[PyMOL] EDS maps switched upon fetch?

Hello all - I have been looking at some electron density from the EDS and wondering why it didn't appear to match up with the coordinates. Then I found that it appears PyMOL (v 1.3), when requesting a "2fofc" map, actually reads in the fofc, and vice versa. Here's a script to illustrate the

Re: [PyMOL] change label position

On Jul 19, 2011, at 6:53 AM, leila karami wrote: my system contains 2 residues. I labeled them. Now I want to change the position of one of labels as position of other be fixed. how do I do that? Hello leila, In addition to the GUI method Zhijian recommended, here are two options to do this f

Re: [PyMOL] Select smart

Hi Troels, Jason - I've often wondered about these as well, so I've just updated the wiki page http://www.pymolwiki.org/index.php/Single-word_Selectors#More_selectors to reflect the single-word selectors from Selector.c. I think I got them all, but feel free to double check! Cheers, -- Jared

Re: [PyMOL] fink install pymol help

On Mar 15, 2012, at 10:14 PM, Shane Neeley wrote: I've installed all of the packages for pymol-py27 with fink. And my terminal went back to normal. Now what? How do I make PyMol an application? Short answer: You don't. The fink version of PyMOL is run from the command line. Open up a new Term

Re: [PyMOL] Creating dummy zones

Hi Anasuya - One way to generate the dummy zones (i.e. get_zones() from Jason's script) might be to step through the protein chain and create one selection around each residue. Of course these aren't really random, but you could fairly easily select random values from the list. # initia

[PyMOL] Script to calculate Fab elbow angle

Hello all - I'd like to share with you this script that I recently added (with Troels' help) to the PyMOL Wiki. http://www.pymolwiki.org/index.php/Elbow_angle Given a PyMOL object containing an antibody Fab fragment complex, light and heavy chain IDs for the Fab, and residue numbers for the bo

Re: [PyMOL] displaying cartoon helix and sheet in multiple identical chains

Hi Hena - You can type the following commands in the command line of the pymol graphics window, one at a time. color red, ss h color yellow, ss s color white, ss l+'' If you don't mind the loops being green, you could also use the first preset under the Color menu for your object. [C] > by

Re: [PyMOL] displaying cartoon helix and sheet in multiple identical chains

simultaneously. But, the problem is when I am using alter resi 10-23, ss='H' is not working at all. Hena On Tue, Jul 10, 2012 at 1:50 PM, Sampson, Jared mailto:jared.samp...@nyumc.org>> wrote: Hi Hena - You can type the following commands in the command line of the pymol graphics

Re: [PyMOL] ribbon trace, visualizing polymers (resent)

Hi Erik - A more general question. It seems like there must be a better way to visualise a polymer, say as a ball an stick image. Is there a more straight forward way of doing this in pymol? Not sure if you've found a solution to this already, but have a look at http://www.pymolwiki.org/index.p

[PyMOL] Export to COLLADA format

Hi all - I'm working on generating some interactive 3D figures, and have found that PyMOL is able to write .obj and .wrl files, which is nice. However, I would like to be able to use COLLADA (.dae) format. I have found tools (MeshLab and Blender, for example) that can convert among various fo

Re: [PyMOL] Write vector graphics of session

Hi Jason - I see that COLLADA is listed as one of the choices for vector output, but I would argue that the selection of another choice of format in the poll shouldn't exclude it from consideration as development-worthy. As an open 3D format, it is useful for applications involving user interac

Re: [PyMOL] symmetry operation to generate the whole virus particle

Hi Yeping - Try using: fetch 2buk, type=pdb1, multiplex=1, async=0 This will fetch the biological assembly (type=pdb1) from the pdb, split the 60 states into separate objects (multiplex=1), and tell PyMOL to wait for all this to be completed before moving to the next command in a .pml script (

Re: [PyMOL] [PyMol] How to visualize surface within a given radius

Hi Yarrow - If you add "br. " to the show surface command, you will get more continuous surfaces, as the selection will be made by residue instead of by atom. show surface, br. protein within 0.5 of pocket_selection If you don't want to show the surface from a particular residue (e.g. if it's

[PyMOL] Mesh Cavity Mode?

Hi all - Is there a way to show internal cavities as meshes instead of surfaces? Something like `set surface_cavity_mode, 1` except with mesh? Thanks in advance for responses. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center Old Public Health Building, Room 610 341

Re: [PyMOL] Mesh Cavity Mode?

older mailto:thomas.hol...@schrodinger.com>> wrote: Hi Jared, how about: PyMOL> as surface PyMOL> set surface_cavity_mode, 1 PyMOL> set surface_type, 2 Cheers, Thomas Sampson, Jared wrote, On 03/22/13 23:31: Hi all - Is there a way to show internal cavities as meshes instead of surf

Re: [PyMOL] sphere_scale help

[Re-posting to the list because, as usual, I forgot to Reply All...] Hi Greg - If I understand correctly (and just on a quick visual inspection in PyMOL it looks like I'm at least close), the sphere_scale setting will scale the size of the sphere relative to the van der Waals radius of the atom

Re: [PyMOL] Applying the DISTANCE command to a docking ensemble

Hi Amit - I'm not sure about working with your AutoDock file, but the way to run PyMOL without opening the GUI is via "pymol -c" on the command line. For more command line options, see: http://www.pymolwiki.org/index.php/Command_Line_Options. You can run a .pml script with PyMOL commands as

Re: [PyMOL] Segmentation Fault

Hi Narin - Hope you don't mind me reviving an old thread, but I just ran into this same problem trying to build Pymol from source (and using fink for the dependencies) on my laptop. What solved it for me was the following: fink remove libpng16 libpng16-shlibs I guess pymol was trying to use l

Re: [PyMOL] residue B factor

Hi Yeping - There is a script on the PyMOL Wiki that will help with this. http://pymolwiki.org/index.php/Average_b Save the code in a plain text file as average_b.py in your working directory, then run it from the PyMOL prompt: run average_b.py Then you can analyze any residue you like, for

Re: [PyMOL] Drawing chain to visualize backbone

Hi Simon - I don't think you need to do any deleting of atoms at all--there are a few settings that will be helpful here. Here's how I would do what I think you're asking for: # load and set basic representation load structure.pdb as cartoon # create the smooth version create smooth, structu

Re: [PyMOL] UCSD pymol workshop

Hi Spencer - You may already be aware of this, but the PyMOL Wiki is a great resource. Depending on the scope of what you want to cover and the experience levels of your members, there are several tutorials that may be helpful. I'd recommend Practical PyMOL for Beg

Re: [PyMOL] minimum rotation between views

Hi Jonathan - There is a script by Christoph Gohlke on the PyMOL Wiki called transformations.py which may be useful. It provides several functions that can be used to manipulate quaternions. I used it to calculate pseudo-twofold axes for my Fab

Re: [PyMOL] Drawing chain to visualize backbone

Hi Simon - Glad you figured out a method that worked for you. However, I'm wondering why you ended up with "un-smoothed" helices using the `cartoon_smooth_loops` method. Are you sure you typed the last two commands in my example correctly (`alter` and `rebuild`)? I'm getting a single, relati

Re: [PyMOL] Working with the pdb ensemble

Hi James - If I understand you correctly, you just need to give a selection argument to the save command. save ligand1.pdb, sele1 save ligand2.pdb, sele2 etc... See http://pymolwiki.org/index.php/Save for more info. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center 5

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

Hi Om - Here is another option that loads only one mutant at a time. You can save the following as a Python script (e.g., "mut-rmsd.py") and run it from the PyMOL command line by typing `run mut-rmsd.py` (with a full or relative path if it's not in PyMOL's working directory). For more informa

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

o see what the command looked like when you ran the script. PyMOL log files are very widely useful for finding out how to translate GUI actions into scriptable commands. Hope that helps! Cheers, Jared On Wed, Jan 8, 2014 at 1:13 AM, Sampson, Jared mailto:jared.samp...@nyumc.org>> wrote

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

Thanks, Carsten. I thought it would turn out to be something related to the paths, but couldn't put my finger on it. (I was able to run the script fine without either of those fixes on Incentive PyMOL 1.5.0 32-bit on a Win XP VirtualBox VM guest on a Mac OS 10.8 host. Not sure why that might

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

Hi Riccardo - Looking at the source (pymol/layer1/Ray.c, in RayRenderIDTF(), starting around line 2254) I can confirm that Sphere, Cone, Cylinder and Sausage representations are not implemented in the IDTF exporter. Currently only triangle mesh representations (cartoon, surface) are supported.

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

ule Viewer<http://chembioscripting.hol.es/> | Gioacchino Riccardo Volpe 2014-02-10 23:15 GMT+01:00 Sampson, Jared mailto:jared.samp...@nyumc.org>>: Hi Riccardo - Looking at the source (pymol/layer1/Ray.c, in RayRenderIDTF(), starting around line 2254) I can confirm that Sphere

Re: [PyMOL] generate solvent exclusive surface with scaled VDW radii

Hi Ye - The solvent excluded surface is the default surface representation in PyMOL. (Solvent accessible surface can also be generated using `set surface_solvent, on`.) View the surface with: show surface, myobj You can modify van der Waals radii like this: alter myobj, vdw=vdw*1.2 rebuild

Re: [PyMOL] Yaw, Pitch and Roll of CGO

Hi Pawel - If you can determine the primary axis of the cone from the tip and the center of the circle at the base, you can give `rotate` an arbitrary [x,y,z] float vector as its first argument instead of x, y or z. For example, if you generate your cone using something like the following Pyth

Re: [PyMOL] Yaw, Pitch and Roll of CGO

of cone. The problem was, that in 'translate' function I didn't use 'camera=0' option, what in did in 'rotate'. Moreover I should set 'origin=[X,Y,Z]' option as well as 'camera=0' in rotate option. Now it work smoothly and pretty nice ;) Than

Re: [PyMOL] selecting atoms ..

Hi Sampsa - The long list of ids crashes for me as well. Instead of listing each id separately, you can use ranges to define your selections. select paska, id 36-58 select isopaska, id 36-350 If you need to use non-continuous ids, you can use Boolean logic to join the ranges: select isopaska

Re: [PyMOL] color each polymer chain differently

Hi Chandan - It seems like you're being limited by the 26 numbered colors in the util.cbc function. You could create your own randomized list of evenly-spaced colors, something like the following (untested, but should be approximately usable--sorry, I'm away from my computer today): from pymol

Re: [PyMOL] color each polymer chain differently

_colors[i] print "%s will be colored %s (%s)" % (sel, color, color_tuple) cmd.color("%s" % color, sel) ### -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center 550 First Avenue New York, NY 10016 212-263-7898 http://kong.med.nyu.edu/ On Mar 17, 2014, at 2:0

Re: [PyMOL] Pymol insertion code

Hi Nick - This PDB employs non-standard usage of the PDB insertion code column. Typically, it is used to insert one or more residues between adjacent numbers in a canonically numbered structure, e.g. residue 42A (along with 42B, 42C, … , 42P, etc.) is between residues 42 and 43. As for whethe

Re: [PyMOL] Pymol insertion code

Sorry - one quick correction to my previous email: On Mar 20, 2014, at 10:50 AM, Sampson, Jared wrote: > If you don’t need the cartoon representation to be continuous (e.g. if you’re > zooming in on a different section of the protein you can replace the 3rd line > with: > >

Re: [PyMOL] Ligand surface: color issue after ray

Hi Tobias - It seems to me that you may not have hidden the lines/sticks from the object where you’ve shown the surface. For overlapping objects, the normal non-ray-traced view appears to give precedence to the object that was present in the viewer first. Try disabling and re-enabling your two

Re: [PyMOL] boundaries/outlines of overlapping regions on surface

Hi Sid - I don’t think there is a way to accomplish this directly in PyMOL, but you can get partway there using the `ray_trace_mode` setting and named selections for the various regions you wish to depict. http://pymolwiki.org/index.php/Ray#Modes Ultimately, you’ll need to create a composite

Re: [PyMOL] animation showing conformational change

Hi Yeping - With incentive PyMOL version 1.6 or later, you can use `morph`. From what I read at http://pymolwiki.org/index.php/Morph, you’ll need to put both conformations of the protein into one object, as different states. See http://pymolwiki.org/index.php/Load for more info on that. Chee

Re: [PyMOL] [ccp4bb] Farewell

Jason - I’d also like to express my appreciation for all you’ve done to benefit the PyMOL community. You have, time and again, proven yourself to be an extremely responsive and helpful leader both in developing the software and in enabling others to learn to use it. Like many on these lists,

Re: [PyMOL] gradually changed colors with b-factor colum

Hi Yeping - I was about to suggest Sean Law’s new spectrumbar script, but I see he beat me to it. You’ll have to adjust the positioning of the bar with some trial and error. Also, in case you get a “NameError: global name 're' is not defined” error

Re: [PyMOL] RE： gradually changed colors with b-factor colum

stion is the same with above: how could I correctly label the bar according my data set? Best regards, Yeping ------ 发件人：Sampson, Jared mailto:jared.samp...@nyumc.org>> 发送时间：2014年4月29日(星期二) 04:36 收件人：孙业平 mailto:sunyep...@aliy

Re: [PyMOL] Pymol wrl output

Hi Bob - The reason you're getting these errors is because having negative values in a color tuple is not meaningful (you can't have a negative amount of color), and results in undefined behavior. RGB colors use a number in the range 0.0-1.0 (inclusive) for each value in the tuple. What color

Re: [PyMOL] Pymol wrl output

g in particular anywhere you see a negative color value? Thanks, Jared -- Jared Sampson Xiangpeng Kong Lab NYU School of Medicine kong.med.nyu.edu ________ From: Grateful Frog [gratefulf...@gmail.com] Sent: Saturday, May 03, 2014 1:53 PM To: Sampson, Jared Cc: Marcelo Marcet;

Re: [PyMOL] using a pseudoatom for distance measurement

Hi Mary - There are a couple problems here. First, you’re giving the pseudoatom command a positional argument out-of-order (and after keyword parameters). Keyword parameters can appear in any order, but only if you use the keyword. Otherwise, you must list them in the order specified by the

Re: [PyMOL] using a pseudoatom for distance measurement

fer to a real coordinate in the file and it can take any of the twenty models, but when it knows which model to take, it is more probable to work because it refers to the right coordinates. Any comments on that? Cheers Mary On Mon, May 5, 2014 at 4:17 PM, Sampson, Jared mailto:jared.samp...@n

Re: [PyMOL] Ray trace mode 1 outline thickness

Hi Martin - Try increasing the `ray_trace_gain` setting. Default value is 0.12, so maybe try 1 or 2. If you go much higher, you’ll start to see additional lines or spots. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On May 14, 20

Re: [PyMOL] how to count all the Polar contacts

Hi Merlin - Try limiting the distances shown to those between atoms in specific selections using the `distance` command. For example, to show H-bonds to solvent, disable the “my_obj_pol_conts” object created by the technical preset and use the command: distance my_dist, my_obj and not solvent

Re: [PyMOL] align or pair_fit display problem

Hi I-Ji - You say the superimposed atoms are still there; that seems like normal behavior to me. If you disable one of the objects, can you see the other one, and vice versa? If the two structures are nearly identical, you may not be able to differentiate them visually after alignment. If th

Re: [PyMOL] Visualize Sheets from C-alpha Only Structure

Hi Sean - I can confirm this behavior, but I’m not sure it’s unintentional on PyMOL’s part. Rather, I think it may have something to do with two facts: 1) unlike loops, sheets represented in automatic mode are not radially symmetric; and 2) unlike helices, the orientation of the sheet at a par

Re: [PyMOL] Visualize Sheets from C-alpha Only Structure

Hi Sean - By “radially symmetric” I mean that a particular representation (e.g. anything in cartoon tube or putty modes, or loops in automatic mode) is drawn as a series of truncated cylinders or cones, so for PyMOL to draw them, basically all it needs for each short section are two end points

Re: [PyMOL] filled rings

Hi H. Adam - Try the cartoon_ring_color setting. You can do this per-selection as well. set cartoon_ring_color, blue, my_selection Hope that helps! Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On Jun 16, 2014, at 4:57 PM, H. Adam

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

Hi Suzanne - The reason you have been getting only one distance in your output file is that your script is opening the file in “write” mode: f=open('distnew.txt','w') This will overwrite the contents of distnew.txt each time the script is run. If you want to keep all the distances without chan

Re: [PyMOL] paste pictures

Hi Yeping - The best way is to upload your image to a file sharing website (e.g. Dropbox, Box, Google Drive, etc.) and include a link to the image (or folder of images) in your message. That way, people only have to download the image if they want to do so. It is also possible to send attache

Re: [PyMOL] what is the pymol representation in this figure?

Hi Yeping - Looks like the following settings are in play here: # different cartoon modes cartoon automatic, alpha1 # for the alpha1 helix cartoon tube, chain P # for the orange, green and blue peptides # hide backbone sticks/lines where cartoon is shown set cartoon_side_chain_helper, on # s

Re: [PyMOL] FW： RE： what is the pymol representation in this figure?

Hi Yeping - I followed Jared's instruction and then show surface, but the surface is still an incomplete plane, unlike what I wish as in the sample. You will probably have to create new objects for those individual residues to show their surfaces in whole. Otherwise, you only get the portion

Re: [PyMOL] Faster installation of plugins during development

Hi Matt - Does your plugin require a GUI, or can you rely on scripted commands and output files for your tests? For any tests that don’t need the GUI, you might consider running them with something like `pymol -ckq my_test.pml`. http://www.pymolwiki.org/index.php/Command_Line_Options Cheers,

Re: [PyMOL] Faster installation of plugins during development

Hi Matt - Does your plugin require a GUI, or can you rely on scripted commands and output files for your tests? For any tests that don’t need the GUI, you might consider running them with something like `pymol -ckq my_test.pml`. http://www.pymolwiki.org/index.php/Command_Line_Options Cheers,

Re: [PyMOL] How to show the surface border of a specific residue?

Hi Ooker - As I understand it, you want to overlay a line to show which part of the surface belongs to which residue. There is currently no way to do this directly within PyMOL. However, is possible to achieve something similar using multiple layers in a composite image. See this previous th

Re: [PyMOL] Problems with superposing small molecules and transformation

Hi German - I’m not sure I follow exactly what you’re asking, but `align` does its superimposition based on sequence alignment, which isn’t really meaningful for small molecule ligands. I would suggest using `fit`, `super`, or `cealign` instead, which all use just the coordinates, although it’

Re: [PyMOL] RMSD for selected residues

Hi Nidhi - The “Align” feature in the GUI uses PyMOL's `align` command, which performs a sequence alignment to use as the basis for structural alignment. It only uses those residues which match exactly, which can throw off the RMSD. Try using `super` or `cealign` instead, which are structural

Re: [PyMOL] Show cation-pi/pi-pi interactions

Hi Markus - It’s already possible to highlight polar interactions using the `distance` command with mode=2. http://www.pymolwiki.org/index.php/Distance For pi-cation stacking, it might be useful to create pseudo atoms at the average position of the atoms in each charged group or ring in questi

Re: [PyMOL] Other coloring strategies based on user-provided properties

Hi Chen - As you guessed, this is commonly done by modifying the B-factor column directly. You can do this with data available to you in PyMOL (e.g. distances, charges, and so forth) using alter and iterate and a fe

Re: [PyMOL] cartoon and line representation

Hi Yeping - I’m unable to reproduce the behavior you’re seeing—using your commands in Open Source PyMOL 1.7.2.0, I get the whole capsid displayed properly as a cartoon. What version of PyMOL are you using? You could also try using the `all_states` setting instead: fetch 3j2v, type=pdb1, async

Re: [PyMOL] re： cartoon and line representation

iences -- 发件人：Sampson, Jared mailto:jared.samp...@nyumc.org>> 发送时间：2014年9月2日(星期二) 22:23 收件人：孙业平 mailto:sunyep...@aliyun.com>> 抄　送：pymol-users mailto:pymol-users@lists.sourceforge.net>> 主　题：Re: [PyMOL] cartoon and line representation Hi Yeping - I’m unable to repro

Re: [PyMOL] Residue-residue contacts from PDB

Hi Bhumika - Have a look at the CCP4 program NCONT: http://www.ccp4.ac.uk/html/ncont.html. You can run it within the CCP4 GUI or from the command line. For example, for contacts between helices 1 and 2, type these lines at the prompt (or copy and paste), substituting the correct path to the PD

Re: [PyMOL] Access to pymol commands from the terminal

Hi James - What version of PyMOL are you using? For me, using Open Source PyMOL 1.7.2.0, a typical PDB file I tested ends up with more information in that column, not less, after saving from PyMOL: Before: ATOM 1312 NH1 ARG A 198 0.544 14.093 19.655 1.00 34.61 N After: A

Re: [PyMOL] Access to pymol commands from the terminal

Hi James - I don’t have any experience with Profit. However, instead of using "something like” PyMOL’s `super` command as you asked, you could actually use `super` in your shell session by launching PyMOL in command line mode. Of course

Re: [PyMOL] Access to pymol commands from the terminal

tarlight mailto:jmsstarli...@gmail.com>>: Hi Jared, many thanks for the suggestion! your method works perfect (i only slightly modified dir for input file) 2014-09-19 20:19 GMT+02:00 Sampson, Jared mailto:jared.samp...@nyumc.org>>: Hi James - I don’t have any experience with Pro

Re: [PyMOL] measure angles in programming

Hi Lei - The `get_angle` command needs an atom selection for your “tunnel" atoms, which, like the B-factor as Matt mentioned, you can also get using `iterate`: ### # create a list stored.centers = [] # get the macro selection string for each atom in tunnel cmd.iterate("tunnel", 'stored.centers

Re: [PyMOL] Show all residues forming H-bonds

es* as dashes, but not the actual residues. I don’t want the dashes, but I want the residues (i.e. the donors and acceptors) in selectable objects. I hope it’s clearer now what I’m after … Cheers M From: Sampson, Jared [mailto:jared.samp...@nyumc.org] Sent: Friday, October 10, 2014 3:33 PM To:

Re: [PyMOL] Show all residues forming H-bonds

:10 PM, Sampson, Jared mailto:jared.samp...@nyumc.org>> wrote: Hi Markus - Ah, sorry, I misunderstood your request at first. What about the “acceptors” and “donors” selectors? http://www.pymolwiki.org/index.php/Single-word_Selectors e.g. select hbond_residues, byres ((acceptors within

Re: [PyMOL] colour surface meshes

Hi David - Yes, indeed, PyMOL can save VRML2 (.wrl) files, although it outputs vertex colors rather than face colors. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On Oct 13, 2014, at 11:18 AM, David Pattinson mailto:dj...@cam.ac.uk

Re: [PyMOL] Show all residues forming H-bonds

Jared, I'm a newbie to pythom/PyMOL; how do I get this to work in a pml script? A pointer to an example script would be enough . Thanks Markus From: Sampson, Jared [mailto:jared.samp...@nyumc.org] Sent: Friday, October 10, 2014 4:17 PM To: Markus Heller Cc: pymol-users@lists.sourcefo

Re: [PyMOL] PyMOLWiki Update

Hi Justin - I see this same “weirdness" using the https protocol. If you remove the ’s’ from ‘https’ in your URL, however, it will load properly. It must be on a shared server that has something goofy happening with the handling of https traffic. I think Jason is still the admin for the wiki

Re: [PyMOL] How to calculate Hinge angle

Hi Shoeib - It’s hard to say exactly what you need, because it will vary depending on your specific case. If you’re looking for the change in a hinge angle between two structures of multi-domain proteins A and B, you can first superimpose domain 1 of B to domain 1 of A, get the matrix of B, su

Re: [PyMOL] ligand binding site visualisation

Hi James - You could put in a feature request to ask that non-canonical residues be included in the preset. In the meantime, the Property Selectors, Single-Word Selectors

Re: [PyMOL] Access API without the GUI

Hi Doug - You can launch PyMOL with the -c flag for command line only (no GUI). See http://www.pymolwiki.org/index.php/Command_Line_Options for more details. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On Nov 11, 2014, at 2:56 PM,

Re: [PyMOL] View Matrix operation

Hi Louris - If your view is centered on the atom from which you would like to draw the line, and oriented the way you want it, you can achieve something similar to what it sounds like you want with the following commands. center myAtom move x, -4 # `move` works in camera space pseudoa

Re: [PyMOL] Super, algorithm

Hi Spencer - If you need a superposition algorithm with a published reference, try CEAlign. Some references are listed on the page for the former CEAlign Plugin from before it was incorp

Re: [PyMOL] homebrew pymol

Hi Ryan - Have a look at this post, which may also help you in creating an app out of your Homebrewed PyMOL. I’d recommend using a symlink within the app bundle to /usr/local/bin/pymol, so when you update with homebrew, you don’t have to ch

Re: [PyMOL] selection of a set of amino acids

Hi Alireza - For renumbering a chain, the program PDBSET in the CCP4 suite is my tool of choice. If your protein is chain A, the command would look something like this: pdbset xyzin my_protein.pdb xyzout my_protein_renumbered.pdb

Re: [PyMOL] Dot representation

Hi Yarrow - 1. Yes, according to the wiki, the dots are located on the vdW surface unless the `dot_solvent` setting is turned on (in which case they’re on the solvent accessible surface). 2. Based on the settings listed with “dot” in their names, it does

Re: [PyMOL] raytracing a transparant surface, with reflections only on the cofactors inside

Hi Floris - Tsjerk is correct. You can set spec_reflect for a selection. Something like: set spec_reflect, 0, all and not organic This would turn of specular reflection on anything that’s not a “ligand” atom. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://

Re: [PyMOL] raytracing a transparant surface, with reflections only on the cofactors inside

8 objects. > > So it seems okay. But however when I raytrace, I still get all reflections. > When I subsequently type > set spec_reflect, 0 > and then raytrace, the reflections are really turned off. > > Could this be a bug, or do I forget something? > > Thanks > >

Re: [PyMOL] unable to export obj

Hi Albert - Surface mode 2 outlines the mesh edges with thin cylinders, but if I remember correctly, I think PyMOL’s OBJ export doesn’t do cylinders (or spheres or cones), only triangle meshes. You could try exporting to VRML2 (.wrl) or COLLADA (.dae) format and using something like, e.g. Blen

Re: [PyMOL] Chain Selection doesn't work (MacPymolEdu)

Hi Simon - It looks like your default Python is now 3.x rather than 2.x. The built-in function reduce() was moved to functools.reduce() as of version 3.0. You can confirm whether this is the case via “python --version” on the command line. One solution might be to make 2.7 the default again,

Re: [PyMOL] Colouring nucleic acids, without changing the colouring of amino acids

Hi Brenton - To avoid coloring e.g. Glycine when you only want to color e.g. guanine, prefix the residue name with “D” (as the residues are shown in the Sequence viewer) for DNA. I believe RNA works the same way with “R” as well. set cartoon_color, green, resn DG To color the DNA backbone, yo

Re: [PyMOL] Pymol molecular visualisation

Hi James - Here is how I would label your objects in grid_mode: # For each object, create a pseudoatom at its center of geometry to position the label pseudoatom myobj_label, myobj # Set the label text for the pseudoatom label myobj_label, "My Object" # To show the label and the object in the

Re: [PyMOL] cartoon putty present in pymol

Hi Wenfu - Cartoon putty representation varies the diameter of the putty tube based on the B-factor column in the loaded PDB file. In your example file, all the B-factors are 0.00. Perhaps you could use `cartoon tube` instead, which is similar to putty, but uses a single cartoon_tube_radius s

Re: [PyMOL] MacPyMol working dir

Hi Luigi - To get the right working directory, you can use the full path to the binary followed by the `-d` flag to run a command (`cd $PWD`) once PyMOL opens. Personally, I'd alias it in ~/.profile like this: alias macpymol='/Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL -d "cd $PWD"' Al

Re: [PyMOL] moving objects

Hi Marcelo - Is Object 2 actually a pseudoatom? Or, if not, can it be placed separately from Object 1? If either of those are the case, it would be much easier to place the pseudoatom at a point equidistant from the two ends of Object 1 than mess with rotation matrices, etc. Here’s what I wo

Re: [PyMOL] Load very similar molecules into distinct objects?

Hi Jorge - As long as the filenames are different, the molecules should end up in separate objects. If the filenames are in fact the same (e.g. same filename but in different folders), try explicitly naming the objects using the PyMOL command line: load path/to/the/first/mol1.pdb, first_mol lo

Re: [PyMOL] Add fragment

Hi Ben - Try this: editor.attach_fragment("pk1", "methane", 1, 0) Here's how I tracked this down, not having known about this function before your email. cmd._alt() and likewise cmd._ctrl() are functions (you can see for yourself in the source code in pymol/modules/pymol/cmd.py), and they are

[PyMOL] Bug report: cmd.fab() with existing object name produces unexpected results and downstream segfault

In the process of investigating Ben Bobay's question about keyboard shortcuts for adding a methyl group, I may have found a bug, or at least unexpected behavior, in cmd.fab(). When first creating a peptide, it works fine: fab ,

Re: [PyMOL] MacPyMOL in command line mode

Hi CY - If you're using the -c flag, you shouldn't need a windowing system at all. The following works for me between a MacBook Air and an iMac, both running 10.9.5, with MacPyMOL 1.7.6.0 installed on the iMac. ### begin shell ### (macbook-air)~ › ssh jared@imac Password: Last login: Fri May 2

Re: [PyMOL] efficiency assigning b-factors

Hi Jordan - I think you're doing it exactly the way I would, given an existing dict containing the values. Note, however, that if you have multiple loaded, or multiple chains with the same residue numbers, you may wish to be more specific with your selection string; your current script will al

Re: [PyMOL] how to measure the distance of 2 hydrophobic residues

Hi Smith - This won't tell you anything about the hydrophobic interaction itself, but if you want to get the distance between the average positions (like center of mass, but without mass) of two groups of atoms to use as an "approximate" distance between the two residues/sidechains/etc., you ca

Re: [PyMOL] how to measure the angle between two protein complexes

Hi Yeping - To calculate such an angle, you will need two vectors, which you can create with some pseudoatoms and the orient command. Before you start, you should create named selections for the ring and

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