Re: [PyMOL] Deprecation of MMTF-format files for the PDB archive

Jose, I have a few questions about the BCIF format. Adding pymol-users because there might be interest there as well (at least among developers). First, at PDBe, where is the link for downloading BCIF files for a given structure? I only see this, for example, at https://www.ebi.ac.uk/pdbe/entry/

[PyMOL] open source installation on Windows broken?

At https://pymolwiki.org/index.php/Windows_Install the process fails for 3. Download the appropriate wheel files , which is a dead link. Does anyone know how to run open source PyMOL on Windows OS? Bob Hanson

[PyMOL] BCIF

t; > . > RCSB PDB support is ready to assist with any issues or questions at i...@rcsb.org. --- Jose Duarte RCSB Protein Data Bank San Diego Supercomputer Center UC San Diego La Jolla CA, USA -- Robert M. Hanson Professor of Chemistry, Emeritus St. Olaf College Northfield, MN http://www.s

Re: [PyMOL] Installing in Linux

gt; trouble installing in Windows but don't know how to proceed in Linux? > Can anyone point me in the right direction? > > Thanks, > Peter -- Robert L. Campbell, Ph.D. Undergraduate Chair (Acting), Biochemistry Program Academic Advisor, BHSc Program Assistant Professor, D

Re: [PyMOL] list_hb.py

out the correct hydrogen-bonding pairs? > > > > Thanks! > > ___ > > PyMOL-users mailing list > > Archives: > > http://www.mail-archive.com/pymol-users@lists.sourceforge.net > > Unsubscribe: > > https://sourcef

Re: [PyMOL] How to iterate commands in pymol

rget) <--- This third line doesn't work since > colorbyrmsd does not have a cmd.colorbyrmsd. > > Is there a way I can run something like: > cmd.executecommand("colorbyrmsd {0}, target".format(obj)) ? > > Best regards, > > Zuben -- Robert L. Campbell,

Re: [PyMOL] Effect of different align method

yOjTtIS59OZnLnYEAG2spdQJXLzlpGzA%3D&reserved=0 > Unsubscribe: > https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsourceforge.net%2Fprojects%2Fpymol%2Flists%2Fpymol-users%2Funsubscribe&data=02%7C01%7Crobert.campbell%40queensu.ca%7C4e290e0f1c4044d3b1fc08d812bf8cca%7Cd61e

Re: [PyMOL] hydrogen bond list for a series of files

%26s%3D6cyeevFFP1ip0quoSgRLS9fqrvVtj8JlnLJWMpJWqFg%26e%3D&data=02%7C01%7Crobert.campbell%40queensu.ca%7C5a300643d81e4d7ea3f608d812359b34%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C637279368764004254&sdata=Wvtb4FDbK8ph8tIPtB3XZwSj8GR%2FaKTwqu%2FFxqwGsS8%3D&reserved=0>> > impo

Re: [PyMOL] Extract all phi and psi angles

able with: p = cmd.phi_psi('obj_1') where p will be a dictionary with keys representing the residue numbers and pointing to a list of the phi/psi values for that residue. Cheers, Rob -- Robert L. Campbell, Ph.D. Assistant Professor, Dept. of Biomedical & Molecular Sciences, Queen

Re: [PyMOL] Drawing lines between residues

figure like this one: > > > [image: 2019-10-15.png] > > What commands can I use to get this done in PyMOL? > > Thanks -- Robert L. Campbell, Ph.D. Adjunct Assistant Professor, Dept. of Biomedical & Molecular Sciences, Botterell Hall Rm 644 Queen's

Re: [PyMOL] Pymol recolour B factors

rbOBvO5agrVsRdkuUKYJA9A26w%3D&reserved=0 > Unsubscribe: > https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsourceforge.net%2Fprojects%2Fpymol%2Flists%2Fpymol-users%2Funsubscribe&data=02%7C01%7Crobert.campbell%40queensu.ca%7C664f1bfa0c934c52f40108d6aebdf161%7Cd61ecb3

Re: [PyMOL] ExecutivesSymexp-Error: No Symmetry loaded!

D0&data=02%7C01%7Crobert.campbell%40queensu.ca%7C6261ebf5a5494e8b230808d4b877938b%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636336271090533556&sdata=6U5D%2BZOPnIAx3X61eeK77XLW23mroFnaM8sxiX7n1Ow%3D&reserved=0 > > Any help will be highly appreciated. > > Best,

Re: [PyMOL] ExecutivesSymexp-Error: No Symmetry loaded!

t; > https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.dropbox.com%2Fs%2Fmt7toc0wtenr779%2Ftemp.pdb%3Fdl%3D0&data=02%7C01%7Crobert.campbell%40queensu.ca%7C6261ebf5a5494e8b230808d4b877938b%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636336271090533556&sdata=6U5D%2BZOPnIAx3X

Re: [PyMOL] Scripting coloring method via own calculations

e direct me to a way of doing that? I saw scripts coloring > by atom type, but I'm not sure how to apply it for a molecule already > loaded in PyMol. > > Best, > > Peleg -- Robert L. Campbell, Ph.D. Adjunct Assistant Professor Dept. of Biomedical & Molecular Scie

Re: [PyMOL] Fw: symmetry and pdb remark

nformation decide the > mate arrangement, as in the remark added PDB for 2zan fitted to > 2zam? Why after pymol alignment, the same remark information leads to > different mates arrangement? > > > I am looking forward to getting a rep

Re: [PyMOL] how to convert .pse to html?

Albert, I just note that JSmol reads PyMOL PSE files directly - fully JavaScript/HTML5 - and allows interactive viewing of them in JavaScript as well as all the functionality of Jmol; nothing to change in terms of the PyMOL file. Just load it. Of course, not every capability of PyMOL is reproduced

Re: [PyMOL] 3D printing

- >> -- >> > Check out the vibrant tech community on one of the world's most >> > engaging tech sites, SlashDot.org! http://sdm.link/slashdot__ >> _ >> > PyMOL-users mailing list (

[PyMOL] 3D printing

Can someone give me a summary of capabilities and limitations in PyMOL re 3D printing? For example: Q: What output file types are supported? (WRL, X3D, STL[ASCII/binary], other) Q: Does the generation of these include algorithms for ensuring closure or for stitching together objects in order to

Re: [PyMOL] dump_binary and PyMOL 1.8 PSE files

To finish this thread -- Jmol and JSmol can now read (basic) PyMOL 1.8 PSE files that have set dump_binary, 1 for faster loading and smaller file sizes. Jmol only implements a small, basic range of PyMOL functionality, of course. https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.6/Ve

Re: [PyMOL] dump_binary and PyMOL 1.8 PSE files

Almost have it. Having trouble fitting all that into 120 bytes, though. I'm good through bytes 96-99, visrep. Somehow, though I count 124 bytes total, not 120 (which is clearly the case in the PSE file). What is sizeof(AtomInfo_1_8_1) ? I calculate: ... 100-105 (six booleans) 106-111 (six characte

Re: [PyMOL] dump_binary and PyMOL 1.8 PSE files

Ah, that is what I needed. For some reason that file is not in the download I unzipped. Much more sensible! Bob On Mon, Aug 8, 2016 at 3:18 PM, Thomas Holder wrote: > On 08 Aug 2016, at 16:01, Robert Hanson wrote: > > > I see this in 1.8.2.1: > > > > #define

Re: [PyMOL] dump_binary and PyMOL 1.8 PSE files

U (will indeed write an unused NULL pointer), at the time it > was work in progress for a specific use case which didn't require ANISOU. > > Cheers, > Thomas > > On 08 Aug 2016, at 11:32, Robert Hanson wrote: > > > I do like the compactness of that and the quicker lo

Re: [PyMOL] dump_binary and PyMOL 1.8 PSE files

for "AtomInfoTypeConverter" if you're > interested in the details. > > The default (in 1.8.2) is to save PyMOL 1.7.6 compatible PSE files, and > with the "pse_export_version" setting you can also export for older PyMOL > versions. > > Cheers, > Tho

[PyMOL] dump_binary and PyMOL 1.8 PSE files

there a way to turn that off? Q: In order to do this properly, how many versions of the atom info data structure do I need to be able to process? Bob -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature doe

Re: [PyMOL] Function signature

ication > problems quickly and reduces your MTTR. Get your free trial! > https://ad.doubleclick.net/ddm/clk/302982198;130105516;z > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-user

Re: [PyMOL] The Wiki appears outdated or in error

In case you are interested, Jim, Jmol will read (most/some) PyMOL session files, and Jmol can then create both an idtf for generating a u3d file, and a small sample TeX file also that can be used to create a PDF containing it. I had some interest in u3d back in 2009, when I wrote this exporter. Yo

Re: [PyMOL] PyMOL split_states error on [PDB: 1hho]

Ioannis, I suggest using the CIF file from EBI instead: http://www.ebi.ac.uk/pdbe/static/entry/download/1hho-assembly-1.cif.gz It looks good to me -- just one model. For reference, the RCSB site is using Jmol and is simply loading 1HHO itself and constructing the assembly *in situ *using the sy

[PyMOL] status of Uppsala EDS server?

Does anyone know the status of http://eds.bmc.uu.se? Is it gone forever? Does anyone know the replacement URL for getting electron density maps and difference maps? (Which I think is at EBI, right?) Bob -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Department of Chemistry

Re: [PyMOL] Version question -- PSE session file format

ith partial=1, it will also not store the viewport. > > Cheers, > Thomas > > On 23 Dec 2015, at 19:12, Robert Hanson wrote: > > > I have a question about the PSE file format. > > > > Newer PSE files, perhaps those created using PyMOL 1.8, seem to have no >

[PyMOL] Version question -- PSE session file format

size? Bob -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Department of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture X

Re: [PyMOL] JyMOL vs JSMol

Don't worry. No apology necessary. It's a closely held secret that JSmol can do this. In any case, trust me, you will find plenty that JSmol cannot handle. There are many mysteries of the PSE format that I could only guess at. Enjoy! ​ --

Re: [PyMOL] JyMOL vs JSMol

I guess I should chime in here. JSmol does read (some fraction of) PyMOL session files. To be sure it has not been a priority to keep up to date with all the amazing PyMOL capabilities, but certainly as a proof of concept it has worked well, and it would be great to collaborate on this to improve i

Re: [PyMOL] Problems loading new mrc-format electron density files into pymol

orge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Department of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not a

Re: [PyMOL] secondary structure disappears

pdb file? > > Thanks! > > > > H. Adam Steinberg > 7904 Bowman Rd > Lodi, WI 53555 > 608/592-2366 > -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Dept. of Biomedical & Molecular Sciences, Botterell Hal

Re: [PyMOL] efficiency assigning b-factors

> >> its taking forever in my script. Is there something inherently > >> inefficient about alter? And is there anyway to fix it? Perhaps, > >> assign a bunch of b-factors at once. > >> > >> Jordan > >> > >> > >> -

Re: [PyMOL] Superimpose small non-protein molecules?

gt; Deep dive visibility with transaction tracing using APM Insight. > http://ad.doubleclick.net/ddm/clk/290420510;117567292;y > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lis

Re: [PyMOL] sulfated tyrosine's losing connection

actually -- I see there are just CONECT records for all the HETATMs, as usual. Nothing odd about that. But, nonetheless, in this case those CONECT records are not there. The point is that it has nothing to do with PyMOL. ​

Re: [PyMOL] sulfated tyrosine's losing connection

This unusual file has all the backbone bonds indicated with CONECT records -- except the missing links you note. I'm guessing that PyMOL is respecting that, and that it could be an RCSB file error. CONECT 9606 9593 9607 CONECT 9607 9606 CONECT 9608 9609 ... CONECT 1674 1661 1675 CONECT 1675 1674 C

Re: [PyMOL] CGOs

Great. Thanks very much. The ones perhaps missing there are: #define CGO_INDENT 0x18 #define CGO_RESET_NORMAL 0x1E #define CGO_PICK_COLOR 0x1F And I think #define CGO_LIGHTING 0x0B50 may be an internal flag, not a CGO command.

Re: [PyMOL] CGOs

OK, that explains it. I think I made that one up. It was a while ago that I worked on this. :) I see the list at https://github.com/speleo3/pymol/blob/master/modules/pymol/cgo.py Thanks​, David. Bob -- Dive into the World

Re: [PyMOL] CGOs

O objects. You can have > a look in modules/cgo.py and in the example scripts in examples/devel/ in > the pymol directory to get some more information. If there is something > specific you want to do, please let us know. > > Cheers, > > Tsjerk > > > On Sun, Dec 21, 2014

Re: [PyMOL] CGOs

I'm looking for something that is relatively comprehensive. There are far more commands than VERTEX, CYLINDER, CONE, and SPHERE, I think. -- Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! In

[PyMOL] CGOs

Happy holidays! Q: Is there a resource that describes the syntax for compiled graphical objects in PyMOL? I see http://pymol.sourceforge.net/newman/user/S0500cgo.html, but that is pretty minimal. Bob -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Department of Chemistry

Re: [PyMOL] View Matrix operation

_ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Robert M. Hanson Larson-Anderson Professor of Chemist

Re: [PyMOL] How to draw clashes in pymol -> integration/plug-in of Molprobity in PyMol???

omeone would write a plug-in to integrate the Molprobity > output in PyMol? > > I can definitely not do it, but maybe this could be an interesting feature > request to the PyMol developers? > > All the best, > Tim > > > > Am 30/08/14 01:53, schrieb Robert Immormino:

Re: [PyMOL] Backbone RMSD

d backbone RMSD. Please advise > something. You simply need to include a selection on the command line. At the PyMOL prompt, you could type align 2hr1 & backbone, 1f88 & backbone Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Dept.

Re: [PyMOL] How to draw clashes in pymol

Hi Bondurant, I really like the merging of the graphic beauty of pymol with the detailed depictions of reduce and probe. I have a method that is a bit clunky for doing what you ask, but I don't know if it ever made it to the mainstream in MolProbity. The caveat of wanting to work with a ligand m

[PyMOL] mmCIF -- multicharacter chain labels

What's the trick to loading mmCIF files with multi-character chain IDS? Maybe I just need to upgrade? (Using PyMOL 1.6.0.0) What I see now is just the first character of _atom_site.auth_asym_id Bob -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Department of Chemist

Re: [PyMOL] Fwd: color by RMSF or RMSD

ve? Can I visualize all 5? Yes, as Andreas said to turn on the display of all states: set all_states, 1 and to revert to just showing a single state: set all_states, 0 Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Dept. of Biomedical & Mole

Re: [PyMOL] command question RE printing out distances to text file

ing shown in the viewer. I will be doing lots > > of these at the same time and the screen will get crowded. Thank you in > > advance. > -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Dept. of Biomedical & Molecular Sciences Bo

Re: [PyMOL] command question RE printing out distances to text file

al gui as well as being shown in the viewer. I will be doing lots > > of these at the same time and the screen will get crowded. Thank you in > > advance. > -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Dept. of Biomedical & Molecula

Re: [PyMOL] Corrupted IDTF file from small molecule (sticks representation)

My only real objection is that WebGL is not supported on iOS in browsers. Beyond that, I probably just don't know enough about it to do it right. On Wed, Feb 12, 2014 at 1:50 PM, Thomas Holder < thomas.hol...@schrodinger.com> wrote: > Hi Bob, > > On 10 Feb 2014, at 20:43,

Re: [PyMOL] Corrupted IDTF file from small molecule (sticks representation)

So JmolData.jar can read a .pse file as is (with lights, > transparences, hidden no-polar hydrogens, colors, ray, etc)? Sounds good. > > Thanks a lot to you. > > Regards, > Riccardo Volpe > > > *ChemBioScripting | X3D PyMOL Molecule Viewer > <http://chembioscrip

Re: [PyMOL] Corrupted IDTF file from small molecule (sticks representation)

So in the mean time, Riccardo, I guess what you are already using: xxx.pse -- JmolData.jar --> idtf is your best bet. Q: What sort of size of PDF file are you seeing in the end? Q: Do you see this a practical and useful in some way? If so, in what way? Bob Hanson --

Re: [PyMOL] ccp4 question

ard command line format for CCP4 programs is such that coordinate files are indicated by the "xyzin" (and "xyzout") logical names. It can also be run from the ccp4i interface. Did you try that? Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adju

Re: [PyMOL] combining multiple objects into one multistate object

to > separate objects that have been aligned, and I want to combine them into > one object in order to run Robert Cambell's rmsf_states script (and, > also since it's just easier to compare and manipulate). You probably have a reason for loading the models into separate objects, bu

Re: [PyMOL] How to automate RMSD calculation for large no of structures

On Tue, 2014-01-07 12:05 EST, Jed Goldstone wrote: > Check out Robert Campbell's Pymol script repository. > I think align_all_to_all.py should do what you want, including exporting > RMSD values. > > http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ Actually, I th

Re: [PyMOL] minimum rotation between views

st (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www

Re: [PyMOL] new "metals" keyword

roubleshooting in minutes. > http://pubads.g.doubleclick.net/gampad/clk?id=48897031&iu=/4140/ostg.clktrk > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Arc

Re: [PyMOL] Reducing the surface rendering load for JSmol export

your free trial of AppDynamics Pro today! > http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk > _______ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-

Re: [PyMOL] Problem Compiling v 1.6.0.0 in 64 bit Debian Testing

ately, I don't have the faintest idea as to what is missing. > Any assistance will be appreciated. Thanks in advance. I would appear that you are just missing the python-pmw package on this machine, whereas it must have been present on your Wheezy version. Cheers, Rob -- Robert L. Campbell,

Re: [PyMOL] PyMOL 1.6 pre-release announcement

15/13 10:45: >>> > Hi Rob, >>> > >>> > this has not been fixed yet, I'm really sorry. We'll look into this >>> > ASAP. It only affects the open-source code, apparently we missed >>> > something when syncing with the incentive codeba

Re: [PyMOL] PyMOL 1.6 pre-release announcement

SAP. It only affects the open-source code, apparently we missed >> > something when syncing with the incentive codebase. >> > >> > Cheers, >> > Thomas >> > >> > On Jun 14, 2013, at 9:23 PM, Robert Campbell < >> robert.campb...@queensu.ca>

Re: [PyMOL] PyMOL 1.6 pre-release announcement

th SVN rev 4028 . On a side note, > others who would like to beta test can use devel:languages:python repo > in openSUSE: > https://build.opensuse.org/package/show?package=pymol&project=devel%3Alanguages%3Apython > > -David > -- Robert L. Campbell, Ph.D. Senior Research Asso

Re: [PyMOL] Cartoon transparency

I guess I understand the idea that in PyMOL a cartoon is like a bond -- between two elements rather than being associated with one (perhaps?) -- but why change the helix to a loop before it ends? Is there a way around that? Bob -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Ol

Re: [PyMOL] Possible hydrogen addition bug

> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Robert M. Hanson Larson-Anderson Professor of Chemi

Re: [PyMOL] scenes and atom-wise colors

throwing me off. For my purposes, it just means that I have to be careful to use only the COLOR command if I want scenes to reproduce changes in color. Might be nice to explain that on the wiki. (Or, of course, maybe I missed it there) Bob On Thu, Jun 6, 2013 at 9:47 AM, Robert Hanson wrot

[PyMOL] scenes and atom-wise colors

contain a text message to display on playback. I get all of that except colors. How does that work in terms of "atom-wise colors" ? When does the scene change colors? That is, what commands would I issue that would set colors that would be recalled by a scene change? -- Robert

Re: [PyMOL] Cartoon transparency

rprise services > 3. A single system of record for all IT processes > http://p.sf.net/sfu/servicenow-d2d-j > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Arc

Re: [PyMOL] settings

Thanks, Thomas On Mon, Jun 3, 2013 at 9:36 AM, Thomas Holder wrote: > Hi Robert, > > you got the levels right. > > The cmd.get method actually doesn't support querying atom level settings, > even though you can set them with cmd.set. > I see. That's helpf

Re: [PyMOL] scenes and states

face > representation only in one state, such that looping over the states, the > surface would suddenly pop up for one. > > Hope it helps, > > Tsjerk > > > On Mon, Jun 3, 2013 at 2:38 PM, Robert Hanson wrote: > >> Questions: >> >> Can two objects be

[PyMOL] scenes and states

Questions: Can two objects be in two different states -- object1 in state 3 and object2 in state 10, for instance, at the same time? If so, how is that set up? How is that then incorporated into a scene? Do CGO, measurements, mesh, and volume objects have states as well? Bob -- Robert M

[PyMOL] settings

I'm trying to understand settings. I see that there are at least these levels of settings: - global - object - state - unique atom/bond Are there more? I'm unclear on when one overrides another. It looks to me that the general "getSetting" methods have the option of up to three levels of setting

Re: [PyMOL] PyMOL measurements

ic_measures, 1 > > In newer versions of PyMOL this is enabled by default. > > Cheers, > > -- Jason > > > On Fri, May 31, 2013 at 8:27 AM, Robert Hanson wrote: > >> Is there a way to tie measurement ends to specific atoms, so that when >> th

[PyMOL] PyMOL measurements

Is there a way to tie measurement ends to specific atoms, so that when the structure is tweaked, those measurements update automatically? -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr

[PyMOL] surfaces involving more than one object

, "One surface, one object"? That is, all atoms involved in a surface must originate from a single object? Bob -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does

[PyMOL] PyMOL session file reader for Jmol

/jsmol.zip (HTML5/JavaScript and also applet files, with demo pages) I'm hoping this will interest some of you, and you might get involved in future efforts as we develop this connection further. Bob Hanson -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department S

Re: [PyMOL] new to list -- simple questions

w and will have some programming questions. Bob -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. --

[PyMOL] new to list -- simple questions

ects such as Surface object, that sort of thing. I think I'm just about done with our current sample set of about 100 PSE files. Anyone interested in contributing PSE files to the Jmol project? Is there a repository somewhere of those? Thanks in advance, Bob Hanson -- Robert M. Hanson Lars

Re: [PyMOL] PyMOL-users Digest, Vol 82, Issue 1

ates. Or you could split the states out into separate objects. > I would like just like to know how to conclude multimeric states > informations from the pdb file without doing transformations ? just this > information Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associa

Re: [PyMOL] PyMOL-users Digest, Vol 82, Issue 1

ates. Or you could split the states out into separate objects. > I would like just like to know how to conclude multimeric states > informations from the pdb file without doing transformations ? just this > information Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associa

Re: [PyMOL] SS in a trajectory

ng you are loading a multi-model .PDB file as the trajectory. If you are using the load_traj command to load an AMBER trajectory, there is no similar option. Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Dept. of Biomedical & Molecular Sciences

Re: [PyMOL] Splitting a PDB file into its constituent chains, and making multiple (smaller) PDB files

l) answers, there is a script on the PyMOL wiki that does exactly this. See: http://www.pymolwiki.org/index.php/Split_chains Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Dept. of Biomedical & Molecular Sciences Botterell Hall Rm 644 Queen

Re: [PyMOL] About draw_links.py by Dr. Robert Campbell

how how the C-alphas were moving so then it made sense to have the two selections be the same atoms, but in different molecules. Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Dept. of Biomedical & Molecular Sciences, Botterell Hall Rm 6

[PyMOL] Coloring molecule after color_ramp

=ocean set surface_color, proximityRamp, (XX*) After that we would like to color defined residues for example in red using the selection tool. Although the color is changed in the sequence pane, the color is not applied to the molecule. Any suggestions? Best Robert

Re: [PyMOL] drawing a bond between the same Calpha atom in different states

Hi, (replying to my own message) On Thu, 2012-12-13 15:52 EST, Robert Campbell wrote: > Hi Jon, > > On Thu, 2012-12-13 16:09 EST, Jonathan Grimes > wrote: > > > Hi All, > > > >I have 2 different states of the same molecule..different > &

Re: [PyMOL] drawing a bond between the same Calpha atom in different states

ordinates of the vector in place of atom1 and atom2. Hope that helps. Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Dept. of Biomedical & Molecular Sciences Botterell Hall Rm 644 Queen's University,

[PyMOL] Reducing VRML file size

Hi folks, we are currently facing problems with large VRML files. We have a quite complex .pse file with several molecules in surface representation. Once we save this .pse file as VRML it has a size of about 1.2 gigabyte. We could reduce the file size to about 700mb after combining all molecul

Re: [PyMOL] sequence file extraction

&aid=3466472&group_id=4546&atid=104546 Another bug (I guess I should report it via the bug tracker) is that if a structure has multiple conformations (at least at the CA atom), then the residue appears twice in the sequence. Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Asso

Re: [PyMOL] about super_all.py Plugin installation.

d, then you can call the "super_all" function from the command line within PyMOL. You can see the options by typing super_all ? and you can get more information by typing help super_all I hope this helps. Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct

Re: [PyMOL] Forced Linux/Python upgrade, killed PyMol, please help!

s using the simple routine of: CC=gcc-4.5 python setup.py build python setup.py install --prefix=/software/Linux python setup2.py install The "--prefix" option just allows me to put the software on an NFS mounted disk, rather than on my own machine, so it is available to all the lab compu

Re: [PyMOL] Pymol: Cartoon representation for .pdb file with multible entries

simply load the pdb file with the "discrete=1" flag: load md_file.pdb, discrete=1 dss md_file Setting the "discrete" flag causes PyMOL to store more information (B-factors, secondary structure) with each atom of each state -- so it can also be noticeably slower to load

Re: [PyMOL] Script for Torsion angles

Martin, If you end up wanting to do this a lot then it might be worth looking into Dangle ( http://kinemage.biochem.duke.edu/software/dangle.php ). This is one of the tools from the Richardson Lab which allows quick output of various bond length, angle, torsion and plane measurements. -bob On Fr

[PyMOL] Help for surface coloring

residues with a gradient depending on the distance from these xyz coordinates. Can anyone please help me out? All the best Robert Robert Münch - Dipl. Biologist / PhD-Student Paul-Ehrlich-Institut Federal Institute for Vaccines and

Re: [PyMOL] change transparency for only a selection

and not sel_01 disable rest set stick_transparency, 0.8, rest set stick_transparency, 0.0, sel_01 I think you'll find that the transparency settings only work with whole objects and not with selections that are subsets of objects. Cheers, Rob -- Robert L. Campbell,

Re: [PyMOL] slab mode fine-tuning

also control the front and rear clipping planes independently by holding down the "Shift" key along with the right mouse button (assuming you are in the standard 3-button viewing mode). Moving the mouse vertically changes the front clipping plane and moving it horizontally changes the r

Re: [PyMOL] Selecting ASP and GLU

y to write that is: color tv_red, resn asp+glu You can string several sorts of selections together that way, for example: select actsite, resi 105+262+286 select aliphatic, resn ala+val+leu+ile Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Profes

Re: [PyMOL] set sphere_scale question

value". Typing "help set" at the PyMOL command prompt shows the following: cmd.set(string name, string value, string selection, int state, int updates, int quiet) So you need to change your command to: cmd.set ("sphere_scale", value=1, selection='&#

Re: [PyMOL] Loading multiple ligands into a single view

On Fri, 21 Jan 2011 10:10:02 -0500 Robert Campbell wrote: > Hello Tom, > > On Fri, 21 Jan 2011 15:28:26 +1100 Tom Dupree wrote: > > > Hello all, > > > > I have a *.sdf (it can be a *.mol2 if that makes it easier) that contains > > multiple ligands. I'

Re: [PyMOL] Loading multiple ligands into a single view

own state. Is there a way to > over-ride this behaviour? You don't need to over-ride the loading behaviour. You can simply set the "all_states" variable to 1 (or "on"): set all_states, 1 (or use the "Settings -> Edit all" menu item). Cheers, Rob --

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