RE: [PyMOL] electrostatic
Are you using the same platform for both Grasp and Pymol? I don't think that big-endian maps (written by an SGI computer) can be read by a little-endian platform, such as a x86 based PC. - Esben The problem is getting the phi map in grasp. Can somebody explain me how to do it? This is what we did and worked (we now using Delphi), try it. -- *On the SGI computers: 1) Start up the computer, log in and in a command line prompt, change the directory to where the .pdb fi le, .siz file and .crg files are located. 2) Run grasp (command: /hhmi/software/grasp/grasp) 3) Open up the menu by right-clicking on the window 4) With the menu open, right-click on the Read option. 5) Right-click on the PDB File option and load the .pdb file. 6) Open the read menu again (steps 3-4), and select the Radius/Charge File option, then load the raidus file. Repeat again, loading the charge file. 7) Open the main menu, click on display, show, molecular surface. 8) Open the main menu, click on calculate, new potential map. 9) Open the main menu, click on calculate, Pot. via map at surface/atoms 10) Open the main menu, click on write, potential map, internal map, let me enter it. In the command lin e prompt, type in the name of the file (namefile.phi) === Yu Chen Howard Hughes Medical Institute Chemistry Building, Rm 182 University of Maryland at Baltimore County 1000 Hilltop Circle Baltimore, MD 21250 phone:(410)455-6347 (primary) (410)455-2718 (secondary) fax: (410)455-1174 email:c...@hhmi.umbc.edu === --- This SF.Net email is sponsored by: SourceForge.net Broadband Sign-up now for SourceForge Broadband and get the fastest 6.0/768 connection for only $19.95/mo for the first 3 months! http://ads.osdn.com/?ad_id=2562alloc_id=6184op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Ball Stick representation
I have mad a lot of these pictures, and the solution is to create two objects for the substrate. object1, displayed as sticks in the desired color, and object2 dipslayed as spheres in the desired color(s) and then set sphere_scale, 0.3, object2 Example (if the file contains a residue named NAD) load molecule.pdb, complex create prot, complex and not resn NAD create nad1, complex and resn NAD create nad2, nad1 disable complex show sticks, nad1 color grey70, nad1 show spheres, nad2 set sphere_scale, 0.3, nad2 Hope this helps Esben -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Zach Sent: 18. maj 2004 23:36 To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Ball Stick representation Hello to all, I have a protein that contains a substrate and for which I want to create a picture. For the substrate I would like to use a ball and stick representation such that the spheres are colored by atom type and the sticks are on a single color. My problem is that I have not been able to give different color schemes to the sticks and spheres. How do I do that? Any help is greatly appreciated. Thanks, Zach --- This SF.Net email is sponsored by: SourceForge.net Broadband Sign-up now for SourceForge Broadband and get the fastest 6.0/768 connection for only $19.95/mo for the first 3 months! http://ads.osdn.com/?ad_id=2562alloc_id=6184op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Linux Beta Version with Sequence Viewer
Thanks for the input. * sequence colors could (optionally?) match atom (C-alpha) colors in the 3D view. Good idea. * When a 3D-alignment is done, there is a sequence alignment behind. Having this transferred to the sequence window would be extremely useful. Planned -- but this is nontrivial. * The heteroatoms should not appear in the sequence windows - at least not in residue modes. Hmm. Some heteroatoms you definitely want, like S-met and modified bases. Others like water aren't quite so useful. What we may need in PyMOL is a set of categories/selection keywords such as the following: polymers: all natural bases/amino acids and any hetatms connected through main chain chemistry waters: all recognized waters (HOH, WAT, TIP, etc.) ions: isolated atomic cations, anions, metals, etc. ligands: anything not contains in the above By default, polymers and ligands make sense in the sequence view and waters can probably be omitted. Ions we should also probably keep in by default since they often play important roles in coordinating ligands. Does this sound like a useful addition? 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 EPF (Esben Peter Friis) Sent: Wednesday, May 19, 2004 4:58 AM To: Warren DeLano; pymol-users@lists.sourceforge.net Subject: RE: [PyMOL] Linux Beta Version with Sequence Viewer Hi Warren This is GREAT! I was going to suggest this for the future development, but (as usual :-) you're ahead. Very good points: * possible to chose between atoms/1-letter residues/3-letter residues etc. * The background color of the scrollbar area shows a complete overview of the selections. Proposals: * sequence colors could (optionally?) match atom (C-alpha) colors in the 3D view. * When a 3D-alignment is done, there is a sequence alignment behind. Having this transferred to the sequence window would be extremely useful. * The heteroatoms should not appear in the sequence windows - at least not in residue modes. How are the sequences represented in the data structure? It could be fun to interface with an extrenal modelling program, such as Nest. That goal seems relatively close with this new feature. Cheers, Esben -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Warren DeLano Sent: 18. maj 2004 10:22 To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Linux Beta Version with Sequence Viewer PyMOLers, I just finished the first beta version of PyMOL with a built-in sequence viewer (96beta6) and am looking for some experienced LINUX PyMOL users who are willing to poke around with this new stuff and provide feedback or suggestions. Screenshot download at: http://delsci.com/beta NOTE: don't install this over your main version -- try this in a separate directory instead. Load your favorite structure, click on the S on the lower right hand corner to enable the sequence viewer, and then see what you can do with it. Try various button combinations on the sequence, and try mixing in shift and/or control with the left middle buttons. Please let me know what you think... Cheers, 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 is sponsored by: SourceForge.net Broadband Sign-up now for SourceForge Broadband and get the fastest 6.0/768 connection for only $19.95/mo for the first 3 months! http://ads.osdn.com/?ad_id=2562alloc_id=6184op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users --- This SF.Net email is sponsored by: SourceForge.net Broadband Sign-up now for SourceForge Broadband and get the fastest 6.0/768 connection for only $19.95/mo for the first 3 months! http://ads.osdn.com/?ad_id%62alloc_ida84op=ick ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Creating a .pymolrc file in Windows
Actually, this too was anticipated ; ). On Windows: for PyMOL commands, simply use pymolrc (no extention -- I suppose pymolrc.txt or pymolrc.pml would've made more sense...) or for Python code: pymolrc.py pymolrc.pym 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 EPF (Esben Peter Friis) Sent: Wednesday, May 19, 2004 2:30 PM To: pymol-users@lists.sourceforge.net Cc: TAPO (Thomas Agersten Poulsen); SMIN (Stefan Minning); LBEI (Lars Beier) Subject: [PyMOL] Creating a .pymolrc file in Windows Hi PyMOLers Seems like it is somewhat difficult to create a .pymolrc file in Windows (whatever version). The standard Windows explorer file browser simply doesn't accept this as a filename. The workaround is to call the file something else, eg. pymolrc.txt and put the desired commands in it using Notepad. The file must be saved in C:\Program Files\DeLano Scientific\PyMOL\ Then open a terminal (command) window by running Start/Run and type cmd (win2000/XP) or command (Windows 98/ME). Then change to the correct directory and rename the file: cd c:\Program Files\DeLano Scientific\PyMOL ren pymolrc.txt .pymolrc That should do the trick! You can edit the file aftrewards by right-clicking it and choose open with/Notepad. Cheers, Esben --- This SF.Net email is sponsored by: SourceForge.net Broadband Sign-up now for SourceForge Broadband and get the fastest 6.0/768 connection for only $19.95/mo for the first 3 months! http://ads.osdn.com/?ad_id%62alloc_ida84op=ick ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Linux Beta Version with Sequence Viewer
Warren. I can't speak to the alignment tools, as I don't spend a lot of time in homology model building, but I would like to second the idea of adding the selection keywords. They would make my use of pymol that much easier. Andy --On Wednesday, May 19, 2004 09:32:17 -0700 Warren DeLano war...@delanoscientific.com wrote: Thanks for the input. * sequence colors could (optionally?) match atom (C-alpha) colors in the 3D view. Good idea. * When a 3D-alignment is done, there is a sequence alignment behind. Having this transferred to the sequence window would be extremely useful. Planned -- but this is nontrivial. * The heteroatoms should not appear in the sequence windows - at least not in residue modes. Hmm. Some heteroatoms you definitely want, like S-met and modified bases. Others like water aren't quite so useful. What we may need in PyMOL is a set of categories/selection keywords such as the following: polymers: all natural bases/amino acids and any hetatms connected through main chain chemistry waters: all recognized waters (HOH, WAT, TIP, etc.) ions: isolated atomic cations, anions, metals, etc. ligands: anything not contains in the above By default, polymers and ligands make sense in the sequence view and waters can probably be omitted. Ions we should also probably keep in by default since they often play important roles in coordinating ligands. Does this sound like a useful addition? Cheers, Warren
