: set opaque_background, off png test.png, dpi=300, ray=1 *PNG fi

Re: [PyMOL] Detecting holes/cavities in surface

Hi Daniel CAVER is another possible PyMOL plugin http://www.caver.cz >From the CAVER website, "CAVER provides rapid, accurate and fully automated calculation of tunnels and channels in static and dynamic structures. The molecules amendable to analysis of CAVER include proteins, nucleic acids, or i

Re: [PyMOL] visualize mode

Hi What about Modevectors? http://www.pymolwiki.org/index.php/Modevectors Emilio On Fri, Jun 19, 2015 at 10:23 AM, Command Line wrote: > Hi, that works for me. Albeit I would be more happy if there would be an > option directly inside pymol. Anyway, thanks. > > 2015-06-18 16:30 GMT-05:00 Osvald

Re: [PyMOL] Is it possible to write PNG images in PyMOL of higher resolution than the viewing window?

Hi Brenton >From the PyMOL command line the PNG file creation/saving command is: PyMOL> png filename, width, height, dpi, ray=1 Notice that ray equals 1 to create a ray-traced image. The dpi option can be set to your desired resolution in dots-per-inch and the width and height options use the unit

[PyMOL] select by size

ligands with > 10 atoms. Xevi -- Xavier Fradera -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/___ PyMOL-users mailing list (PyMOL-users@lists.

[PyMOL] pymol 3D movies

Hi, I am looking into making a quad-buffered stereo 3D movie. Is this possible with mpeg or any other format ? I know I could just play the movie from pymol, but would like to be able to save as mpeg with x-ray traced images for higher quality. Xevi -- Xavier Fradera

[PyMOL] Winners of the Teach-Discover-Treat 2014 Challenge

! The TDT Steering Committee Hanneke Jansen, Rommie Amaro, Jane Tseng, Wendy Cornell, Patrick Walters and Emilio Xavier Esposito -- The best possible search technologies are now affordable for all companies. Download your

[PyMOL] Still time to participate in the Teach-Discover-Treat 2014 Competition!

tools. Detailed information about the 2014 Competition can be found here: http://www.TDTproject.org/2014-competition.html Submissions deadline is February 3, 2014. The TDT Steering Committee Hanneke Jansen, Rommie Amaro, Jane Tseng, Wendy Cornell, Patrick Walters and Emilio Xavier Esposito

[PyMOL] creating anaglyphic 3D images in PyMOL

Hi I know that I can create cross-eye stereo images with PyMOL but I was curious how to create anaglyphic (Red/Blue, Red/Cyan or Red/Blue-Green) 3D images similar to those created in Spartan. Other than post-processing the images with Photoshop, is there a way to have PyMOL natively construct thes

Re: [PyMOL] Question about measuring volume

to used to run voidoo to find cavities. The resulting log files have information about volumes. To visualize the cavities, the resulting .ezd files have to bee converted to .ccp4 with mapman. Hope this helps, Xavier Xavier Deupi Laboratory of Computational Medicine Biostatistics Unit. School

Re: [PyMOL] interior protein-surfaces

e.g. 5 Ang. around the ligand). Hope it helps, Xavier Xavier Deupi Laboratory of Computational Medicine Biostatistics Unit. School of Medicine Universitat Autonoma de Barcelona Bellaterra, 08193 (Barcelona) Catalunya, EU

[PyMOL] grid_mode?

Hi, I've just noticed the grid_mode command announcement in the wiki. I've checked the latest beta, but it seems to be 1.1 beta 3, which is the same I have installed (without the grid_mode command). This seems a great feature, so... how can I enable it? Thanks, Xavier Deupi Lab

[PyMOL] Pymol update and plugins?

I have to completely reinstall Pymol and the plugins or does there is a way to update only the software without removing plugins? Thanks for your help, Xavier.   Xavier HANOULLE, Ph.D. UMR 8576 CNRS–USTL Structural and Functional Glycobiology Unit NMR Laboratory 59655 Villeneuve d’

[PyMOL] Distances and Python scripts

A/3/       7.249     /MyProt/MyProt/A/2/N   /MyProt/MyProt/A/4/  8.762     ... ? Furthermore, would it be possible to add a limit for these distances ? For exemple, only get the N-N distances in MyProt which are <7Ang. ? Thanks for your help. Sincerely, Xavier.     Xavier HANOULLE, Ph.

[PyMOL] molecular surface of unnatural amino acids?

the “show dots” command. Does anyone know how to display molecular surface of unnatural amino acids? Thanks in advance. Xavier. Xavier HANOULLE, Ph.D. UMR 8576 CNRS - Unité de Glycobiologie Structurale et fonctionnelle RMN Biologique Université des Sciences et Technologies de Lille

[PyMOL] error on debian w/ pymol -c foo.pml

ol from python2.4 ${PYMOL_PATH}/__init__.py "$*" to python2.4 ${PYMOL_PATH}/__init__.py "$@" --X. -- Xavier Siebert, Ph.D. Laboratoire de Microscopie Électronique Structurale (room 6234) Institut de Biologie Structurale (IBS) J.P. Ebel UMR

[PyMOL] Slerpy & Command:translate

” works pretty well in Pymol (without using Slerpy)… Does anyone know how to solve the problem? Thanks! Xavier. Xavier HANOULLE, Ph.D. UMR 8576 CNRS RMN biologique Université des Sciences et Technologies de Lille - France

[PyMOL] set_dihedral

4 consecutive residues. Is there any restriction on where you can apply this command? Thanks in advance, xavi -- Xavier Deupi, Ph.D. Department of Molecular and Cellular Physiology Beckman Center for Molecular and Genetic Medicine (B161) 279 Campus Drive, Stanford University School of Medici

[PyMOL] direction of rotation

can reproduce this 'bug' changing the conformation of some other residue... So, has anybody experienced this situation before? Any solution to restore the 'normal' behaviour of the 'mutated' conformations? Is it possible that this is a bug? Regards, Xavier -- Xav

RE: [PyMOL] rot+trsl matrices

trix('mono') Note that it diverges also but more slowly when replacing the second transform line by : cmd.transform_object('mono',[cos(1.57), 0, sin(1.57), 0.0, 0, 1, 0, 0.0, -sin(1.57), 0, cos(1.57), 0.0, 0, 0, 0, 0.0]) Can you help us with some of these issues ? Thank you very muc

[PyMOL] rot+trsl matrices

algorithm. Do you know how to get these matrices ? Thank you ! --X. - Xavier Siebert, Ph.D. Laboratoire de Virologie Mole©culaire & Structurale UMR 2472 CNRS-GIF 1 Av. de la Terrasse, Bat. 14 B 91198 Gif-sur-Yvette, FRANCE tel : (++33)-1-69.82.3

[PyMOL] using a variable name within a selection

on't match (0 != 6). ... which seems a pretty straightforward error message. I've tried different 'alternative syntaxes', but I can't get the correct form. Any help? Thanks in advance xavi -- Xavier Deupi, Ph.D. Department of Molecular and Cellular Physiology Beckman Cen

Re: [PyMOL] mouse middle button

Hi Bronwyn, I had the same problem (using a Logitech MX310 under OS X 10.4.2). As somebody previously suggested, I just uninstalled the Logitech software, so the os treats the mouse as 'generic'. And now the middle button behaves as expected. hope this helps, Xavier Bronwyn Carl

[PyMOL] torsion + movie

command (as in "load foo1.pdb,mov") expects a pdb file as an argument, but I want to load the current state as shown in PyMOL (after modifying the torsion angle, for instance). Any help? Thanks in advance, Xavier -- Xavier Deupi, Ph.D. Department of Molecular and Cellular Physiology

[PyMOL] conformational states in the mutagenesis wizard

X 10.4.2) Thanks in advance, Xavier -- Xavier Deupi, Ph.D. Department of Molecular and Cellular Physiology Beckman Center for Molecular and Genetic Medicine (B161) 279 Campus Drive, Stanford University School of Medicine Stanford, CA 94305 (USA) E-mail: xavier.de...@stanford.edu Phone: +1 (65

[PyMOL] transparent sticks

selection "ret", as I was expecting. I've been trying a few variations in the syntax, but I can't figure out the correct way... any help? Thanks in advance, Xavier -- Xavier Deupi, Ph.D. Department of Molecular and Cellular Physiology Beckman Center for Molecular and Genet

[PyMOL] movies in MacOSX

Thanks everybody. Framed (<http://www.likelysoft.com/framed/>) works fine. x -- Xavier Deupi, Ph.D. Department of Molecular and Cellular Physiology Beckman Center for Molecular and Genetic Medicine (B161) 279 Campus Drive, Stanford University School of Medicine Stanford, CA 94305 (USA)

[PyMOL] movies in MacOSX

#x27;t find the mpng codec. I downloaded a codecs.conf file and copied to ~/.mplayer, but it doesn't help. Are any of you using mencoder in a mac? If so, I'd like to get some advice. Thanks in advance, Xavier -- Xavier Deupi, Ph.D. Department of Molecular and Cellular Physiology Bec

[PyMOL] atom number labels?

Hi, I'm a new user, so my question is *extremely* basic... I want to display atom numbers as labels, but this property does not appear in the list of properties that can be displayed using the command 'label'. How can I do it? Thanks in advance, xavi -- Xavier Deupi, Ph.D

[PyMOL] ray tracing and cross-eyed stereo

Pymolers, I am trying to make an image (png file) in cross-eyed stereo, but it seems that I cannot make the stereo image and ray trace. Does anyone know either how to do this or how to manually make the image by making two images with the proper angles/distance/etc.? Thanks, Xavier