Re: [PyMOL] making a plane

I have a script for calculating principal moments of inertia and displaying them as axes: https://github.com/sbliven/principal_axes If you look over the code it should be pretty easy to draw the first two axes as a cgo plane instead of as arrows. -Spencer On Tue, Jan 17, 2017 at 3:38 PM, Tsjerk

Re: [PyMOL] Save command output to a file in pymol

This can be done using normal python file i/o: f=open("ss.txt","w") iterate n. CA, f.write(resi + ':' + ss+"\n") f.close() On Fri, Jan 13, 2017 at 10:38 AM, Academic Research wrote: > That would be good as well, How? > > keep in mind, my protein is synthetic, it is not from the PDB database, >

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

There is a cartoon variant too, although everything will look like a loop set cartoon_trace_atoms, on show cartoon, polymer On Wed, Oct 26, 2016 at 12:27 AM, Yuxing Liao < yuxing.l...@utsouthwestern.edu> wrote: > Hi Mohsen, > > The PDB file of 3B5D only contains CA atoms, so most rendering like

Re: [PyMOL] PDB Format not correct for use in CHARMM

It would be nice to have a setting that adds TER records only where the chain or segi change (as opposed to whenever the residue numbers are non-sequential). I believe that better captures the original intent for terminating polymers. Of course, the real answer is that everyone should switch to mmC

Re: [PyMOL] Pair_fit syntax

First off, when the documentation includes square brackets in the command it indicates optional arguments. You don't include them in the command itself. In this case, pair_fit takes alternating selections from obj1 and obj 2. It also requires that the number of atoms in each selection be equal. I u

Re: [PyMOL] 3D printing

I've done a bit of 3D printing of proteins. I found links in the previous thread VRML2 export and edu pymol helpful. STL is the best supported format for the printers, but since it's not supported by pymol I've used VRML2 (.wrl). Fortunate

Re: [PyMOL] Rotate protein to align principal axes

Jingjie, I've used a script for calculating the principal components ( https://github.com/sbliven/principal_axes). The computeprincipalaxes function returns the axes. With a bit of linear algebra you should be able to use that to get a transformation matrix to apply to the coordinates. This can be

Re: [PyMOL] Problem with feedback push

> _ feedback enable, cmd parser, warnings errors results > _ feedback pop > > Hope that helps. > > Cheers, > Thomas > > On 11 Mar 2016, at 04:48, Spencer Bliven wrote: > > > Here's a minimal .pymolrc to demonstrate the issue: > > > > #prints

Re: [PyMOL] Problem with feedback push

<http://pymolwiki.org/index.php/Feedback> docs don't mention the push/pop commands. I likely got them from MacOSX-specific_.pymolrc_file <http://www.pymolwiki.org/index.php/MacOSX-specific_.pymolrc_file> On Fri, Mar 11, 2016 at 10:41 AM, Spencer Bliven wrote: > Since ti

[PyMOL] Problem with feedback push

Since time immemorial my .pymolrc file has been wrapped by the construct _ feedback push_ feedback disable,all,everything ..._ feedback pop However, I've noticed that my `get` command doesn't print anything unless I specifically re-enable all feedback after starting pymol (or use the unwieldy `p

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

This looks like a bug in the PDB's file, and you should definitely let them know about it. It's a particularly weird case since the second model doesn't correspond to any of the valid crystallographic operators. Probably it is a problem with the very non-standard crystal frame specified by the SCAL

Re: [PyMOL] ignore_case in next PyMOL version

Restoring the old ignore_case behaviour seems pragmatic. Can you explain the difference with the new ignore_case_chain setting? Is the idea that we would want case-insensitive element symbols (ignore_case=off) but case-sensitive chains (ignore_case_chain=on)? Are there other places where case is i

Re: [PyMOL] regarding show_bumps

cp4 pymol wrote: > Dear Spencer > > Thank you for the suggestion. Well, I actually wanted to do it as a part > of making a movie, so would have liked some automation. > > Thank you. > > Best Regards > Priyan > > On Thu, Jan 28, 2016 at 2:39 PM, Spencer Bliven >

Re: [PyMOL] regarding show_bumps

Priyan– You can use the split_states command to divide it into multiple objects, then run the script on each state individually. -Spencer On Thu, Jan 28, 2016 at 3:45 AM, ccp4 pymol wrote: > Hi > > I have a multi-state object loaded in PyMOL which

Re: [PyMOL] show the long helix filament

For such cases I generate the symmetry partners using either the symexp command or the supercell script. Both scripts result in lots of extra objects, which you then have to winnow down to a single helix. Supercell c

Re: [PyMOL] Problem using pymol

> Please let me know how can I renumber protein chains to avoid overlap and > give it a uniqu chain id. > You can manually modify chain IDs with the alter command. For instance, to rename chain A to X: alter chain A, chain = "X" To automatically select uniq

Re: [PyMOL] PyMOL with Python 3

Nice work! It will be very nice to have python3 compatibility in the future. It would be nice to organize a section of the pymol-script-repo for python3-compatible scripts once this gets merged to SVN. -Spencer On Fri, Dec 4, 2015 at 8:12 PM Thomas Holder wrote: > Hi all, > > We have refactore

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

cy, I know that selection #2 does not > give me this. This is corroborated by an independent calculation I did in a > different program (the Bio3D pacakge in R). > > All best, > Andrew > > On Wed, Dec 2, 2015 at 10:53 AM, Spencer Bliven > wrote: > >> Andrew, >>

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

Andrew, The 'byres' selector expands the inner selection to include all covalently bonded atoms. Thus, your selection #2 should be a superset of selection #1. Are you sure that's not the case? What do your 'wats' and 'solute' selections refer to? Are you trying to find the water molecules to some

Re: [PyMOL] on axis of the subunit

Note that the elbow formula assumes that the two vectors are normalized. Remember the dot product equation = |x| * |y| * cos( theta ) -Spencer On Tue, Dec 1, 2015 at 4:34 AM Sampson, Jared M. wrote: > Hi Smith - > > Check out how I did it in the h

Re: [PyMOL] on PDB

Smith– The code is intended to be saved to a file ("save_transformed.py") and then loaded into pymol using `run /path/to/save_transformed.py`. There's some general info on running pymol scripts: Simple_Scripting Running_Scripts

Re: [PyMOL] Is it possible to install PyMOL .app on Mac?

Luke, You have the right download. .app files are for mac programs, not for Linux. However, I believe that macpymol 1.3 doesn't work on recent os x versions. You'll need at least version 1.4. You can install the open source version 1.7 from a number of places, including macports and homebrew. -Sp

Re: [PyMOL] PyMol Question

Mohsen– set transparency , .5, sele Cheers, Spencer On Tue, Nov 3, 2015 at 3:18 AM, Mohsen Chitsaz < mohsen.chit...@flinders.edu.au> wrote: > Hi there, > > > > I was wondering how I can make the surface of a selected part of a protein > transparent?

Re: [PyMOL] Biological assembly unit

Faiza– If what you're actually interested in is a model for the structure of the human dimeric Phenylalanine-4-hydroxylase, I suggest that rather than building it in pymol you use one from the protein model portal: http://www.proteinmodelportal.org/query/up/P00439 If you want to make such a model

Re: [PyMOL] Biological assembly unit

Dealing with multi-state models is tricky. I wrote a flatten_obj script to combine the multiple states into a single object. (Thanks for the motivation to finally upload my script to the wiki!) This allows you to use the normal align/super/cealign comman

Re: [PyMOL] Common atoms in two selections (and their indices)

Tsjerk– You might be able to extract the ids of the aligned residues from an alignment object: cmd.align(sele1,sele2copy,object="aln") [a.id for a in cmd.get_model('aln').atom] Since the alignment is sequential, I think this should contain all the aligned atoms from sele1 concatenated with the a

Re: [PyMOL] superimposing and aligning

Or cealign ! On Tue, Oct 20, 2015 at 4:14 PM, Osvaldo Martin wrote: > Hi Raag, > > You can use align or super > , the main difference is that > super does not use sequ

[PyMOL] Interrupting slow commands

Is there any way to interrupt slow commands without killing pymol? For instance, if you accidentally add an extra 0 to the raytracing resolution. On a related note, it would be nice to programmatically access the progress bar and abort button from scripts and plugins (I know it has been discussed

Re: [PyMOL] Pymol crash when deleting callback object

lso be fixed. > > Cheers, > Thomas > > On 29 Sep 2015, at 10:47, Spencer Bliven wrote: > > > I'm using the callback version of the Axes script (third script at > http://www.pymolwiki.org/index.php/Axes). In MacPyMol 1.7.6.3 syspython, > deleting the constructed axes

[PyMOL] Pymol crash when deleting callback object

I'm using the callback version of the Axes script (third script at http://www.pymolwiki.org/index.php/Axes). In MacPyMol 1.7.6.3 syspython, deleting the constructed axes object causes Pymol to crash. It's an old script and I'm guessing not well maintained, but the crash is still unfortunate. As an

Re: [PyMOL] Pymol crash when raytracing empty graphics

- so we use ribbon > instead with the command > > pymol.cmd.set("ribbon_trace_atoms", 1) > > This test allows us to make images such as those shown on the entry page > for 1a1q at PDBe > > http://www.ebi.ac.uk/pdbe/entry/pdb/1a1q > > The images are made wi

[PyMOL] Pymol crash when raytracing empty graphics

We have a pipeline that uses pymol to create images using the headless command line interface. I've discovered that PyMOL 1.7.4 and 1.7.6 (at least) crash if you try to ray-trace an empty viewport. Example: pymol -q -c -d 'fetch 1a1q,async=0;as cartoon;ray' This particular example only has CA at

Re: [PyMOL] Interleaved atoms when creating from two objects

n, also check your pymolrc if you're setting it there. > > > > http://www.pymolwiki.org/index.php/Retain_order > > http://www.pymolwiki.org/index.php/Pymolrc > > > > Cheers, > >Thomas > > > > On 22 Apr 2015, at 20:39, Spencer Bliven wrote: &

[PyMOL] Interleaved atoms when creating from two objects

I'm working on a script which involves joining two objects together, which I do using the create command. The input objects have different chain identifiers, but identical residue numbers. When I create the joined object, I would expect all atoms from the first object to be added, followed by all a

Re: [PyMOL] holes in isosurface representation

Hey Jacob, Are Lagging_A and Leading_B selections or objects? Generally for surfaces to display right you have to create a new object for the part you want (using either the create or extract commands). Otherwise you get holes in the surface where the selection contacts the rest of the object. -S

Re: [PyMOL] select state not working

I noticed that my response didn't go through due to the attachment being to big. The PDB file is here: https://dl.dropboxusercontent.com/u/41995424/4BVNAa-2Z73Aa.pdb -Spencer On Thu, Nov 6, 2014 at 2:44 PM, Spencer Bliven wrote: > I hadn't heard about any plans to convert biologic

Re: [PyMOL] Is it possible to move different subunits independently using Pymol

You can translate and rotate objects using the Editing mouse mode ('Mouse' > '3 Button Editing'). Objects can be rotated with shift-left click or translated with shift-middle click. You can also modify just a segment by 'picking' the boundaries (command/ctrl left click). Use the 'unpick' command to

Re: [PyMOL] sequence alignment function

PyMOL includes Biopython, so I would just use their sequence aligner. For instance: from Bio import pairwise2 alignments = pairwise2.align.globalxx("ACCGT", "ACG") See http://biopython.org/DIST/docs/api/Bio.pairwise2-pysrc.html -Spencer On Wed, Dec 3, 2014 at 9:33 AM, Jordan Willis wrote: >

Re: [PyMOL] Problem with MacPyMOL's linalg package

lib/python') > import scipy.linalg > > Hope that helps. > > Cheers, > Thomas > > On 25 Nov 2014, at 04:46, Spencer Bliven wrote: > > > Importing scipy.linalg in MacPyMOL crashes the program for me. Probably > the linalg module shipped with MacPyMOL is corr

Re: [PyMOL] wiki.pymol.org

of > pymolwiki.org, and it's up-to-date with sometimes a few days delay. > Thanks for your suggestion about the sitenotice - we've put it into place. > > Cheers, > Thomas > > On 26 Nov 2014, at 05:48, Spencer Bliven wrote: > > > What's the deal with

Re: [PyMOL] Super, algorithm

I would also be interested if there is any documentation about the super algorithm and the differences to align. -Spencer On Fri, Nov 14, 2014 at 10:25 PM, Osvaldo Martin wrote: > Hi, > > Exactly which algorithm is behind the super command? How the outliers > pairs are defined? The is some sci

[PyMOL] wiki.pymol.org

What's the deal with wiki.pymol.org? It looks like a mirror of pymolwiki.org from June 9th. Are there plans to move the community wiki into the pymol namespace? Since google indexes them both now, it would be nice to have a indication on wiki.pymol.org that the information is not fully up-to-date

[PyMOL] Problem with MacPyMOL's linalg package

Importing scipy.linalg in MacPyMOL crashes the program for me. Probably the linalg module shipped with MacPyMOL is corrupt or incorrectly linked. I've reproduced it with MacPyMOL 1.6 and 1.7, with both X11 and aqua, and on Mac OS 10.9 and 10.10. I discovered this problem because importing the full

Re: [PyMOL] select state not working

rtoon representation does not work on states which don't match the atoms of state 1. Does anyone familiar with the code know if that's the case? If so it's probably not a trivial fix. -Spencer On Thu, Nov 6, 2014 at 10:18 AM, Spencer Bliven wrote: > Thanks for the response, D

Re: [PyMOL] select state not working

b has an rms of 1.155 > > intra_fit 2kgx and chain b > > now, chain a has an rms of 0.952 and chain b has an rms of 1.130 > > Note, it can take a target state, that all other states are aligned to, > etc. > > > On Wed, Nov 5, 2014 at 5:23 AM, Spencer Bliven wrote: >

[PyMOL] select state not working

Hey, I've been doing a lot of work with PDB assemblies, which are distributed as multi-state structures. I would like to be able to align them based on individual chains from individual states. However, I haven't been able to figure out any way to uniquely identify atoms by state. The select state

Re: [PyMOL] naming of chain id

Are there plans to support 4-letter chain IDs, as defined by the current xPDB/mmCIF specification? -Spencer On Tue, Sep 16, 2014 at 3:36 PM, Thomas Holder < thomas.hol...@schrodinger.com> wrote: > Hi Folmer and Yeping, > > to support upper and lower case letters, set this setting: > > PyMOL> set

Re: [PyMOL] symmetry mates

Sometimes it is easier to see the overall structure when looking at a single unit cell rather than the symmetry mates within a certain distance. You might want to try the supercell script. Otherwise I tend to generate symmetry mates multiple times and

Re: [PyMOL] how to get the surface representation look better?

Yeping– You have to make a new object with the desired atoms. Try 'help extract' or 'help create'. Also, dropbox lets you share a link to any file. The file is visible at https://www.dropbox.com/s/j2lkd2lvu0eb2l1/surface1.tif?dl=0. I would change your password. -Spencer On Wed, Aug 27, 2014 at

Re: [PyMOL] Detecting Plugins menu

I just found the pymol._ext_gui property, which seems to be None if X11 is off and a positive number if X11 is present. Seeing as it's a private variable, is it ok to use this to check for X11 presence? -Spencer On Thu, Apr 17, 2014 at 10:21 AM, Spencer Bliven wrote: > Here&#x

Re: [PyMOL] Detecting Plugins menu

Tk: try: import Tkinter except ImportError: hasTk = False return hasTk On Mon, Apr 14, 2014 at 10:46 AM, Spencer Bliven wrote: > I'm working on a plugin with a command line interface and a light-weight > tk interface through the plugins

[PyMOL] Detecting Plugins menu

I'm working on a plugin with a command line interface and a light-weight tk interface through the plugins menu. This works fine on Linux, Windows, and open-source Mac builds, but not on MacPyMol.app. Importing Tkinter causes PyMol to quit with a prompt to install X11 (but not an ImportError, as far

Re: [PyMOL] manual superposition with pymol--and another question

Suzanne, There isn't an easy way to do this, as far as I know. `pair_fit` can be used to do a superposition based on an arbitrary alignment, but it is very tedious to specify each aligned pair individually, and it's hard to modify the alignment. I've used NCBI's Cn3D program for detailed manual a

[PyMOL] UCSD pymol workshop

We've been discussing putting together a PyMol workshop for the UCSD undergrad bioinformatics club (http://ubic.ucsd.edu/). I wanted to ping this list and see if anyone in the San Diego area would be interested, either as attendants or as an instructor or assistant. I would like hearing if anyone

Re: [PyMOL] new "metals" keyword

Excellent! I had previously been using things like 'not elem c+n+o+h+s' in my scripts. Using 'metal' will match my intent much better. 'Sidechain' will be appreciated as well. I would suggest 'ligand' and 'ptm' selectors to distinguish nonbonded and covalently bonded hetatms. Although I'm not sure

Re: [PyMOL] Fwd: Script writing

James, If the CA position is acceptable as the residue coordinate (as assumed in Jason's answer), then you don't need to bother with pseudoatoms. Here's the easiest way to display all the distances for a figure: select resn LYS and n. CA dist (sele), (sele) Aside: this doesn't work for me as `di

Re: [PyMOL] Passing parameters to pymol aliases

en issue > an extend command to the module.function with the wanted new shortcut name > Den 16/05/2013 01.29 skrev "Spencer Bliven" : > >> I have a number of python scripts that I use regularly. I would like to >> create shortcuts for these in my .pymolrc. For instance, &

[PyMOL] Passing parameters to pymol aliases

I have a number of python scripts that I use regularly. I would like to create shortcuts for these in my .pymolrc. For instance, alias co, color_obj Unfortunately, aliases cannot take arguments (using MacPyMOL 1.3). Is there a way to create aliases for commands that require arguments? I could mod