Re: [PyMOL] STRIDE plugin for Pymol

Hi Thomas, Thanks for looking into it! Unfortunately, I don't currently have access to a Linux system. These plugins don't seem to be compatible with Pymol on Windows? Best, Chris On Tue, Nov 1, 2022 at 8:35 PM Thomas Holder wrote: > Hi Chris, > > The plugin works for me

[PyMOL] STRIDE plugin for Pymol

ys. Cheers, Chris ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] conversion of the small molecules from sdf to mol2

tle> Chris > On 14 Jan 2022, at 12:03, 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 Wide Web, visit > https://lists.sourcefor

Re: [PyMOL] PyMOL for M1 macs

Hi, Thanks all will give it a try Cheers, Chris > On 6 Dec 2021, at 06:08, Jarrett Johnson > wrote: > > IIRC when we tried with Rosetta2, PyMOL was still faster (about 2x I think) > than the previous x86. Your mileage may vary. > > Best, > Jarrett J > > O

[PyMOL] PyMOL for M1 macs

Hi, Is there a build of PyMOL for M1 Macs yet? Cheers, Chris ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] May I hire you to assist me

Hello   I wish to hire someone to assist me with the demonstration of active sites and molecular structure and function. A knowledge of the use of  PDB is also helpful. my email is dr.cmor...@yahoo.ca  ___ PyMOL-users mailing list Archives: http://www.m

Re: [PyMOL] Coloring different carbons differently

Hello again, Here’s a simple command for selecting four specific atoms in the ligand hemoglobin (HEM): sele resn HEM & n. C1A+C3A+CHA+C4D sele = select resn = residue name n. = atom name Best, Chris On Tue, May 5, 2020 at 10:38 Chris Fage wrote: > Hello, > > You can alwa

Re: [PyMOL] Coloring different carbons differently

d line, but you'll need to know the PDB-formatted names of those atoms to do. That likely requires clicking on the atoms of interest anyway. Best, Chris <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> Virus-fre

Re: [PyMOL] [EXTERNAL] Apply valence settings to an object

Many thanks for your assistance, Blaine! For the second point, I wanted to use the stick_ball setting on the ligand only. I was able to modify your command as follows: hide sticks; set stick_ball, on, ligand; show sticks Best wishes, Chris On Fri, Apr 10, 2020 at 9:37 PM Mooers, Blaine H.M

[PyMOL] Apply valence settings to an object

of the protein. Many thanks in advance! Best, Chris ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] HELIX and SHEET records not read by Pymol

Hi Thomas, I have no idea why, but it seems to work for me when following your instructions. Perhaps because I deleted everything except for the ATOM records? Thanks for looking into it! Best wishes, Chris <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_c

[PyMOL] HELIX and SHEET records not read by Pymol

tride Web Interface and converted them to PDB format with Emma Rath's website ( http://www.canoz.com/sdh/STRIDEtoPDBsecondarystruct.pl). Does anyone have any ideas? Thanks! Best wishes, Chris <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-emai

Re: [PyMOL] PDB structure to .obj or .fbx

A short how-to https://www.macinchem.org/reviews/3D/augmented.php <https://www.macinchem.org/reviews/3D/augmented.php> Cheers Chris > > Message: 1 > Date: Fri, 31 Aug 2018 12:26:03 -0400 > From: Abel J Baerga Ortiz > To: pymol-users@lists.sourceforge.net > Subject:

Re: [PyMOL] Pymol under El Capitan

That seems to have sorted things. Many Thanks Chris > On 11 Dec 2015, at 13:14, David Hall wrote: > > Try the last comment on: > > https://github.com/Homebrew/homebrew-science/issues/2273 > <https://github.com/Homebrew/homebrew-science/issues/2273> > > -David

[PyMOL] Pymol under El Capitan

ol: line 4: 3628 Segmentation fault: 11 "/usr/local/opt/python/bin/python2.7" "/usr/local/Cellar/pymol/1.7.6.0/libexec/lib/python2.7/site-packages/pymol/__ini

[PyMOL] Stereo issues on Mac Pro with Quadro FX 4800

meone with experience of this setup suggest a way around these problems? nVidia's support seems to have only a tenuous appreciation of the existence of the Mac platform. The 4800 is quite* expensive, so I'm keen to get this working. Regards, Chris * For "

Re: [PyMOL] [Apbs-users] Strange behaviour with APBS

Hi, I noticed the latest version of the PDB file format description was posted today. http://www.wwpdb.org/docs.html Chris On 17 Sep 2008, at 20:21, DeLano Scientific wrote: The PyMOL and APBS programs have differing views as to whether PDB & PQR files are column-based or s

[PyMOL] Small VRML export bug

Hi Warren, In the current SVN sources, line 1214 of layer1/Ray.c sets "shininess" equal to 8 for exported VRML files. The VRML97 specification, however, wants shininess to be between 0.0 and 1.0. So, I would recommend changing the shininess to 0.8. Che

[PyMOL] How can I stop PyMOL sleeping when idle?

ng, and/or am I barking up the wrong tree looking for a sleep? Any help is appreciated, Chris _ Invite your mail contacts to join your friends list with Windows Live Spaces. It's easy! http://spaces.live.com/spacesapi.a

[PyMOL] set_dihedral command

Dear PyMol users, I am trying to set dihedral angles in a protein. Unfortunately, the set_dihedral command is not documented, but it looks like it is the same as the get_dihedral with an additional value for the angle to set. I tried to set the dihedral angle for the protein crambin (PDB cod

[PyMOL] Some VRML improvements

hrown out after the surface is created. Regards, Chris -- ____ ( Chris Want ) ( Research Computing Support ) ( Academic Information and Co

[PyMOL] VRML patch

the attached patch (diff-ed against cvs, and tested with two VRML2 readers) can be regarded as being in the public domain. Regards, Chris -- ( Chris Want ) ( Research

[PyMOL] Cheap VRML hack for 3D printing surfaces

using the "chainbow" coloring scheme: http://bebop.cns.ualberta.ca/~cwant/pymol_wrl/pymol_1tii.jpg http://bebop.cns.ualberta.ca/~cwant/pymol_wrl/pymol_1tii_print.jpg Anyways, maybe somebody else will find the patch useful

Re: [PyMOL] movies in presentations

uite well. The only problem is that I don't have a laptop so when I give presentations it has to be done on someone elses computer and rarely can you gaurantee what codecs etc they will have installed - hence forcing the use of lower compression more ubiquitous codecs Chris Mar

[PyMOL] Reference

Hi Warren Could you tell me how I should reference Pymol in papers etc? I've tried finding it one the web and i've not seen it Ta Chris

Re: [PyMOL] Pymol & 3D printing

The only thing to note here is that we had to scale all of the molecules by the same factor for the output to be meaningful. Regards, Chris -- Chris Want Research Computing Support Computing & Network Services University of Alberta Tel: 1-780-492-9418

Re: [PyMOL] Pymol & 3D printing

lable' yesterday -- might have been an effect of the Sobig e-mail worm, maybe. Cheers, Chris -- Chris Want Research Computing Support Computing & Network Services University of Alberta Tel: 1-780-492-9418

[PyMOL] Pymol & 3D printing

Hello, My name is Chris Want, and I do visualization support at the University of Alberta -- and in particular I run the university's 3D printer. I'm not a pymol user per se, but I have had a client who really liked the 'surface' visualization from pymol and wanted to prin

[PyMOL] Interscript communication

Hi guys I just wondered how I would go about getting pdb data for an object in pymol so that a python script act on it eg. if I wanted to perform a calculation on the object which produces a pdb file back into pymol again.?? any ideas Thanks in advance Chris

[PyMOL] Pymol and Autodock

.trj) from simulated annealing dockings into Pymol ? for doing animations in Pymol Cheers in advance Chris

Re: [PyMOL] Script Box

ssPDB viewer. Any way my question is, can anybody think of a way to write a script that would iterate through any pdb file and create individual objects MET1, ALA2, ASP3... to AAn etc at the push of a scriptbox button?? My python/scripting isn't so good but I'm learning! Cheers, Chris.

Re: [PyMOL] New PyMOL Release for Win/Linux/SGI

ipts menu that could also list all the scripts in a given directory?? Cheers, Chris. _______ Dr Chris Winfield Lab: N317/318 Post-Doctoral Researcher Tel: +44 (0)1179 546 324 School of Chemistry Fax: +44 (0)1179 298

Re: [PyMOL] Zooming in animations

Cheers Warren I had a bit of a play last night and it seem to work fine. Do you know what the last number in the seqence corresponds to? movie.zoom 1,100,1,0 Chris - Original Message - From: "DeLano, Warren" To: "Chris Arthur" ; "pymol-users" Sent: Mon

[PyMOL] Zooming in animations

Hi Guys Sorry if this question has been asked before but does anyone know a way to zoom in on an area as an animation (eg an active site or interface). Thanks in advance Chris

[PyMOL] OT: BioMT

BioMT matrix to transform the structure. Is there a nice easy way of doing this? Thanks in advance Chris Snippet from the PDB file... REMARK 300 BIOMOLECULE REMARK 300 THE BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 300 MOLECULE IS A DIMER. REMARK 350 REMARK 350 GENERATIN

Re: [PyMOL] MacOSX and Three button mice.

middle-click. I am using a Kensington 5-button optical mouse. You can program this mouse so that the buttons mean different things for different programs, which is quite useful. Chris Department of Biochemistry 606 Light Hall Vanderbilt University Nashville, TN Phone: (615) 343-5682

[PyMOL] labels

? Thanks, Chris

Re: [PyMOL] Re: image quality

Hi, Thanks to Andrey and Warren, that was certainly what was needed! Chris On Tuesday, April 30, 2002, at 12:03 PM, DeLano, Warren wrote: Image quality: As Andrey indicated, on typical color lasers and inkjets, you need 300 dots per final printed inch (~120 pixels/cm) for maximum

[PyMOL] image quality

g and printing from different programs, but with no luck. Any suggestions? Thanks, Chris