Re: [PyMOL] SHARP map not opening in PyMOL

map (ccp4 format, i.e. .map format), but it does not open the map. According to the pymol users manual, it should open ccp4 format maps. Has anyone had this problem before, and what can I do to get around it? Thanks! Sivaram Mylavarapu. -- Jacob Corn The Berger Lab UC Berkeley -

Re: [PyMOL] Angstrom-squared values for solvent/protein contact surface per residue

/pymol-users -- Jacob Corn The Berger Lab UC Berkeley - Molecular and Cell Biology jc...@uclink.berkeley.edu phone: 510-643-8893 fax: 510-643-9290

Re: [PyMOL] B & W Molscript & David Goodsell look-alike modes

PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Jacob Corn The Berger Lab UC Berkeley - Molecular and Cell Biology jc...@uclink.berkeley.edu phone: 510-643-8893 fax: 510-643-9290

Re: [PyMOL] biological unit

iling list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Jacob Corn The Berger Lab UC Berkeley - Molecular and Cell Biology jc...@uclink.berkeley.edu phone: 510-643-8893 fax: 510-643-9290

Re: [PyMOL] biological unit

Hi Surendra, Just to make sure, are you downloading the "biological unit" PDB from RCSB? That should be a 5MB gzipped file. The normal PDB for 1c8e does not contain coordinates for the biological unit (which you need to use split_states); only a monomer and then info on crystal symmetry. If you

[PyMOL] Mysterious crash bug

e has bitten me on two occasions, but before I spend time trying to track down a reproducible case, I would like to find out if anyone else has noticed it, or if it's an isolated problem. Jacob -- Jacob Corn The Berger Lab UC Berkeley - Molecular and Cell Biology jc...@uclink.berkeley.edu

Re: [PyMOL] symmetry and density maps

Hi Richard, Unfortunately, PyMOL will not do symmetry expansion. You could use ccp4s mapmask to extend an existing map around a molecule. An example script is below (BORDER is the number of angstroms around the input model to calculate the new map) mapmask \ XYZIN model.pdb \ MAPIN previous_m

[PyMOL] problems using selection wildcards?

r nitrogen, name N+", but that only gets backbone amides. "color nitrogen, name NH+" (or NH*) does nothing. This seemed to work reliably in the last release. For the nonce I'm using the "symbol" selector, but I found atom selection wildcards oh-so-convenient... Am I do

[PyMOL] select/deselecting objects via script?

I'd like to write a jiffy that binds the up and down arrow keys to move up/down the list in the object/selection pane. I'd like (for example) pressing the down arrow to equate to clicking the currently active object (thus hiding its representation) and clicking the next object down (thus sh

Re: [PyMOL] select/deselecting objects via script?

OK, I'm feeling a little silly now... I found enable/disable (sorry for not rtfm'ing closely). But is there a way to get whether an object is currently dis/enabled? Jacob On Apr 22, 2009, at 9:04 AM, Jacob Corn wrote: I'd like to write a jiffy that binds the up and dow

[PyMOL] Rocking on the y axis

lity to pass the function an argument for the axis of rotation. However, in my desperation, I've even gone so far as changing this last variable to axis='y' within movie.py itself, but the molecule continued to rock on the x axis. Any suggestions? Jacob Corn Gladstone Institute of Neurological Disease jc...@gladstone.ucsf.edu

[PyMOL] Labeling stretches

So here's yet another question, oh-so-soon after the first. Is there a way to label long stretches of residues with a single user-defined label? So far I've only been able to label *every* residue along a stretch according to a some property. I could instead just create 2 selections, one being the

Re: [PyMOL] image resolution

nd size of images exported from pymol? Thanks Joel M. Harp ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Jacob Corn Gladstone Institute of Neurological Disease 415.695.3745 jc...@gladstone.ucsf.edu

Re: [PyMOL] image resolution

_names,pymol_names) File "", line 1, in ? AttributeError: get_povray after the line containing cmd.get_povray. I am assuming that python doesn't understand get_povray without being told to? So how do I tell it to? Or whatever. Bronwyn Carlisle Biochemistry Department University

Re: [PyMOL] image resolution

ack (most recent call last): File "/usr/local/pymol/modules/pymol/parser.py", line 208, in parse exec(com2[nest],pymol_names,pymol_names) File "", line 1, in ? AttributeError: get_povray after the line containing cmd.get_povray. I am assuming that python doesn't unders

Re: [PyMOL] atom picking on windows

UK. http: http://www.cse.clrc.ac.uk == ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Jacob Corn Gladstone Ins

re: [PyMOL] Fancy images

Hi Robert, To do that, you'll need to become moderately well acquainted with working with a POVRay scene file. It sounds like what you're thinking of would be covered by the "plane" object in POVRay. As described in the POVRay manual, planes are defined as follows #begin plane definition plane {

[PyMOL] Separate surfaces

Hi all, It's possible that I've run into a bug/undocumented feature, but I'd like to see if anyone has a solution to the following problem. I'm working on a movie script that will (in part) make two separate surfaces for each subunit in a dimer (excluding a drug bound between the subunits), the

[PyMOL] v0.93 ribbons sampling

Hi, Someone sent out a question about this a month or so ago, but I never saw a reply, so I'll ask it again. In the Windows v0.93 pyMOL, it seems that I'm stuck with ribbon_sampling=1 (CA trace, instead of smoothed ribbon). I can change the setting, but the representation does not change. This beha

[PyMOL] v0.95 breaking pymolrc

tion, no matter where I started PyMOL from). However, after updating to v.095 the parser can no longer find these files. I've tried calling the files as C:\thing\thing\thing.py and so on, but so far, no luck. Is this a bona-fide bug or have others run into this problem and found a solution? Jac

Re: [PyMOL] creating objects from pdb w/out chain id

Hi Hanspeter, If you want to use a stock pdb that does not contain chain IDs, you should create the object using either a residue or atom selection. For example (using residue ids for kinesin) create kin=(/1BG2///3:325/) However, for your convenience I've attached a modified pdb that contains dif

Re: [PyMOL] showing sequence conservation on the surface

the B-factor column replaced with relative conservation. If you open this PDB and run the color_b script (http://adelie.biochem.queensu.ca/~rlc/work/pymol/) with a two-color ramped gradient (eg - white->green) you'll have a very intuitive view of potential "hot spots". Enjoy!

[PyMOL] reiterating a ccp4 map problem

aps only displayed over part of the unit cell? Jacob -- Jacob Corn UC Berkeley - Berger Lab Lab: 510-643-8893 Fax: 510-643-9290 jc...@uclink.berkeley.edu

Re: [PyMOL] reiterating a ccp4 map problem (erratum)

Oops. I actually used mapmask to extend the map over the unit cell. Apologies. Jacob Corn wrote: This question was posted by someone else in January, but no solution was ever described. I'm currently running up against the same problem and would very much like to know if there is a sol

Re: [PyMOL] rtools from .pml scripts

pdb 1kv2 ^ SyntaxError: invalid syntax [...] pymol launches as usual after that, and I also can use rtools commands without problems within it. ideas? thanks, christian -- Jacob Corn UC Berkeley - Berger Lab Lab: 510-643-8893 Fax: 510-643-9290 jc...@uclink.berkeley.edu

Re: [PyMOL] rtools from .pml scripts

ists/listinfo/pymol-users -- Jacob Corn UC Berkeley - Berger Lab Lab: 510-643-8893 Fax: 510-643-9290 jc...@uclink.berkeley.edu

[PyMOL] Plugins segfaults

the non-working Debian boxes set up identically to the working Debian box. Since this is clearly not the case, we're looking for clues about how PyMOL interfaces with the plugin scripts. That is, where should we start looking for broken things on one Debian box versus another? Jacob -- Ja

Re: [PyMOL] Problem with pml script and png command

Hi Gregori, If you are just saving an image without rendering it (eg - "png" without "ray") then the raw OpenGL output is sent to the file. Meaning, if you have the command line/menu window open in front of the graphics window, your images will be cut off where they overlap. This might or migh

[PyMOL] Creating one object from two

just the two objects I want and try create objectx, (all) the problem still occurs. Since this has happened with two independent pdbs, I'm wondering if any one else has run into the problem. If so, is there a workaround? Jacob -- Jacob Corn UC Berkeley - 315 Hildebrand Ha

Re: [PyMOL] Creating one object from two

ted monomer PDBs and collating them. I don't know about anyone else, but I think that task would be nice to do in PyMOL. Would it be hard to alter the create command so that it makes sure there are no clashes between atom/chain/etc. naming? Jacob Robert Campbell wrote: Jacob, * Jaco

[PyMOL] Raytracing "lies" in v0.98

e is two objects with different cartoon transparencies. But if I set them to both have the same transparency, no dice. This behavior occurs with this session across computers and across OSes (WinXP and OSX). Has anyone else seen this? Warren, if this is a bug, shall I send you the scene file? Jacob

Re: [PyMOL] Raytracing "lies" in v0.98

346-1154 . mailto:war...@delsci.com -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Jacob Corn Sent: Wednesday, May 25, 2005 3:52 PM To: pymol-users Subject: [PyMOL] Raytracing "lies" in v0.98 Hi all, I have a