Re: [PyMOL] manipulate standard error ?
Hi,
If you are getting unwanted PyMOL standard errors you can turn them off
using the cmd.feedback() commands:
cmd.feedback('disable', 'selector', 'everything')
cmd.feedback('disable', 'executive', 'everything')
to turn them on again:
cmd.feedback('enable', 'selector', 'everything')
cmd.feedback('enable', 'executive', 'everything')
cmd.feedback('disable', 'all', 'everything') will do exactly as it says on
the tin.
otherwise maybe use a Python try:/except: clause?
eg:
try:
Instructions to load the map (cmd.load(map)?)
except:
raise IOError('')
Jules
Sebastien Moretti wrote:
Hello,
yes. maybe. if you are talking about printing to standard error, then :
import sys
sys.stderr.write(hello, stderr!)
will do it.
if, on the other hand, you mean something more complicated to do with
manipulating the shell (redirection...?) than I don't know, sorry.
gilleain torrance
I would like to change the current path for stderr to /dev/null by example.
I have a plugin which creates a legend box from a fake (empty) apdb map.
Instruction, which loads the map, sends an error message and I would
like to hide it.
How can I do ?
Thanks
Hello,
I would like to know if there is a way to manipulate standard error
redirection into pymol scripting language ?
Thanks
Re: [PyMOL] Re:
Kostas, This command: dist name, sel1, sel2, mode=3D2 doesn't work because the move value should be a whole number ie. 1,2,3 etc. Also unless you have some objects actually called sel1 and sel2 you won't get anything meaningful back. something like this: dist name, resn lys, resn glu, mode=2 will give you a new object called name, which shows the distances between all lysine and glutamate N-O atoms within approxmately 3.5 Angstroms. Is this clearer? Jules Kostas Tripsianes wrote: On Tuesday 18 October 2005 16:36, pymol-users-requ...@lists.sourceforge.net wrote: Hi Warren It's been a long time since my last post. Anyway I tried the polar contacts identifier as written below dist name, sel1, sel2, mode=3D2 and I get the following error Traceback (most recent call last): File /home/kostas/pymol/modules/pymol/parser.py, line 191, in parse result=apply(kw[nest][0],args[nest],kw_args[nest]) File /home/kostas/pymol/modules/pymol/querying.py, line 400, in distance str(selection2),int(mode),float(cutoff), ValueError: invalid literal for int(): 3D2 using the last version pymol-0_99beta20 Any clue Another important notion regarded the 0.99 versions and on is that incorrectly draw bonds between methyl protons. As you understand I work with NMR structures but I don't have this misinterpretation with previous versions. The same appeared with 13 and 20 releases. Please keep it in mind. cheers kostas --- This SF.Net email is sponsored by: Power Architecture Resource Center: Free content, downloads, discussions, and more. http://solutions.newsforge.com/ibmarch.tmpl ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] Using a seperate python installation
Hello All, Can someone tell me wether it is possible to use a stand-alone python installation alongside the latest PyMol releases? I have a few things set up in my main python installation which an older (python free) version of Pymol was happy to use, having installed the newer version it uses it's own version of python. Is this possible to specify in the .pymolrc? If so what do I write? I've tried the obvious PYTHON_PATH = 'C:\\Python24\\' Many thanks, Jules
Re: [PyMOL] selection help + align question
Hi,
I've written a script for aligning all structures loaded against your
structure of choice:
def __init__(self):
cmd.extend('allalign',allAlign)
def allAlign(id=''):
Aligns all models in a list to the
specified model where '' is the model id you want to
align all others against. Written by Jules Jacobsen
(jacob...@ebi.ac.uk). Feel free to do whatever you like with this code.
id = id.lower()
pdbList = cmd.get_names()
for entry in pdbList[:]:
entry = entry.strip()
if entry not in id:
cmd.do('align %s, %s\n'%(entry,id))
cmd.do('zoom %s'%(id))
cmd.do('show cartoon, %s'%(id))
just save the section above as a seperate file ie allalign.py and put it
in the PyMOL\modules\pmg_tk\startup directory.
the script is run using the command 'allalign x' where x is the model
you wish to align all others against.
This is one of my first teetering steps into Python so if anyone can
suggest a better way of writing it i'd be keen to hear
Jules
Douglas Kojetin wrote:
Thanks for that one; it works as advertised.
Another question: if I have 10 different structures read into PyMOL,
what is the best (most accurate) method for aligning the structures as
an ensemble? Currently, I'm aligning all to the first structure read in
(i.e. 21, 31, etc.) using a for loop and the 'align' command. Since
the structures have different sequences, I cannot use 'intra_fit', etc.,
is that right? Are there any other commands or methods of aligning that
might be easy to script?
Thanks,
Doug
On Jan 20, 2005, at 2:12 PM, Warren DeLano wrote:
Doug,
Setwise logical ANDs and ORs are tricky at first. In this case, you
want to
create a new set that contains atoms in a1 *or* a2. There aren't any
atoms
that are in both a1 and a2 which is why you're ending up with an empty
object.
create one, a1 or a2
-Original Message-
I'm having some problems with selection syntax w/ multiple objects.
I've loaded four different PDB files (in sequence structure):
load 1.pdb, a1
load 2.pdb, a2
load 3.pdb, b1
load 4.pdb, b2
I wanted to create two new selections:
one = a1 a2
two = b1 b2
I've tried many different combinations of PyMOL selection
syntax, but I cannot get the objects to add to the same
selection (using 'create' or
'select'):
create one, a1 + a2
create one, a1 and a2
create one, object a1 + object a2
create one, a*
From what I've read in the manual, I think these commands
are not working because they actually work to select atoms
that are the same between a1 a2. The manual says it
'selects atoms included in both s1 and s2'.
Any clues or hints?
Thanks,
Doug
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[PyMOL] 0.98 beta 18 Selecting bug
Oops! sorry, I just realized that the .pse was quite large. My apologies. The pdbs used were 1hju, 1hjs and 1hjq. The following script will produce the same pse: select Binding, (resi 86,300) label Binding and elem o, (resn+'-'+resi) zoom Binding Jules Original Message Subject: 0.98 beta 18 Selecting Date: Tue, 23 Nov 2004 11:05:01 + From: Jules Jacobsen jo...@hermes.cam.ac.uk To: pymol-users@lists.sourceforge.net Hi all, Has anyone else had the problem of not being able to select several identical residue types in aligned structures? eg in the .pse included, if you single left-click on Trp-86 (the left one of the 'Binding' selection) and try to select them all in the same manner, PyMOL won't add any more residues to the selection if it has the same resn/resi. It will select them if you use a shift-left-click. It will however, happily remove them from the selection with a single left-click. I'm guessing this is a PyMOL rather than platform specific bug? (I'm running on WinXP) Cheers, Jules
Re: [PyMOL] pymol displays c alpha as nonbonded
Hi Matthew, You want: 'set ribbon_trace,1' or 'set cartoon_trace,1' Jules Matthew Bowler wrote: Dear All, I am trying display a c-alpha model in pymol (1qo1), when the file is opened all the atoms are displayed as non-bonded. Is there a way to tell pymol that this is a c-alpha trace and display it as a cartoon? Many thanks in advance, Matt. Matthew Bowler MRC Dunn Human Nutrition Unit Wellcome Trust / MRC Building Hills Rd Cambridge CB2 2XY Tel: 01223 252826 Fax: 01223 252825 --- This SF.Net email is sponsored by: InterSystems CACHE FREE OODBMS DOWNLOAD - A multidimensional database that combines robust object and relational technologies, making it a perfect match for Java, C++,COM, XML, ODBC and JDBC. www.intersystems.com/match8 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] Swissprot
Hello List, I'm trying to make a plugin which will load various features from a swissprot entry onto a model loaded in PyMol but need to know a few things such as: Where are the sequences of the models stored in pymol and how do I retrieve them? Are these taken from the ATOM or SEQRES sections of the PDB file? Is there a PDB parser class somewhere for reading in the PDB files? I had a browse through the pymol directory but couldn't find anything which looked like the above. I'm still very new to python so the chances are I have missed it. many thanks, Jules
Re: [PyMOL] sequence visualisation bug ?
Yes, I've got the same problem. Jules Daniel Rigden wrote: Hi all When I visualise sequences, all Glu residues (as well as all Asp residues) are shown as D! Has anyone else seen this? Daniel
Re: [PyMOL] problem in installation
Yes, i've had the same problem too. Jules On Mon, 5 Apr 2004, Tom Lee wrote: I have trouble installing PyMOL using pymol-0_95-bin-win32-py23.zip. Here is the message I got. The installer is unable to locate Python. Python must be installed before PyMOL. Do you wish to abort? I have Python2.3.2 installed, and there was no problem installing pymol_0.93 with this version of Python. Anyway, I reinstalled Python again, but it doesn't help. Does anyone have this problem? Tom Lee --- This SF.Net email is sponsored by: IBM Linux Tutorials Free Linux tutorial presented by Daniel Robbins, President and CEO of GenToo technologies. Learn everything from fundamentals to system administration.http://ads.osdn.com/?ad_id=1470alloc_id=3638op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] Further functionality
Hi Warren, I was just wondering about a few features that pymol is currently lacking and if/when you were planning on implementing them. 1- calculation of surface potentials- will this be coming soon? 2- Are you thinking of including any kind of sequence viewer and sequence alignment tools to tie in with the fitting - as seen with swissPDB? This would be verh high on my wishlist. 3- Will you be including any more NMR biased features like a quick fitting and RMSD calculation for ensembles of structures? 4- Is there any chance you will be able to include non-continuous selections ie select (resi 10-20,30-40) rather than just 10-20 and ignore residues 30-40? many thanks Jules
Re: [PyMOL] Re: fitting and seq. alignment
I agree, what are the exact criteria for fitting in pymol? Currently i'm using SwissPDB viewer for quick fitting as this is pretty robust and usually comes up with something sensible. This is satisfactory for viewing but saving a swiss pdb fit for use in pymol is not. Pymol still seems to have problems with anything but the easiest fits when using the align command. One further related question- how do you pick different models from and NMR ensemble and align them all to the best fit? cheers Jules On Wed, 19 Feb 2003, Michael Ford wrote: I know it seems like every other question is on this subject but. I saw from an earlier message the following statement from Dr. DeLano PyMOL's fitting abilities are improving: the upcoming version (v0.80) will have the ability to do an on-the-fly sequence-alignment followed by an optimized structure alignment, saving considerable time and hassle. Has this been implemented (I'm running the latest version 0.86) I have 2 proteins that are identical, but for reasons of no great interest, have different numbering schemes. I have the documentation on the align command, but it doesn't work (malformed selection) Any help is appreciated. Mike Ford
Re: [PyMOL] Inter-PyMOL communication?
Wouldn't an easier way to do this be to have a command whereby you tell pymol to rotate/translate all seperate molecules relative to their own centres rather than the group or last loaded molecule centre as it does currently? That way you only need one pymol open and wouldn't need to have a master/slave setup. Jules On 13 Feb 2003, Gareth Stockwell wrote: Is there any way to have more than one PyMOL session respond to the same user input? What I would like to do is the following: Have several PyMOL windows open side-by-side, each containing a different molecule. Then, when I click and drag in any of these windows (to effect a rotation/translation), ALL of them undergo the same transformation. The reason I want to do this is to compare the structures of several related proteins, which have been superimposed and are therefore in the same coordinate frame. At the moment, the only way I can do this is by loading them all into the same PyMOL session, rotating the view, then toggling each object on/off using the menu at the right-hand side, but this is both fiddly and does not permit easy comparison of many structures. So, Warren, would it be very complicated to establish some kind of IPC commumication between PyMOL sessions, where one was designated the 'master', and all commands executed on that session were piped to each of its 'slaves'? Gareth -- - Gareth Stockwell EMBL - European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD gar...@ebi.ac.uk Tel (+44) 01223 492548 http://www.ebi.ac.uk/~gareth --- This sf.net email is sponsored by:ThinkGeek Welcome to geek heaven. http://thinkgeek.com/sf ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] graphics performance
Hi Dirk This might actually be a hardware affect rather than a software effect. The GeForce4 is undoubtably quicker that the GeForce 2 bu there comes a time when the actual CPU is lagging behind in the amount of data it can pass to the GPU- this also includes other limitations such as the graphics apature size setting in the bios, the amount of RAM available to the machine and the speed of the AGP BUS. Putting a GeForce4 into a PIII means the GPU will be idling a lot probably upgrading the motherboard, RAM and CPU will yield improvements, better graphics cards most likely won't. Jules On Wed, 8 Jan 2003, Dirk Kostrewa wrote: Dear Gordon, I assume that you changed the default nv driver in your XF86config(-4) file to the Nvidia driver nvidia. I've replaced on my private Pentium III (733 MHz) PC a GeForce2 GTS against a GeForce4 Ti4200 and I also observe less improvement than expected. Here are my observations: 1. Under Windows98SE with 3DMark2001 I get a ~50 % higher score, which is probably okay. 2. Under Linux I get a ~ doubled frame rate for the simple OpenGL benchmark program gears in full-screen mode and somewhat less than this in the Vulpine OpenGL Mark, which is fine (Nvidia driver 31.23). 3. But, puzzlingly with pymol and on-screen rendering of a complex secondary structure sketch (without ray-tracing) I only get a moderate increase (~ 10 %, or so) of the movie frame rate compared to a Geforce2MX440 running on a Pentium III (450 MHz) in my office! Here, I would really expect a huge difference in frame rate. I also don't understand this. A possible explanation would be that pymol, upon automatic detection of the graphics card, internally changes the complexity of the calculations resulting in a slower but improved image? Best regards, Dirk. On Wednesday 08 January 2003 09:40, gordon wrote: Hi I recently upgraded from a geforce 2 to a geforce 4 ti4200, and I don't really notice a performance improvment (running linux). I judge this based on how smoothly large sized proteins can be rotated with spheres on. Just wondering why?
Re: [PyMOL] multiple objects
Hi Michael, If I understand you right you already can do this- make sure that no atoms are selected first then click on the mouse menu so that when you press 'shift' RotF and MovF are implemented. Then all you have to do is move the mouse over the molecule you want to move/rotate whilst holding down the shift key and that molecule will move. To move all just release the shift key. Finally ensure the molecules are displayed in stick/line form or else they won't move. Jules On Mon, 9 Dec 2002, Michael Ford wrote: So I know how to manipulate objects individually using the rotate and translate commands. But what would be really useful is to be able to control which objects are controlled by the mouse (probably a critical function that will be implemented in the next release??). Insight handles this with the ability to 'clip' to an object or manipulate the 'world' (meaning all objects). Just wondering and eagerly anticipating the new version! Michael Ford --- This sf.net email is sponsored by:ThinkGeek Welcome to geek heaven. http://thinkgeek.com/sf ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] multi-chain pdb (+ clipping)
Hi Luca, To create new objects of chains try this: select R= chain R this will create an object named R from the atoms of chain R. Where chain R is specified in the PDB file. Sorry, i can't help with the Z-plane clipping thing. Jules On Fri, 29 Nov 2002, Luca Fenu wrote: dear Pymolers, can anyone suggest me a way to select in pymol the different chains inside a given pdb file? e.g: 1a07 has 4 different chain, two long ones belonging to the protein, and two small ones belonging to the ligands. It is possible to create an object for every one of them? thanks in advance luca ps: also: how can I set the z-plane clipping in such a way that when I load a new molecule the previous object are kept in view? is there any way of doing that? --- This SF.net email is sponsored by: Get the new Palm Tungsten T handheld. Power Color in a compact size! http://ads.sourceforge.net/cgi-bin/redirect.pl?palm0002en ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] settings of ribbons and cartoons
Hi Kristl The problem is that the secondary structure of your protein hasn't been defined in the PDB file. This is why the cartoon looks ike a tube. What you need to do is type util.ss into the command line and this will calculate some sort of secondary structure for you although it's not that accurate. Alternatively click on the little diamond next to your protein name in the in the OpenGL window and then click on 'assign ss'. As for your best bet on finding out how to do things this is probably it. Jules On Mon, 25 Nov 2002, Kristl Adams wrote: Where can I find a list of what I can set with regard to ribbons and cartoons. Currently the cartoons command just shows a thin round tube and the ribbons command shows just a thin line. I'd ideally like to have cartoonishly round ribbons with some of the residues on them drawn in sticks. I'm a new pymole user and am finding it frustrating to work with because it isn't that well documented ... Am I just not looking in the correct places for documentation? I have the pdf at http://pymol.scourceforge.net/userman.pdf, but it isn't specific enough. Please help the hopelessly confussed. Kristl --- This SF.net email is sponsored by: Get the new Palm Tungsten T handheld. Power Color in a compact size! http://ads.sourceforge.net/cgi-bin/redirect.pl?palm0002en ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
