Re: [PyMOL] new metals keyword

2013-09-10 Thread Spencer Bliven
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

[PyMOL] UCSD pymol workshop

2013-11-20 Thread Spencer Bliven
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] manual superposition with pymol--and another question

2014-04-08 Thread Spencer Bliven
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

[PyMOL] Detecting Plugins menu

2014-04-14 Thread Spencer Bliven
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

Re: [PyMOL] Detecting Plugins menu

2014-04-17 Thread Spencer Bliven
: hasTk = False return hasTk On Mon, Apr 14, 2014 at 10:46 AM, Spencer Bliven sbli...@ucsd.edu wrote: 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

Re: [PyMOL] Detecting Plugins menu

2014-04-22 Thread Spencer Bliven
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 sbli...@ucsd.edu wrote: Here's

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

2014-08-27 Thread Spencer Bliven
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

Re: [PyMOL] symmetry mates

2014-08-27 Thread Spencer Bliven
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 http://www.pymolwiki.org/index.php/Supercell script. Otherwise I tend to generate symmetry mates multiple times and

Re: [PyMOL] naming of chain id

2014-09-17 Thread Spencer Bliven
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

[PyMOL] select state not working

2014-11-05 Thread Spencer Bliven
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

Re: [PyMOL] select state not working

2014-11-06 Thread Spencer Bliven
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 sbli...@ucsd.edu wrote: Hey, I've been doing a lot of work with PDB assemblies, which

Re: [PyMOL] select state not working

2014-11-06 Thread Spencer Bliven
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 sbli...@ucsd.edu wrote: Thanks for the response, David! You

[PyMOL] Problem with MacPyMOL's linalg package

2014-11-25 Thread Spencer Bliven
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

[PyMOL] wiki.pymol.org

2014-11-26 Thread Spencer Bliven
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

Re: [PyMOL] Super, algorithm

2014-11-26 Thread Spencer Bliven
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 aloctavo...@gmail.com wrote: Hi, Exactly which algorithm is behind the super command? How the outliers pairs are

Re: [PyMOL] wiki.pymol.org

2014-12-01 Thread Spencer Bliven
, 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 sbli...@ucsd.edu wrote: What's the deal with wiki.pymol.org? It looks like a mirror of pymolwiki.org from June

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

2014-12-01 Thread Spencer Bliven
. Cheers, Thomas On 25 Nov 2014, at 04:46, Spencer Bliven sbli...@ucsd.edu wrote: 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

Re: [PyMOL] sequence alignment function

2014-12-03 Thread Spencer Bliven
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

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

2014-12-05 Thread Spencer Bliven
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] select state not working

2014-12-05 Thread Spencer Bliven
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 sbli...@ucsd.edu wrote: I hadn't heard about any plans to convert

Re: [PyMOL] holes in isosurface representation

2015-01-06 Thread Spencer Bliven
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.

[PyMOL] Interleaved atoms when creating from two objects

2015-04-22 Thread Spencer Bliven
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

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

2015-04-22 Thread Spencer Bliven
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 sbli...@ucsd.edu wrote: I'm working on a script which involves joining two objects together, which I do using the create command

[PyMOL] Pymol crash when raytracing empty graphics

2015-08-17 Thread Spencer Bliven
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

Re: [PyMOL] Pymol crash when raytracing empty graphics

2015-08-18 Thread Spencer Bliven
page for 1a1q at PDBe http://www.ebi.ac.uk/pdbe/entry/pdb/1a1q The images are made with pymol (currently 1.6, but also works in 1.7) Regards John PDBe On Monday 17 August 2015 15:40:14 Spencer Bliven wrote: We have a pipeline that uses pymol to create images using the headless

Re: [PyMOL] superimposing and aligning

2015-10-26 Thread Spencer Bliven
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 >

[PyMOL] Interrupting slow commands

2015-10-26 Thread Spencer Bliven
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] Common atoms in two selections (and their indices)

2015-10-27 Thread Spencer Bliven
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

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

2015-11-08 Thread Spencer Bliven
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.

Re: [PyMOL] Biological assembly unit

2015-10-30 Thread Spencer Bliven
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

Re: [PyMOL] Biological assembly unit

2015-11-02 Thread Spencer Bliven
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

Re: [PyMOL] PyMol Question

2015-11-03 Thread Spencer Bliven
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?

[PyMOL] Pymol crash when deleting callback object

2015-09-29 Thread Spencer Bliven
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

Re: [PyMOL] Pymol crash when deleting callback object

2015-09-30 Thread Spencer Bliven
lso be fixed. > > Cheers, > Thomas > > On 29 Sep 2015, at 10:47, Spencer Bliven <spencer.bli...@gmail.com> 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, >

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

2015-12-02 Thread Spencer Bliven
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

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

2015-12-02 Thread Spencer Bliven
Based on the above discrepancy, 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 <spencer.bli...@gm

Re: [PyMOL] PyMOL with Python 3

2015-12-07 Thread Spencer Bliven
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:

Re: [PyMOL] Problem using pymol

2015-12-10 Thread Spencer Bliven
> 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

Re: [PyMOL] on axis of the subunit

2015-12-01 Thread Spencer Bliven
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 - >

Re: [PyMOL] show the long helix filament

2016-01-13 Thread Spencer Bliven
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

Re: [PyMOL] regarding show_bumps

2016-01-28 Thread Spencer Bliven
ymol <ccp4.py...@gmail.com> 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

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

2016-02-22 Thread Spencer Bliven
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

Re: [PyMOL] Problem with feedback push

2016-03-13 Thread Spencer Bliven
> _ feedback enable, cmd parser, warnings errors results > _ feedback pop > > Hope that helps. > > Cheers, > Thomas > > On 11 Mar 2016, at 04:48, Spencer Bliven <spencer.bli...@gmail.com> wrote: > > > Here's a minimal .pymolrc to demonstrate the issue:

[PyMOL] Problem with feedback push

2016-03-11 Thread Spencer Bliven
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

Re: [PyMOL] Problem with feedback push

2016-03-11 Thread Spencer Bliven
ttp://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 <spencer.bli...@gmail.com> wr

Re: [PyMOL] making a plane

2017-01-18 Thread Spencer Bliven
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] Rotate protein to align principal axes

2016-09-01 Thread Spencer Bliven
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

Re: [PyMOL] 3D printing

2016-10-04 Thread Spencer Bliven
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).

Re: [PyMOL] Pair_fit syntax

2016-10-25 Thread Spencer Bliven
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

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

2016-11-28 Thread Spencer Bliven
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

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

2017-01-13 Thread Spencer Bliven
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

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

2016-12-02 Thread Spencer Bliven
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