Re: [PyMOL] A faster way of unbonding things?
If you have a PDB file of the ligands and know the number of atoms in
each ligand, then you could introduce a TER card after the each ligand.
That way PyMOL will not draw bonds between the ligands. If you want to
visualize it one after the other then MODEL and ENDMDL cards before and
after each ligand would work too.
-Kaushik
On Tuesday, August 17, 2004, at 01:02 PM, Michael George Lerner wrote:
Hi,
I have a file which contains a protein and a bunch of ligands. The
ligands come from a Monte Carlo simulation where they were allowed to
talk
to the protein, but not to eachother. So, lots of the ligands overlap.
When PyMOL sees this, it draws bonds between the ligands. Every time I
load up one of these structures, I have to unbond things with something
like
for i in range(160,660):cmd.do('unbond resi %s, not resi %s'%(i,i))
which takes a *really* long time. Is there a faster way to do this? I
once hacked up the PyMOL source so that HETATMS with resi N didn't
get
bonded to anything else in the first place, but that's obviously a bad
way
to do things (and I can't seem to compile things myself on our SGIs, so
it doesn't work there anyway).
Thanks,
-michael
--
This isn't a democracy;|_ |Michael Lerner
it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan
-Torrence, Bring It On| - against HTML email X | Biophysics
| / \ | mler...@umich
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[PyMOL] More on Plugins
Hello, Since it is plugin season, I thought of contributing too. I have a plugin which is very specific to my research needs in structure based drug design. It marries the PyMOL interface with other command line software packages, such as DivCon and AMBER. Both these packages can be obtained from other sources. AMBER is a popular simulation package from UCSF. DivCon was developed at the Merz research group at Penn State and can be obtained from http://www.quantumbioinc.com I did not write this with the aim to distribute it but just as a way to learn Python and PyMOL. But my colleagues who have used it, describe it as useful. So, PyMOL users who have access to these programs might find it useful too. In addition to the features that use the above programs, there are other features not dependent on any external programs and could be helpful during visualization and analysis of biomolecular structures. Anyway, a short description of the plugin can be found at the following location from where it can be downloaded too: http://www.personal.psu.edu/kxr205/research/divscore.html The introduction to the plugin in the above webpage is pretty ambitious and was written when the realization that a PhD has to be finished had not sunk in. But the features that have been described will all work once the programs are installed correctly. The installation is straightforward and follows the pymol plugin philosophy. If anybody is interested and has problems installing it then please e-mail me. As for platform dependence -- Since it uses external programs such as AMBER and DivCon, they need to be compiled for the specific platform. I have tested it out on RedHat Linux and it works fine. The features that do not need external programs (not too many of them yet) are platform independent. I just checked out the sequence viewer in 0.96 and its great. Kaushik -- Kaushik Raha Merz Research Group Penn State University On Wednesday, July 14, 2004, at 03:56 PM, Warren DeLano wrote: Charles, Simply awesome! It works great on Windows and Mac too... Folks, I think we've finally hit on a workable paradigm for extending PyMOL's capabilities via these lightweight, end-user-installable plugins. You have my full encouragement -- go crazy with this stuff! This grass-roots user-driven development is exactly what PyMOL was supposed to enable... To help the sharing process along, I've created a new plugins page on the SourceForge site and welcome your submissions. http://pymol.sf.net/plugins.html I can already see that we'll need a user-friendly Install Plugin... menu item in the next release that will automatically copy plugin files to the correct location. In the meantime, installation directions can be found on that page... Provided that plugins are released under a suitable (non-viral) open-source license, I don't see any reason why good ones couldn't become part of the standard PyMOL distribution, which would of course save users the trouble of having to download and install them. Cheers, Warren -- mailto:war...@delsci.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Charles Moad Sent: Wednesday, July 14, 2004 11:32 AM To: Michael George Lerner Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Plug-in Menu Thanks for the info. Using your APBS as an example I made a very simple remote pdb loader. You can check it out at http://euclid.uits.iupui.edu/~cmoad/pymolPlugins/; or download it directly from http://euclid.uits.iupui.edu/~cmoad/pymolPlugins/remote_pdb_load.py;. It is inspired from chimera's remote pdb loading feature. Thanks again, - Charlie Michael George Lerner wrote: Hi, There's some example code in pymol/modules/pmg_tk/startup/__init__.py. You can see how it works by copying it (uncommented) into a new file and placing that file in pymol/modules/pmg_tk/startup. You'll see the new plugins the next time you start PyMOL. I have a larger plugin that I've written .. I'll be sending out an announcement about it later today. -michael -- This isn't a democracy;|_ |Michael Lerner it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan -Torrence, Bring It On| - against HTML email X | Biophysics | / \ | mler...@umich On Wed, 14 Jul 2004, Charles Moad wrote: I am interested in developing some simple plugins for the new release, and I was wondering if there was a document or api specifying how to go about this. As the subject says, for example, how do you add a plugin entry to the new menu bar list. Thanks, Charles Moad Scientific Data Analysis Lab Indiana University --- This SF.Net email
[PyMOL] Coloring atoms by charge
Hi, Is there a way to color atoms by charge in PyMOL? Can PyMOL read the charges in a PDB file use those charges to color the atoms? Thanks, Kaushik.
[PyMOL] Using Numeric from PyMOL
Hi Warren, I am trying to use the Numeric module from within my PyMOL pluggin but I can not get it to work. It complains while importing Numeric. The message is: ImportError: /usr/lib/python2.2/site-packages/Numeric/multiarray.so: undefined sybmol: _Py_NoneStruct I had to change the PYTHONPATH variable in PyMOL 9.3 to get it to see Numeric since in 9.3 it seems like PyMOL uses ext as PYTHONPATH. In any case I dont think the problem is with changing the PYTHONPATH. Have you been able to import Numeric to PyMOL? Please do let me know and any suggestions would be appreciated. Regards, Kaushik.
[PyMOL] N-Terminal hydrogens with Chempy
Hi Warren, I found out that it is possible to write out AMBER style atom name formats with hydrogens added using the Chempy which is pretty neat. However it seems like this does not recognize the N-terminal residue for adding hydrogens. Is that still the case? I am still using PyMOL 088 (I will soon upgrade). Thanks, Kaushik. -- Graduate Student Penn State University University Park PA-16801
[PyMOL] AMBER Style Hydrogen
Hi, I was using the add hydrogen functionality in PyMOL which works fine but it places the hydrogens after the heavy atoms in a protein. Is it possible to have AMBER style hydrogens added where the Hydrogens go after the heavy atom it is attached to? Better still can I have the names of the hydrogens similar to the AMBER hydrogens. I notice that the Chempy has AMBER libraries so is it possible to use that library to protonate proteins? Thanks, Kaushik Raha.
Re: [PyMOL] Electrostatic potential maps in PyMOL
Yu Chen, I think it is because of endianess. My phi files were generated by Delphi on an SGI in the GRASP format. My PyMOL 088 on Linux does not seem to mind it. I think Warren has fixed the problem of endianess and it should be fine in the next release. Kaushik. On Thursday, July 10, 2003, at 10:11 AM, Yu Chen wrote: Thanks everybody for suggestiones, and Warren for fixing the problem. I will see if we could generate some phimap not 65x65x65. Ksushik, I don't know why your Delphi is working fine, here is my output from load phimap, which it should be cause of the endianess: PHIMapToStr: now starting phimap PHIMapToStr: potential PHIMapToStr: qdiffxas: qdiffxs4 with an improved surfacing routine PHIMapToStr: j# ObjectMap: Map Read. Range = -3388. to 37 Crystal: Unit Cell1.0001.0001.000 Crystal: Alpha Beta Gamma90.000 90.000 90.000 Crystal: RealToFrac Matrix Crystal:1.0.0. Crystal:0.1.0. Crystal:0.0.1. Crystal: FracToReal Matrix Crystal:1.0.0. Crystal:0.1.0. Crystal:0.0.1. Crystal: Unit Cell Volume1. Executive: object map created. Best Yu === Yu Chen Howard Hughes Medical Institute Chemistry Building, Rm 122 University of Maryland at Baltimore County 1000 Hilltop Circle Baltimore, MD 21250 phone: (410)455-6347 (410)455-2718 fax:(410)455-1174 email: c...@hhmi.umbc.edu === On Wed, 9 Jul 2003, Warren L. DeLano wrote: Okay, scratch that -- I fixed the problem, relying on standard Fortran unformatted IO conventions to automatically determine endianness and map size. PyMOL should now be able to read a PHI map of any dimensionality, so long as record size is implicitly and correctly specified in the map file. This may or may not be the case for .phi files written from C (for example, fld2phi is hard-coded for a 65x65x65 map, because the data block's record length specifier is hardcoded to be 0x10c304 = 65*65*65*4). Can someone send me a PHI map which is not 65x65x65 for testing purposes? Please include the associated PDB file for visual verification. Thanks! Looks like we'll need to push out another release sooner rather than later... Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Warren L. DeLano Sent: Wednesday, July 09, 2003 2:20 PM To: 'EPF (Esben Peter Friis)'; 'Kaushik Raha '; 'Yu Chen ' Cc: pymol-users@lists.sourceforge.net Subject: RE: [PyMOL] Electrostatic potential maps in PyMOL Yes, you have identified the problem: PyMOL 0.90 currently only reads PHI files in one of the two endian formats (not sure if it is big or little). The problem is, how it PyMOL to determine which format the incoming map is in? The file format is so darn implicit, I haven't yet come up with any effective way of doing it without risking a floating exception on finicky hardware. Any ideas? If we can just determine the enddian-ness of the incoming file, then the rest is a snap. Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 --- This SF.Net email sponsored by: Parasoft Error proof Web apps, automate testing more. Download eval WebKing and get a free book. www.parasoft.com/bulletproofapps ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] Electrostatic potential maps in PyMOL
There has been some talk on the list regarding failure of PyMOL in reading Delphi generated potential maps that I missed. I have generated phimap using a modified version of Delphi in the GRASP format that PyMOL reads and displays without any problem. So I am not sure what the problem is. Can anybody please let me know what was the problem with PyMOL reading Delphi generated GRASP potential maps? Was wondering if PyMOL is doing the right thing?? Thanks, Kaushik Raha Penn State University On Wednesday, July 9, 2003, at 10:48 AM, EPF (Esben Peter Friis) wrote: Hi PyMOL users, MEAD's potential maps can be used in PyMOL, but it requires a little more than a bit of tweaking, as the maps are in the AVS .fld format, which can not be read by PyMOL. (These maps can be read by Dino, as Paulo just mentioned). Also, PyMOL reads (as far as I can see) only big-endian phi-maps. I have written a small program, which does the conversion from .fld to big-endian-.phi, so the maps can be read by PyMOL. It just finished it today, and it has only been tested on Linux (i386), so beware ;-) To create a nice electrostatic surface, you need: * Gromacs (not strictly necessary, but makes life easier) Download from http://www.gromacs.org * MEAD. Download from http://www.scripps.edu/bashford/ * fld2phi, source code quoted below (sorry, but I don't have access to our external web server, and it's only about 4kb). * PyMOL, of course (v0.88 or newer). Here is an example how to create everything from scratch for 4PTI.pdb Gromacs steps - 1) use pdb2gmx to create .gro and .top files: pdb2gmx -f 4PTI.pdb -o 4PTI.gro -p 4PTI.top 2) use grompp to create .tpr file: grompp -f 4PTI.mdp -p 4PTI.top -o 4PTI.tpr -c 4PTI.gro The file 4PTI.mdp contains the parameters for the Gromacs simulation. But as we are not going to do any simulation this time, an empty file is ok. It can be created with touch 4PTI.mdp. 3) use editconf to create a MEAD-readable pdb file: editconf -f 4PTI.tpr -mead -o 4PTI.pqr.pdb The output pdb file must then be renamed to be recognized by MEAD: mv 4PTI.pqr.pdb 4PTI.pqr MEAD steps -- 1) create a .ogm file which specifies the grid size. Notice that PyMOL can only handle grids which are 65x65x65 points, so your only option is to change the spacing between points. You can specify focussing options in the .ogm file, but only the coarsest grid is written anyway, so you only need one line in the 4PTI.ogm file: ON_GEOM_CENT 65 1.0 See documentation for other centering options (first parameter). Next number is the number of grid points on each side (must be 65 to be readable by PyMOL). The last number is a real specifying the distance between grid points. 2) Run 'potential' to create the grid: potential -epsin 2 -CoarseFieldOut 4PTI 4PTI The epsin option is mandatory and specifies the internal (in the protein) dielectric constant. The program will say something like: WARINING from potential main program: Could not open field point file, 4PTI.fpt, for reading. Exiting without giving any potentials. This can be ignored. The program still writes out a 4PTI.fld file with the grid. Notice that this file in not overwritten, so you must delete it manually if it already exists. Convert to PyMOL readable grid -- 1) Use the fld2phi to convert the .fld file to a big-endian .phi grid file: fld2phi 4PTI.fld 4PTI.phi This sould create a 4PTI.phi file which is readable by PyMOL. PyMOL steps --- 1) Load the structure including the hydrogens built by Gromacs: load 4PTI.pqr, 4PTI 2) Create a selection of the water: select water, 4PTI and resn SOL 3) Remove the water atoms: remove water 4) Show the surface of the 4PTI object: show surface, 4PTI 5) Load the electrostatic grid: load 4PTI.phi, map You can show the extent of the grid box by clicking on the object called map in the object list to the right. 6) Create a color ramp object: ramp_new e_lvl, map, [-0.02,0.00,0.02] 7) Color the surface according to the grid and map: set surface_color, e_lvl, 4PTI Thats it. You can change the color scale on the fly by issuing another ramp_new command with other numbers. The 3 numbers are red-point, white-point and blue-point, respectively. The scale can also be changed by ctrl+mid-click while you drag the color scale. It is also possible to create one or more contour surfaces: isosurface contour1, map, -0.05 where contour1 is the object name of the surface (choose whatever you want), map is the object name of the electrostatic potential map and the number is the contour level. The commands isomesh and isodot have the same syntax and do exactly what you think. Best regards (and please forgive me for quoting source code here :) Esben ** * Source code for fld2phi * * save as: fld2phi.c
[PyMOL] 1-4 Lists
Hi, The sculpting feature of PyMOL indicates that it creates 1-4 neighbor list. Does it create all (1-2, 1-3 and 1-4)? Is it possible to access it? Kaushik Raha. Penn State
Re: [PyMOL] Disulfide Bonds
A similar question: Does PyMOL have a PDB file parser that can read disulphide linkages from the file and connect the atoms or one has to explicitly issue bond commands. Also, can PyMOL display hydrogen bonds without the user having to write out a list? thanks, Kaushik Raha. Penn State University. On Friday, September 20, 2002, at 04:07 PM, DeLano, Warren wrote: Alex, If the sulfurs are within disulfide bonding distance, PyMOL should connect them by default. If this is not happening, please send me the PDB file so I can take a look-see. Otherwise, you can use the bond command to attach them: bond 24/sg,26/sg bond 56/sb,99/sg unpick (unpick will hide the bond baton which gets displayed) Cheers, Warren -- mailto:war...@sunesis.com Warren L. DeLano, Ph.D. -Original Message- From: Alex Morla [mailto:alex...@uic.edu] Sent: Friday, September 20, 2002 8:48 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Disulfide Bonds Sorry if this is a novice question, but how do I display the disulfide bonds in my models? Thanks, and keep up the great work!! Alex Morla Univ. of Illinois, Rockford. --- 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 --- 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
