[PyMOL] Antwort: PyMOL-users Digest, Vol 169, Issue 20

-pymol-users-requ...@lists.sourceforge.net schrieb: - An: pymol-users@lists.sourceforge.net Von: pymol-users-requ...@lists.sourceforge.net Datum: 15.06.2020 22:47 Betreff: PyMOL-users Digest, Vol 169, Issue 20 Send PyMOL-users mailing list submissions to pymol-users@lists.sourcef

Re: [PyMOL] Renumber

problems due to duplicate residue numbers. I would offer to send you my macro collection, but right now I am in the middle of fixing a number of things that broke due to the update to EXCEL 2019, so I have to ask you for patience. best regards Annemarie Honegger Hi Vaheh, I susoect that your issue

[PyMOL] incomplete secondary structure

When you look at the coordinate file for 3jav in a text editor, you'll see that for the parts of the structure which give you a "AssignSS-Warning: Ignoring incomplete residue" feedback, the coordinate file contains C-Alpha coordinates only, while in the parts which render the secondary structure

[PyMOL] Antwort: interface surface Area and distances in two dimeres (Ashwani Kumar)

mass script - it returns the coordinates of the cog as well as a pseudo atom indicating the position. Annemarie Honegger Message: 1 Date: Sat, 8 Jul 2017 02:12:05 +0530 From: Ashwani Kumar To: pymol-users@lists.sourceforge.net Subject: [PyMOL] interface surface Area and distances in two

Re: [PyMOL] PyMOL-users Digest, Vol 131, Issue 10

> > -- > Jo?o M. Damas > PhD Student > Protein Modelling Group > ITQB-UNL, Oeiras, Portugal > Tel:+351-214469613 > -- next part -- > An HTML attachment was scrubbed... > > -- > > Message: 3 > Date: Thu, 13 Apr 2017 10:03:20 +0800 (GMT+08:00) >

[PyMOL] Pymol fab ss = 4 introduces bends in the structure

You get kinks wherever there is a proline in the sequence, because the ring of the PRO residues restrict the phi angle Annemarie > > -- > > Message: 4 > Date: Fri, 7 Apr 2017 14:26:34 +0200 > From: Ahmad Abdelzaher > Subject: [PyMOL] Pymol fab ss = 4 introduces b

[PyMOL] Antwort: PyMOL-users Digest, Vol 129, Issue 9

Dear Vivian If you just want to get rid of shadows in exported ray-traced images, you can specify set ray_shadows, 0 (https://pymolwiki.org/index.php/Ray_shadow) set depth_cue,0 (https://pymolwiki.org/index.php/Depth_cue) will get rid of the color modulation due to dept cueing Annemarie -

[PyMOL] Antwort: course or tutorial to make nice pictures

Hi Clarissa I have just deposited the slides to my 1.5 day class on macromolecular visualization on Research Gate https://www.researchgate.net/publication/313877004_Introduction_to_PyMOL https://www.researchgate.net/publication/313877009_Intermediate_PyMOL https://www.researchgate.net/publicatio

[PyMOL] symmetry and pdb remark

You have to generate the symmetry mates before you align the two structures. Then you can generate an object containing all symmetry mates for one structure, e.g by putting them as different frames on one object, and do the alignment with this object. Annemarie Forwarding messages --

Re: [PyMOL] a pymol problem: cannot transit smoothly between representations in animation

oth to the observer. Best regards Annemarie Honegger Message: 1 Date: Fri, 18 Nov 2016 02:37:50 + From: ? ? Subject: [PyMOL] a pymol problem: cannot transit smoothly between representations in animation To: "pymol-users@lists.sourceforge.net" Message-ID: Content-Type: text/plai

[PyMOL] PyMOL] difficulty opening EmrE protein (pdb: 3B5D) in Pymol

/SABBAC/), however, be aware that low resolution structures do not get more precise by modelling in parts that were not resolved in the experimental structure . Annemarie Honegger Message: 4 Date: Tue, 25 Oct 2016 21:34:01 + From: Mohsen Chitsaz Subject: [PyMOL] difficulty opening EmrE protein

Re: [PyMOL] morph issues

t identifiers into your selections best regards Annemarie ___ Dr. Annemarie Honegger PhD Department of Biochemistry Zürich University Winterthurerstrasse 190 CH-8057 Zürich Switzerland e-Mail: honeg...@bioc.uzh.ch websites http://www.bioc.uzh.ch/plueckth

Re: [PyMOL] morph issues

those atoms, the morph should work. best regards Annemarie ___ Dr. Annemarie Honegger PhD Department of Biochemistry Zürich University Winterthurerstrasse 190 CH-8057 Zürich Switzerland e-Mail: honeg...@bioc.uzh.ch websites http://www.bioc.uzh.ch

Re: [PyMOL] pymolrc location (harold steinberg)

files without dot. https://sourceforge.net/p/pymol/mailman/message/30422388/ <https://sourceforge.net/p/pymol/mailman/message/30422388/> Annemarie ___ Dr. Annemarie Honegger PhD Department of Biochemistry Zürich University Winterthurerstras

Re: [PyMOL] shadows commands

rie ___ Dr. Annemarie Honegger PhD Department of Biochemistry Zürich University Winterthurerstrasse 190 CH-8057 Zürich Switzerland e-Mail: honeg...@bioc.uzh.ch websites http://www.bioc.uzh.ch/plueckthun http://www.bioc.uzh.ch/plueckthun/antibody http://www.bioc.uzh.ch/plueck

Re: [PyMOL] running python scripts from within python loops in a pymol scripts

Yes, this works! Thank you very much for your help! Annemarie > On 01 Apr 2016, at 15:17, David Hall wrote: > > I think you can use cmd.do > > cmd.do("com /DARPin2//A/37-135/CA, object=com2”) > > -David > > >> On Apr 1, 2016, at 8:48

[PyMOL] running python scripts from within python loops in a pymol scripts

within the loop. If I try to use it analogous to normal commands, I get the error message: Traceback (most recent call last): File "/Users/ahonegger/Desktop/MacPyMOL1.8.0.2.app/Contents/pymol/modules/pymol/parser.py", line 157, in parse exec(py_block,self.pymol_names,self.pymol_names)

Re: [PyMOL] PyMOL-users Digest, Vol 116, Issue 15

marie ___ Dr. Annemarie Honegger PhD Department of Biochemistry Zürich University Winterthurerstrasse 190 CH-8057 Zürich Switzerland e-Mail: honeg...@bioc.uzh.ch websites http://www.bioc.uzh.ch/plueckthun http://www.bioc.uzh.ch/plueckthun/antibody http://www.bioc.uzh.ch/pluec

[PyMOL] Transformation of cgo objects

is with an arrow using the “AngleBetweenHelices” script, I have to use “turn” rather than “rotate” to get a second view rotated by 90 degree. I suspect that cgo objects are fixed in object space, you can only alter the camera position to look at them from different angles. best regards

Re: [PyMOL] PyMOL-users Digest, Vol 116, Issue 15

Annemarie ___ Dr. Annemarie Honegger PhD Department of Biochemistry Zürich University Winterthurerstrasse 190 CH-8057 Zürich Switzerland -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + M

Re: [PyMOL] PyMOL-users Digest, Vol 115, Issue 7

> On Fri, Dec 11, 2015 at 8:19 AM, Smith Liu > wrote: > >> Dear All, >> >> Suppose by pymol I have opened A.pdb abd B.pdb. Is anyway I close B.pdb >> and have only A.pdb displayed? >> >> Smith >> > > -- > Tsjerk A. Wassenaar, Ph.D. > Date: Fri, 11 Dec 2015 08:53:

Re: [PyMOL] PyMOL-users Digest, Vol 114, Issue 7

I like the way the Protein-Ligand Interaction Profiler (PLIP, https://projects.biotec.tu-dresden.de/plip-web/plip/index , https://pypi.python.org/pypi/plip , http://nar.oxfordjournals.org/content/early/2015/04/14/nar.gkv315.full ) highlights different interactions in its PyMol output file, suc

[PyMOL] creating a virus capsid using supercell.py (Marcelo Marcet)

> Hi Everyone, > > I have been trying to build a virus capsid using pymol. The biological unit > for the complete structure is not available. :( > > My first attempt at getting this done was by using the ?rotate? and > ?translate? commands. Unfortunately, these commands can only move objects >

Re: [PyMOL] PyMOL-users Digest, Vol 107, Issue 14

Hi Wenfu Getting a putty representation out of a series of MD snapshots should be equivalent to producing a putty representation from an NMR ensembles: Multiple models in one pdb files, and you want the putty width to represent the structural variation between the models. This site https://k