[PyMOL] Show sticks for phosphoserine (SEP) side chain

2010-03-25 Thread Sampson, Jared
Hi all - I have a structure where a serine is phosphorylated, so the residue is SEP. If cartoon_side_chain_helper is on, the sticks disappear from the phosphate group oxygens (O1P, O2P and O3P), even if I issue something like show sticks, (obj and i. 54 and n. P,O1P,O2P,O3P) I wonder if

Re: [PyMOL] Bug in Snow Leopard

2010-10-25 Thread Sampson, Jared
Hi Tom - I’ve also experienced this behavior, which led me to a) attempt to learn not to switch Spaces while using Fink-installed X11 PyMOL (other X11 programs, e.g. CCP4i, appear not to have the same issue); b) make all of my figures using .pml scripts so that if I’ve changed something it’s

[PyMOL] Fab elbow angle

2010-12-14 Thread Sampson, Jared
Hello all - I'm trying to calculate the elbow angle of an Fab locally (i.e. without uploading to a server) and decided to try it in PyMOL. I got stuck, and thought maybe someone much wiser than I might be able to shed some light on the error(s) of my ways. I've been trying to use some of the

Re: [PyMOL] Selecting ASP and GLU

2011-03-01 Thread Sampson, Jared
Hi Martin - ** Short answer: Use `resn asp+glu` (although your original command actually works for me). ** Not-so-short answer, with a bonus question about comment syntax: The Asp/Glu line of your script can be condensed slightly using a plus sign, but the original syntax of that line

[PyMOL] EDS maps switched upon fetch?

2011-04-12 Thread Sampson, Jared
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] Select smart

2011-12-05 Thread Sampson, Jared
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, --

Re: [PyMOL] fink install pymol help

2012-03-16 Thread Sampson, Jared
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

Re: [PyMOL] Creating dummy zones

2012-05-01 Thread Sampson, Jared
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. #

[PyMOL] Script to calculate Fab elbow angle

2012-06-15 Thread Sampson, Jared
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

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

2012-07-10 Thread Sampson, Jared
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

2012-07-11 Thread Sampson, Jared
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 jared.samp...@nyumc.orgmailto:jared.samp...@nyumc.org wrote: Hi Hena - You can type the following commands in the command line of the pymol graphics window, one at a time

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

2012-11-28 Thread Sampson, Jared
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

Re: [PyMOL] Write vector graphics of session

2013-01-16 Thread Sampson, Jared
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

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

2013-02-28 Thread Sampson, Jared
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

2013-03-04 Thread Sampson, Jared
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?

2013-03-22 Thread Sampson, Jared
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

Re: [PyMOL] Mesh Cavity Mode?

2013-03-25 Thread Sampson, Jared
thomas.hol...@schrodinger.commailto: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

Re: [PyMOL] sphere_scale help

2013-07-26 Thread Sampson, Jared
[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

Re: [PyMOL] Segmentation Fault

2013-10-03 Thread Sampson, Jared
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

Re: [PyMOL] residue B factor

2013-11-06 Thread Sampson, Jared
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

2013-11-15 Thread Sampson, Jared
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,

Re: [PyMOL] UCSD pymol workshop

2013-11-21 Thread Sampson, Jared
Hi Spencer - You may already be aware of this, but the PyMOL Wikihttp://www.pymolwiki.org/ 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

Re: [PyMOL] minimum rotation between views

2013-11-25 Thread Sampson, Jared
Hi Jonathan - There is a script by Christoph Gohlke on the PyMOL Wiki called transformations.pyhttp://pymolwiki.org/index.php/Transformations 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

2013-12-02 Thread Sampson, Jared
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,

Re: [PyMOL] Working with the pdb ensemble

2013-12-06 Thread Sampson, Jared
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

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

2014-01-07 Thread Sampson, Jared
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

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

2014-01-08 Thread Sampson, Jared
to translate GUI actions into scriptable commands. Hope that helps! Cheers, Jared On Wed, Jan 8, 2014 at 1:13 AM, Sampson, Jared jared.samp...@nyumc.orgmailto:jared.samp...@nyumc.org wrote: Hi Om - Here is another option that loads only one mutant at a time. You can save the following

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

2014-01-09 Thread Sampson, Jared
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)

2014-02-10 Thread Sampson, Jared
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

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

2014-02-10 Thread Sampson, Jared
://chembioscripting.hol.es/ | Gioacchino Riccardo Volpe 2014-02-10 23:15 GMT+01:00 Sampson, Jared jared.samp...@nyumc.orgmailto: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, Cone, Cylinder and Sausage

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

2014-02-14 Thread Sampson, Jared
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

2014-02-18 Thread Sampson, Jared
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

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

2014-02-18 Thread Sampson, Jared
' 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 ;) Thank you Paweł 2014-02-18 19:40 GMT+01:00 Sampson, Jared jared.samp...@nyumc.orgmailto:jared.samp...@nyumc.org: Hi Pawel - If you

Re: [PyMOL] selecting atoms ..

2014-02-18 Thread Sampson, Jared
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

Re: [PyMOL] color each polymer chain differently

2014-03-17 Thread Sampson, Jared
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

Re: [PyMOL] color each polymer chain differently

2014-03-18 Thread Sampson, Jared
Medical Center 550 First Avenue New York, NY 10016 212-263-7898 http://kong.med.nyu.edu/ On Mar 17, 2014, at 2:07 PM, Sampson, Jared jared.samp...@nyumc.orgmailto:jared.samp...@nyumc.org wrote: Hi Chandan - It seems like you're being limited by the 26 numbered colors in the util.cbc function

Re: [PyMOL] Pymol insertion code

2014-03-20 Thread Sampson, Jared
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

Re: [PyMOL] Pymol insertion code

2014-03-20 Thread Sampson, Jared
Sorry - one quick correction to my previous email: On Mar 20, 2014, at 10:50 AM, Sampson, Jared jared.samp...@nyumc.org 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

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

2014-03-31 Thread Sampson, Jared
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

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

2014-04-08 Thread Sampson, Jared
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

2014-04-09 Thread Sampson, Jared
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.

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

2014-04-28 Thread Sampson, Jared
Hi Yeping - I was about to suggest Sean Law’s new spectrumbarhttp://pymolwiki.org/index.php/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

2014-04-29 Thread Sampson, Jared
. But the question is the same with above: how could I correctly label the bar according my data set? Best regards, Yeping -- 发件人:Sampson, Jared jared.samp...@nyumc.orgmailto: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 sunyep

Re: [PyMOL] Pymol wrl output

2014-05-03 Thread Sampson, Jared
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

Re: [PyMOL] Pymol wrl output

2014-05-03 Thread Sampson, Jared
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; pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Pymol wrl output Hi, I tried it in white WRL as you suggested

Re: [PyMOL] using a pseudoatom for distance measurement

2014-05-05 Thread Sampson, Jared
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

2014-05-06 Thread Sampson, Jared
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 jared.samp...@nyumc.orgmailto:jared.samp

Re: [PyMOL] Ray trace mode 1 outline thickness

2014-05-14 Thread Sampson, Jared
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,

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

2014-05-27 Thread Sampson, Jared
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

Re: [PyMOL] align or pair_fit display problem

2014-05-27 Thread Sampson, Jared
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

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

2014-06-04 Thread Sampson, Jared
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

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

2014-06-04 Thread Sampson, Jared
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

2014-06-16 Thread Sampson, Jared
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

2014-06-17 Thread Sampson, Jared
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

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

2014-07-11 Thread Sampson, Jared
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] How to show the surface border of a specific residue?

2014-07-24 Thread Sampson, Jared
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

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

2014-08-05 Thread Sampson, Jared
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

Re: [PyMOL] RMSD for selected residues

2014-08-12 Thread Sampson, Jared
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

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

2014-08-13 Thread Sampson, Jared
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

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

2014-08-29 Thread Sampson, Jared
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 alterhttp://pymolwiki.org/index.php/Alter and iteratehttp://pymolwiki.org/index.php/Iterate and a few

Re: [PyMOL] cartoon and line representation

2014-09-02 Thread Sampson, Jared
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,

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

2014-09-11 Thread Sampson, Jared
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:

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

2014-09-19 Thread Sampson, Jared
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 modehttp://www.pymolwiki.org/index.php/Command_Line_Options. Of course,

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

2014-09-22 Thread Sampson, Jared
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 jared.samp...@nyumc.orgmailto:jared.samp...@nyumc.org: Hi James - I don’t have any experience with Profit. However, instead of using something like

Re: [PyMOL] measure angles in programming

2014-09-24 Thread Sampson, Jared
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,

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

2014-10-10 Thread Sampson, Jared
the *distances* 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

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

2014-10-10 Thread Sampson, Jared
:10 PM, Sampson, Jared jared.samp...@nyumc.orgmailto: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

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

2014-10-16 Thread Sampson, Jared
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.sourceforge.netmailto:pymol-users@lists.sourceforge.net Subject

Re: [PyMOL] PyMOLWiki Update

2014-10-20 Thread Sampson, Jared
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

Re: [PyMOL] How to calculate Hinge angle

2014-11-04 Thread Sampson, Jared
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,

Re: [PyMOL] ligand binding site visualisation

2014-11-10 Thread Sampson, Jared
Hi James - You could put in a feature requesthttp://sourceforge.net/p/pymol/feature-requests/ to ask that non-canonical residues be included in the preset. In the meantime, the Property Selectorshttp://www.pymolwiki.org/index.php/Property_Selectors, Single-Word

Re: [PyMOL] View Matrix operation

2014-11-19 Thread Sampson, Jared
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

Re: [PyMOL] Super, algorithm

2014-11-26 Thread Sampson, Jared
Hi Spencer - If you need a superposition algorithm with a published reference, try CEAlignhttp://www.pymolwiki.org/index.php/Cealign. Some references are listed on the page for the former CEAlign Pluginhttp://www.pymolwiki.org/index.php/Cealign_plugin#References from before it was

Re: [PyMOL] homebrew pymol

2014-12-11 Thread Sampson, Jared
Hi Ryan - Have a look at this posthttps://mathiasbynens.be/notes/shell-script-mac-apps, 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

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

2014-12-15 Thread Sampson, Jared
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 EOF renum 1 chain A EOF To remove the extraneous stuff within

Re: [PyMOL] unable to export obj

2015-01-26 Thread Sampson, Jared
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.

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

2015-01-14 Thread Sampson, Jared
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 Floris On 09-01-15 16:55, Sampson, Jared wrote: set

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

2015-02-17 Thread Sampson, Jared
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] Dot representation

2015-01-05 Thread Sampson, Jared
Hi Yarrow - 1. Yes, according to the wikihttp://www.pymolwiki.org/index.php/Dots, 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

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

2015-01-09 Thread Sampson, Jared
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

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

2015-03-26 Thread Sampson, Jared
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,

Re: [PyMOL] moving objects

2015-04-29 Thread Sampson, Jared
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

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

2015-05-05 Thread Sampson, Jared
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

Re: [PyMOL] MacPyMol working dir

2015-04-16 Thread Sampson, Jared
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'

Re: [PyMOL] cartoon putty present in pymol

2015-04-13 Thread Sampson, Jared
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

Re: [PyMOL] Pymol molecular visualisation

2015-04-13 Thread Sampson, Jared
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] Add fragment

2015-05-20 Thread Sampson, Jared
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

2015-05-20 Thread Sampson, Jared
In the process of investigating Ben Bobay's questionhttps://sourceforge.net/p/pymol/mailman/message/34128680/ 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] efficiency assigning b-factors

2015-06-16 Thread Sampson, Jared
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

Re: [PyMOL] MacPyMOL in command line mode

2015-05-29 Thread Sampson, Jared
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

Re: [PyMOL] .pdb files and rendering software

2015-08-17 Thread Sampson, Jared
Hi again, Joe - Try saving in COLLADAhttp://www.pymolwiki.org/index.php/COLLADA format with `save myfile.dae` (in PyMOL v1.7.3.2 or later). If you're using Blender, you'll need to `set collada_geometry_mode, 1`, because Blender only supports polylists for COLLADA import, and not the more

Re: [PyMOL] How does PyMOL create .obj file?

2015-08-17 Thread Sampson, Jared
Hi Joe - The coordinate system in the .obj file is in camera space, where (0,0,0) is the center of the viewport, positive x to the right, positive y up, and positive z out of the screen toward the viewer. If you want to correlate them, you would need to transform the model coordinates using

Re: [PyMOL] How to get TTT matrix in PyMOL 1.7.6?

2015-08-13 Thread Sampson, Jared
Hi Paweł - Honestly, if you prefer to use matrices, I'd say just go ahead and use get_object_matrix; I doubt it's going away any time soon. You may want to use this in combination with transform_selectionhttp://www.pymolwiki.org/index.php/Transform_selection. Also maybe check out Christoph

Re: [PyMOL] secondary structure disappears

2015-07-23 Thread Sampson, Jared
I'm posting the following solution on behalf of Thomas Holder (whose sourceforge.nethttp://sourceforge.net email address is currently down due to SF server issues), to ensure it is added to this thread in the archive: This is due to chain identifier conflict. He's merging 6 models with

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

2015-07-09 Thread Sampson, Jared
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 can

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

2015-07-09 Thread Sampson, Jared
Hi Yeping - To calculate such an angle, you will need two vectors, which you can create with some pseudoatomshttp://www.pymolwiki.org/index.php/Pseudoatom and the orienthttp://www.pymolwiki.org/index.php/Orient command. Before you start, you should create named selections for the ring and

Re: [PyMOL] reproduce special vrml-output

2017-05-19 Thread Sampson, Jared
Hi Anke - Try `as surface`, which is the equivalent of `hide everything; show surface`. Hope that helps. Cheers, Jared Sent from my iPhone > On May 19, 2017, at 6:43 AM, Anke Schultz > wrote: > > Hi Thomas, > > thanks for the explanation on adjusting

Re: [PyMOL] using "bymol" in combination with "within"

2015-12-03 Thread Sampson, Jared M.
Hi Andrew - If you're just looking to expand the selection from atoms in water molecules to entire water molecules, I would actually use `byres` instead of `bymol`. The `bymolecule` selector is apparently dependent on how PyMOL sees the bonds (e.g. try `fetch 3ghe, async=0; select test, bymol

Re: [PyMOL] on axis of the subunit

2015-11-30 Thread Sampson, Jared M.
Hi Smith - I’m not quite sure what you mean by "axis of a subunit." If you mean the principal axis of that selection of atoms, `orient my_selection` will get it aligned along one of the axes. Then you can create pseudoatoms on that axis and create a dash between them with the distance

Re: [PyMOL] on axis of the subunit

2015-11-30 Thread Sampson, Jared M.
-01 00:51:46, "Sampson, Jared M." <jms2...@cumc.columbia.edu<mailto:jms2...@cumc.columbia.edu>> wrote: Hi Smith - I’m not quite sure what you mean by "axis of a subunit." If you mean the principal axis of that selection of atoms, `orient my_selection` will get it

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