[PyMOL] clipping

Robert Schwarzenbacher, PhD The Joint Center for Structural Genomics phone: 858 822 3637 Hi there, Is there a way to define the clipping planes for only one object in a scene. For example I only want to clip the surface while not affecting residues shown in stick. Or alternatively is there a

[PyMOL] electron density settings

Hi there, 1. How can I reduce the density-map line thickness in the ray-traced image? 2. Is there a way to just display the density around a ligand many thanks robert Robert Schwarzenbacher, PhD The Joint Center for Structural Genomics phone: 858 822 3637

[PyMOL] chainbow on commandline

___ Robert Schwarzenbacher, PhD The Joint Center for Structural Genomics; www.jcsg.org University of California San Diego Phone: 011-858-822-3637 or 011-619-519-9504 Hi there, How do you tell pymol on commandline to do chainbows. I tried 'spectru

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] 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,

[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] 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

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] 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] 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] 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

[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] 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,

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 > &

[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] 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

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] 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] 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

[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] 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] 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

[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 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

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] 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

[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

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

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] 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

[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] 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

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] 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] 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] 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

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] 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] 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] 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] 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] 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] 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] 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] 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] 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)

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] 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] 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] 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

[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] 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

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 -> 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] 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

[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] 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

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

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

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] 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] 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] 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] 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] 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] 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] 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] 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! ​ --

[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] 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] 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] 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

Re: [PyMOL] question on cctbx and pymol

c: http://cci.lbl.gov/cctbx_build/mac_os_x_notes.html Note that you need to use the "Framework" build of PyMOL: http://delsci.com/frameworkpymol/ Unfortunately there isn't a Mac around here for me to test this stuff on. Cheers, Rob -- Robert L. Campbell, Ph.D.

Re: [PyMOL] [colors frozen for rendering modes defined in .pymolrc]

t cartoon_color, default Then the cartoon is not forced to be the colour that you set (slate) but takes on the colour of the atoms in the object. Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associatephone: 613-533-6821 D

Re: [PyMOL] Listing secondary structure assignments

si,ss Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associatephone: 613-533-6821 Dept. of Biochemistry, Queen's University, fax: 613-533-2497 Kingston, ON K7L 3N6 Canada http://adelie.biochem.queensu.ca/~rlc

Re: [PyMOL] label alternate conformations

This series of commands seems to do the job although a little sloppy. label alt a+"", "A%s-%s" % (resn, resi) label alt b+"", "B%s-%s" % (resn, resi) hide labels, alt "" Cheers, -bob On 12/7/05, Seth Harris wrote: > > Hi, > > I'm writing a small script to visit alternate conformations, steppin

Re: [PyMOL] Re: New spectral color pallette

'gy' : green -> yellow 'yg' : yellow -> green 'gray' : black -> white 'reversegray' : white -> black It isn't too difficult to add more gradients by following the recipes in the "make_gradient" function i

Re: [PyMOL] What residues have I selected?

of If you just wanted to see a list of those residues, you could type: iterate near & name ca, print chain,resn,resi to get a list of those residues. Hope that helps. Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate

Re: [PyMOL] delete/create bonds in pymol

they are selected and named pk1 and pk2 and then just type "unbond", or you can explicitly specify the atom selections in the typed command. Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associatephone: 613-533-682

Re: [PyMOL] transparency for nb_spheres

Chad, You can try, show spheres, resn HOH (or whatever your waters are called) set sphere_scale, .2 set sphere_transparency, .5 Good luck, -bob On 3/20/06, Chad R. Simmons wrote: > Hello, > > I am using "nb_spheres" to represent waters in a figure I am generating but > cannot figure out how

Re: [PyMOL] Ray-tracing inner surface backside

Paul, I'm actually quite interested in an answer to this question as well. An example of what I have been able to do is this: http://kinemage.biochem.duke.edu/~immormino/neca_new.png I like using this type of rendering to look at a protein cavity from inside the protein. For me it has been hel

Re: [PyMOL] a scaling question

forth. > How can I put the molecule in the different time frames in exactly the > same size? What you are experiencing is the "auto_zoom" feature of pymol. I have this turned off in my .pymolrc file. You can type: set auto_zoom, 0 to disable this feature

Re: [PyMOL] D-ala

hen the N and C atoms of the main chain of the residue you wish to convert to the "D" configuration. These atoms will not move. Then use that menu item (or type "Ctrl-E") and the Cbeta will flip to the other configuration. Cheers, Rob -- Robert L. Campbell, Ph.D.

Re: [PyMOL] That _cmd thing

mplete scripts are available on my web site: http://adelie.biochem.queensu.ca/~rlc/work/scripts Given the size of the scripts, I've been thinking of breaking it down into a much simpler script that calls a specialized script for each program, but I haven't done it yet. Cheers, Rob

Re: [PyMOL] alternate conformations

Tina, A work-around that does something like what you are looking for is: load protein_with_alts.pdb, A load protein_with_alts.pdb, B hide everything, show sticks, A and alt A show sticks, B and alt B set stick_ball, 1, B set stick_overlap, -1.8, B Cheers, -bob On 5/23/06, Nguyen, Tina (GSBS)

Re: [PyMOL] loosen secondary structure

n the command line. Alternatively, you can create a file of resname, phi, psi and build it with: http://adelie.biochem.queensu.ca/~rlc/work/pymol/build_seq_phi_psi.py if you don't want the phi/psi angles to be the same for every residue. Cheers, Rob -- Robert L. Campbell,

Re: [PyMOL] Problem loading chempy objects to pymol

't used the load_model function, but like the "load" function, there is a "discrete" option. It think you need to say: cmd.load_model(model,name,cont,discrete=1) Then each state will maintain its own values for B-factor etc. Cheers, Rob -- Robert L. Campbell, Ph.D. Sen

Re: [PyMOL] debian: error in opening pymol

open shared object file: No such file or > directory > > > Can somebody please point out the cause and the remedy? I have never used > pymol before and this was my first try. You need to install the freeglut3 package: apt-get install freeglut3 should take c

Re: [PyMOL] Is there a way to show three dimsional movement of residues?

Ronald, You can try the yale morph server: http://molmovdb.mbb.yale.edu/molmovdb/morph/ There are probably other tools that will perform linear interpolation of structures and output "intermeditate" .pdb files, which could be cleaned up and used in pymol to create a similar, but more user contr

Re: [PyMOL] sphere_scale problem

t_ca set sphere_scale=0.5, object_others Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Department of Biochemistry, Queen's University Kingston, ON K7L 3N6 Canada http://adelie.biochem.queensu.ca/~rlc phone: 613-533-6821

Re: [PyMOL] align states

ame ca)",1) SEE ALSO fit, rms, rms_cur, intra_rms, intra_rms_cur, pair_fit Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Department of Biochemistry, Queen's University Kingston, ON K7L 3N6 Canada http://adelie.bioche

[PyMOL] Cutaway surfaces

Hi. I want to make a figure showing a cutaway surface representation of a large complex showing a channel containing a peptide helix. If I show the surface and cartoon representations respectively and fiddle around with the clipping and slabing I can't get it so that the channel is 'open' without

Re: [PyMOL] How can I change the surface_quality of an electron density map surface?

hange the smoothness of the latter, you would need to sample the electron density at a finer interval (i.e. do the FFT with a finer grid). Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Department of Biochemistry, Queen's University Kingston, ON K7L 3

Re: [PyMOL] Paths to loaded objects

g is that I should add code (e.g. a > > dictionary) to the importing.py load() function which saves the > > file information of objects as they're loaded. But then instead of > > just distributing my plugin, I would have to get users to change > > their PyMOL source, as w

Re: [PyMOL] Surface Edge

Paul, I think the reason the surface coloring "spills over" is because there are some surface triangles that are shared by the selection you want (red) and the neighboring residues (grey)... So it should work if you only use one selection, by saying something like: load my_protein.pdb, show surf

Re: [PyMOL] problem getting kabsch.py to run

ic-23.7-2.i386.rpm file that you need to install (I'm assuming that version 23.7.2 works here). Perhaps another RHEL4 user can offer better advice. I use Debian GNU/Linux myself. Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Depar

Re: [PyMOL] thread in pymol

Shivesh, try show ribbon, set ribbon_sampling, 10 -bob

Re: [PyMOL] H-bonds and VDW

Kun, When I'm interested in dimer interfaces, or protein ligand contacts I usually use Molprobity to define the interface. http://molprobity.biochem.duke.edu/ It is a bit of a process, but here's the rundown: Load your .pdb into molprobity Add hydrogens Visualize interface contacts Then select

Re: [PyMOL] change the sphere size of a chosen atom ?

You can go to settings > edit all > sphere scale. Default is set to one, I have found that 0.3-0.4 works best. Bob _ From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of GAO FENG Sent: Wednesday, January 10, 2007 12:00 PM T

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