Re: [ccp4bb] Please Delete: FW: Departmental License for Pymol
Hi Phoebe, We all accidentally mis-forward an email at one time or another, so no worries. Schrödinger has reissued new credentials to your department. Cheers, -- Jason On Wed, Sep 11, 2013 at 9:54 AM, Phoebe A. Rice pr...@uchicago.edu wrote: MANY APOLOGIES the wrong address got auto-filled when I tried to forward this to my lab. Please delete. ++ Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University of Chicago 773 834 1723; pr...@uchicago.edu http://bmb.bsd.uchicago.edu/Faculty_and_Research/ http://www.rsc.org/shop/books/2008/9780854042722.asp From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Phoebe A. Rice [pr...@uchicago.edu] Sent: Wednesday, September 11, 2013 9:50 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] FW: Departmental License for Pymol This may get us a more advanced version than the one embedded in phenix? From: Erin Adams [ejad...@uchicago.edu] Sent: Wednesday, September 11, 2013 9:32 AM To: Shohei Koide; Herbert C Friedmann; Andrzej Joachimiak; Godfrey Getz; James Shapiro; Ronald S. Rock; Robert Haselkorn; Geoffrey L. Greene; Sean Crosson; Nancy Schwartz; Joe Piccirilli; Tao Pan; Keith Moffat; David R. Kovar; Tobin R. Sosnick; Stephen C. Meredith M.D., Ph.D.; Phoebe A. Rice; Francisco Bezanilla; Marvin W. Makinen; Stephen Kent; Donald F. Steiner Md.; Benoit Roux; D Allan Drummond; Glyn Dawson; Erin Adams; Robert Keenan; Theodore L. Steck; Tony Kossiakoff; Eduardo Perozo Subject: Departmental License for Pymol Dear colleagues, Tobin has generously agreed to fund another three year departmental licensing for Pymol. The information is below, please distribute this to your labs. Thanks, Erin Begin forwarded message: From: Schrodinger Licensing licens...@schrodinger.com Subject: PyMOL Invoice #13348 Date: September 10, 2013 5:24:01 PM CDT To: ejad...@uchicago.edu Dear Erin J. Adams, Thank you for your recent purchase of PyMOL. Here is the information you need for downloading the software: Invoice number: 13348 Download documentation URL: http://pymol.org/dsc USER: 16sep10 PASSWORD: xoeklc4y The following links should be helpful to you while using the software: PyMOL-Users mailing list. Please consider joining the community mailing list if you haven't done so already. http://lists.sourceforge.net/lists/listinfo/pymol-users For technical support issues, please email: licens...@schrodinger.com The community-maintained Wiki documentation server: http://pymolwiki.org Additional PyMOL-related links: http://pymol.sourceforge.net/links.html We hope you enjoy PyMOL. Sincerely, Schrodinger PyMOL licensing team Schrodinger Licensing | licens...@schrodinger.com http://www.schrodinger.com | 503-299-1150 | 503-299-4532 (fax) 101 SW Main St. Suite 1300, Portland OR 97204 Erin J. Adams Ph.D. Associate Professor Department of Biochemistry and Molecular Biology University of Chicago 929 E. 57th Street Chicago, IL 60637 office: CIS W236 lab: CIS W229 website: http://ejadamslab.bsd.uchicago.edu Office phone: 773-834-9816 Lab phone: 773-834-0660 Department Fax: 773-702-0439 -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120
Re: [ccp4bb] Superposition of electron density
Hi Jan, If there's no other easy solution at hand, you can consider using PyMOL. In PyMOL you just load your structures and maps, align the structures, and then move the maps with the matrix_copy command: # Fetch two proteins and their densities fetch 1oky 1t46, async=0 fetch 1oky 1t46, type=2fofc, async=0 # align the structures align 1oky, 1t46 # copy the map over matrix_copy 1oky, 1oky_2fofc Cheers, -- Jason (Already sent to Jan, forgot to CC the list.) On Thu, Aug 29, 2013 at 10:17 AM, Jan Lohöfener lohoefener@mh-hannover.de wrote: Dear all, we are trying to superimpose several structures together with their electron density to show the presence of point mutations. Is there any possibility to superimpose the electron density together with its structure or to translate/rotate the electron density alone? Thanks you, Jan -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120
Re: [ccp4bb] Strand distorsion and residue disconnectivity in pymol
Hi Donghui, Bernhard is correct: PyMOL flattens out secondary structure to produce more aesthetically appealing images. You can disable this for beta sheets and loops by typing: # disable smoothing of sheets set cartoon_flat_sheets, 0 # disable smoothing of loops set cartoon_smooth_loops, 0 The cartoon_sidechain_helper setting automatically modulates these settings. If for some reason you need to disable cartoon_sidechain_helper you can imitate the look with: hide show cartoon show sticks, not (n. C+CA+O+N) extend 1 set cartoon_smooth_loops, 0 set cartoon_flat_sheets, 0 Again as Bernhard noted, smoothing representations adjusts the representations' positions in space; therefore, you have the option of being positionally correct or aesthetically more pleasing. Cheers, -- Jason On Wed, May 29, 2013 at 10:29 PM, wu donghui wdh0...@gmail.com wrote: Dear all, I found a problem when I use pymol to prepare structure interface. Strand is distorted when residue from the strand is connected to the strand by turning on side_chain_helper on. However when side_chain_helper is off, the strand turns to normal shape but the residue from it is disconnected to the strand. I attached the picture for your help. I know there must be some tricks for this. Welcome for any input. Thanks a lot. Best, Donghui -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120
Re: [ccp4bb] Strand distorsion and residue disconnectivity in pymol
Hi Jacob, Sure, but I believe Donghui wanted to only show sidechains, not any backbone atoms, as sticks. Doing this will leave fragments floating in space as the original email noted. Cheers, -- Jason On Thu, May 30, 2013 at 10:13 AM, Jacob Keller j-kell...@fsm.northwestern.edu wrote: Can't you just show both cartoon (smoothed) and sticks (not smoothed) for the given area? JPK On Thu, May 30, 2013 at 11:06 AM, Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi Donghui, Bernhard is correct: PyMOL flattens out secondary structure to produce more aesthetically appealing images. You can disable this for beta sheets and loops by typing: # disable smoothing of sheets set cartoon_flat_sheets, 0 # disable smoothing of loops set cartoon_smooth_loops, 0 The cartoon_sidechain_helper setting automatically modulates these settings. If for some reason you need to disable cartoon_sidechain_helper you can imitate the look with: hide show cartoon show sticks, not (n. C+CA+O+N) extend 1 set cartoon_smooth_loops, 0 set cartoon_flat_sheets, 0 Again as Bernhard noted, smoothing representations adjusts the representations' positions in space; therefore, you have the option of being positionally correct or aesthetically more pleasing. Cheers, -- Jason On Wed, May 29, 2013 at 10:29 PM, wu donghui wdh0...@gmail.com wrote: Dear all, I found a problem when I use pymol to prepare structure interface. Strand is distorted when residue from the strand is connected to the strand by turning on side_chain_helper on. However when side_chain_helper is off, the strand turns to normal shape but the residue from it is disconnected to the strand. I attached the picture for your help. I know there must be some tricks for this. Welcome for any input. Thanks a lot. Best, Donghui -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- *** Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Farms Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kell...@janelia.hhmi.org *** -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120
Re: [ccp4bb] Off-topic PyMOL Issue
Hi Greg, Takanori Nakane's suggestion should work for you, which is our workaround for non-compliant video cards/drivers. If it doesn't or you see performance or stability problems, please try these two settings: unset use_shaders unset sphere_mode These two settings are usually only necessary for Intel-based mobile chipsets. Furthermore, PyMOL v1.5.0.5 and later should automatically fallback to the most stable settings. Cheers, -- Jason On Sat, Mar 2, 2013 at 6:12 PM, Greg Costakes gcost...@purdue.edu wrote: Hello Everyone, I am having some difficulties with PyMOL on my windows machine and was wondering if anyone has come across this problem When I load a pdb, nothing shows up except for the waters. Selecting cartoon representation will show the protein, however if I try to show residues as sticks or lines they appear disconnected. I have attached a figure for reference. When I ray-trace the protein, the residues in stick representation appear normal. I tried re-installing PyMOL, but that did not fix the problem. My graphics card drivers are up to date. Any suggestions would be greatly appreciated. Thank you! --- Greg Costakes PhD Candidate Department of Structural Biology Purdue University Hockmeyer Hall, Room 320 240 S. Martin Jischke Drive, West Lafayette, IN 47907 -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120
Re: [ccp4bb] GeForce Graphics cards
Hi Alex, Thanks for asking before buying. You've avoided a common mistake. If you want to do 120 Hz stereoscopic 3D you must have a Quadro card. GeForce cards, even the really expensive ones, are made for games (and DirectX) not science. I've seen people pay upwards of $1000 for a top-of-the-line GeForce card only to be disappointed to find out it won't do in-window and full-screen OpenGL stereoscopic 3D like a $99 Quadro card will. If you're using passive 3D, like anaglyph or Zalman, then a GeForce card should be capable. I've run both off a MacBook Pro before just fine. Last, here's http://www.pymolwiki.org/index.php/Stereo_3D_Display_Optionsthe discussion on the PyMOLWiki from our users. Cheers, -- Jason On Wed, Feb 13, 2013 at 1:47 PM, Alex Kavian alek6...@gmail.com wrote: Hi there, I have an off-toptic question about Graphics card. My searches on pymolwiki and ccp4bb archives resulted in the following conclusion: Coot and pymol are not compatible with the new GeForce graphics cards. Hoewver, most of the posts I found were from 2009 and 2010. Does anyone here have any experience with GeForce 660 or 680 for stereo applications of Coot, Pymol or UCSF chimera? Will quadro cards work equally smooth in the stereo mode of these programs? Do 3D applications put too much pressure on the Graphics card which would justify installing dual Graphics card? (not sure if is relevant, but just for the record, we want to buy passive 3D monitor due to the budget restrictions). Thanks, Alex -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120
Re: [ccp4bb] GeForce Graphics cards
Hi, They might be, but please be aware that nearly all scientific applications use OpenGL for drawing and 3D. Many games use DirectX, an MS standard, for that. The capabilities differ by standard (OpenGL vs DirectX), hardware (NVidia GeForce, NVidia Quadro, AMD, Intel, etc) and operating system. Cheers, -- Jason On Wed, Feb 13, 2013 at 3:15 PM, S K alek6...@gmail.com wrote: Hi Jason, aren't the current gaming monitors all (or mostly) 120 Hz? At least companies like alianware sell GeForce together with 120 Hz monitors. A On Wed, Feb 13, 2013 at 4:02 PM, Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi Alex, Thanks for asking before buying. You've avoided a common mistake. If you want to do 120 Hz stereoscopic 3D you must have a Quadro card. GeForce cards, even the really expensive ones, are made for games (and DirectX) not science. I've seen people pay upwards of $1000 for a top-of-the-line GeForce card only to be disappointed to find out it won't do in-window and full-screen OpenGL stereoscopic 3D like a $99 Quadro card will. If you're using passive 3D, like anaglyph or Zalman, then a GeForce card should be capable. I've run both off a MacBook Pro before just fine. Last, here's http://www.pymolwiki.org/index.php/Stereo_3D_Display_Optionsthe discussion on the PyMOLWiki from our users. Cheers, -- Jason On Wed, Feb 13, 2013 at 1:47 PM, Alex Kavian alek6...@gmail.com wrote: Hi there, I have an off-toptic question about Graphics card. My searches on pymolwiki and ccp4bb archives resulted in the following conclusion: Coot and pymol are not compatible with the new GeForce graphics cards. Hoewver, most of the posts I found were from 2009 and 2010. Does anyone here have any experience with GeForce 660 or 680 for stereo applications of Coot, Pymol or UCSF chimera? Will quadro cards work equally smooth in the stereo mode of these programs? Do 3D applications put too much pressure on the Graphics card which would justify installing dual Graphics card? (not sure if is relevant, but just for the record, we want to buy passive 3D monitor due to the budget restrictions). Thanks, Alex -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120
Re: [ccp4bb] 3D alignment of points (atoms)
Hi Dave, If you're still searching for a quick way to do this, check out PyMOL's Pair Fitting Wizard (Wizard Pair Fitting; see Page 20 http://www.doe-mbi.ucla.edu/CHEM125/pymol_tutorial_060418.pdf). The wizard is interactive and quick to use. This can also be done from the command line or scripted using the pair_fit command (http://www.pymolwiki.org/index.php/Pair_fit). We use the Kabsch algorithm (with the appropriate corrections for reflection) and a faster hand-rolled technique, using if I recall correctly Jacobi rotations, to annihilate off-diagonal values. Cheers, -- Jason -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 On Fri, Dec 28, 2012 at 5:53 AM, Tom Oldfield oldfi...@ebi.ac.uk wrote: Hi In you post you say you want to fit a small number of points. Note that the original algorithm of Kabsch has a number of maths pathalogical conditions where points have symmetry or lie in a plane/line - this is common for a small number of points (fitting residues or your example). The maths for an update to this algorithm can be found here Oldfield St'Fun'Gen (2002) 510-528 (appendix C) where cross terms are used to generate the eigen vectors. This algorithm is very stable for fitting a small number of points and might be more suitable for what you are trying to do. If you want I can email you the code in C or maybe Java, though it has rather a lot of other weighting schemes/masking used in the above paper. Regards Tom Lsqkabsch should do the trick. Herman -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dale Tronrud Sent: Thursday, December 27, 2012 9:10 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] 3D alignment of points (atoms) If you just want the mathematics and are willing to roll your own code, you can use the method of Wolfgang Kabsch. I see this has been enshrined in a Wikipedia page at http://en.wikipedia.org/wiki/Kabsch_algorithm This is what I've used when I've wanted to superimpose points where the mapping between the points is defined. If the points in your tetramer aren't pathological, like lying in a common plane, you shouldn't have to worry about SVD and can just perform the matrix inversion. Dale Tronrud On 12/27/12 11:16, Waugh, David (NIH/NCI) [E] wrote: Greetings, I have what seems like a relatively simple problem to solve, but have not been able to do so using the software tools I know about. I have two sets of 4 points in 3D space (atoms in PDB files). They represent equivalent positions in two tetrameric proteins. I would like to align these points in one PyMol or Coot file. I don't want a NEW set of points representing the LSQ average of the two sets, which is what I get in Coot's SuperPose. Instead I am looking for a way to superimpose one atom from each set and then rotate one set for the best fit. I'm not an intuitive expert on symmetry, but I think there is probably only one best solution to this problem, right? I also need the atomic distances to be on the same scale in the two sets of points. Thanks for any help! Dave Waugh -- David S. Waugh, Ph.D. Macromolecular Crystallography Laboratory Center for Cancer Research National Cancer Institute Bldg. 538, Room 209A Frederick, MD 21702-1201 +1 (301) 846-1842 wau...@mail.nih.gov http://mcl1.ncifcrf.gov/waugh.html --
Re: [ccp4bb] Off topic: Selecting atoms within a given distance from a target atom
Hi Rex, I would like to specify a target atom in a pdb file and then isolate all atoms within a given distance of the target. The selected atoms are then to be placed in a new pdb file. Any suggestions please. This is simple to do in PyMOL. After loading your structure just use the mouse to select your target atom. After that, on the PyMOL command line type, select all within 5 of (sele) That will quickly identify those atoms within 5 Angstroms of your selection. For more help check out the PyMOLWiki (http://pymolwiki.org) especially selections (http://www.pymolwiki.org/index.php/Selection_Algebra). Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120
Re: [ccp4bb] Efficient way of showing residue conservation
Hi Yuri, I once saw a figure showing the protein as surface, but instead of having it coloured by atom type or potential, it was shown by percent conservation in the family. Something like red highly conserved, all the way to white, not conserved at all... Now, I assume the figure was done by uploading aligned sequnces of several members of a family, and the colouring the generated surface accordingly. Does anyone know a way to do this more elegantly than what I tried doing? ps. I quit colouring them manually after I remebered my protein was 407 aa long... PyMOL can do this pretty easily now. First you need to calculate an alignment, then you need to do the coloring. The alignment step is done like this: align protA, protB, object=aln I then wrote a script to automate the coloring of residues by conservation in the sequence alignment. You can find the script on the PyMOLWiki, here http://pymolwiki.org/index.php/Color_by_conservation. The script does a couple other useful things like showing the conservation not only by color but by cartoon putty radius, and expanding the alpha-carbon conservation to surface colors. You can find an example to copy/paste into PyMOL on that page. Hope this helps. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120
Re: [ccp4bb] Mac OSX 10.7 Lion
Phil, On Fri, Sep 9, 2011 at 4:28 AM, Phil Evans p...@mrc-lmb.cam.ac.uk wrote: Is there any opinion or experience about whether Lion is ready for crystallographic use? Should I upgrade? MacPyMOL works fine on Lion. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120
Re: [ccp4bb] structure based superposition
Hi Shilong, On Thu, Aug 18, 2011 at 5:55 AM, Shilong Fan fanshil...@hotmail.com wrote: normaly you can do it in the pymol. In the main interface, on the left menu, there is a:A button, click it, then looking for Aliagn. Then you can do it. But I prefer to use CCP4, in CCp4 there is a tool : Superpose. You can fine any region you want to do superpose. PyMOL can indeed perform alignments. It has three different methods and I'd like to take a second to clear up the differences. First, the align command (A Align ) performs a sequence alignment followed by a few rounds of fitting throw away outliers to improve the fit. The super command is similar to align, but if you indicate seq=0 then PyMOL will ignore the sequence. It then uses a dynamic programming strategy to find the best fit. Last, PyMOL also offers access to the structure-only cealign method as well. Of course, if you already know your paired atoms you can just use any of the 'fit' commands to do the fitting. Here are links to the PyMOLWiki pages for reference: * -- http://www.pymolwiki.org/index.php/Align * -- http://www.pymolwiki.org/index.php/Super * -- http://www.pymolwiki.org/index.php/Cealign * -- http://www.pymolwiki.org/index.php/Fit Hope this helps. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120
Re: [ccp4bb] Pymol question
Hi Chris, set cartoon_side_chain_helper=1, HISA should be set cartoon_side_chain_helper=1 That setting cannot yet be applied just to a specific set of atoms: it's a global setting. This is something we should add to our to-do list. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120
Re: [ccp4bb] PDB data mining
Hi Cale, For any given structure in the PDB, I want to identify all the Histidine ND1 atoms. I then want to consider these atoms in pairs, measure the distance in Angstroms between the ND1 atoms in each pair, and compile these distances (along with residue numbers of the pair) in a table. I then want to repeat this procedure for each unique structure in the PDB and generate a table containing all occurrences of HisND1 pairs with their corresponding separation distance. Amongst other things, I want e.g. generate a histogram from this table and determine e.g. the shortest HisND1 pair distance observed and the structure in which this happens. Does anyone have any suggestions for any tools I might be able to use to perform this search? This looked like a fun little PyMOL task. So, I wrote a script to do it. This will iterate over all the PDBs in a given directory and calculate the non-redundant distances of all HIS ND1s. A table is written to pre_hist.csv. Use R or something similar to create the histogram and do the numerical analysis. To use this, first, you'll need a prepared copy of the PDB, suitable for this task, downloaded locally in pdb_path. You will need to set pdb_path in the script below to wherever your PDBs are. (The other kind folks on this list already pointed you to resources for mirroring the PDB, if you haven't done it already.) To run the script below just save it to disk as his.py and launch it with: # from Linux pymol -cq his.py # or, from Mac /Applications/PyMOLX11Hybrid.app/Contents/MacOS/MacPyMOL -cq his.py If you're a Linux/Mac user, when the script finishes, just type: sort -n -k8 pre_hist.csv | head -2 into your BASH shell to get the shortest distance. For my example PDB it was: $ sort -n -k8 pre_hist.csv | head -2 PDB CHAIN RESI ATOM-A CHAIN RESI ATOM-B DISTANCE 5rla B 187 3729 C 312 7075 2.838208 To view the shortest distance use the ATOM-A and ATOM-B fields from the output file. From my example above I would need to fetch the protein and create a distance from index 3729 to index 7075. Here's how: # fetch the protein fetch 5rla, async=0 # show the distance distance index 3729, index 7075 # zoom on the new distance zoom dist01 Here's the Python script that does the work: import glob, os, pymol, sys from pymol import cmd the_pdb=/Users/vertrees/small_pdb files = glob.glob(the_pdb+os.sep+*.pdb) if not len(files): print Please set 'the_pdb' variable to a valid path containing PDB files. sys.exit(1) else: print Processing %d files. % len(files) s, outFile = resn HIS and name ND1, pre_hist.csv f = open(outFile, 'wb') # write the header f.write(PDB\tCHAIN\tRESI\tATOM-A\tCHAIN\tRESI\tATOM-B\tDISTANCE\n) # for each file in the mirror for x in files: cmd.load(x,finish=1) n = cmd.get_names()[0] m = cmd.get_model(s).atom # pairwise for each atom for aa in m: for bb in m: # avoid duplicates if aa.index==bb.index: continue f.write( %s\t%s\t%s\t%s\t%s\t%s\t%d\t%f\n % (n, aa.chain, aa.resi, aa.index, bb.chain, bb.resi, bb.index, cmd.get_distance( index %s % aa.index, index %s % bb.index))) cmd.delete(n) f.close() print Processed %d files. Please see %s for results. % (len(files), outFile) Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120
Re: [ccp4bb] help with pymol error message
Hi Rakesh, My guess is that PyMOL is getting confused by your map's name when loaded into PyMOL as an object. When you call isomesh/isosurface the 2nd parameter is the name of the map object loaded into PyMOL, not the filename you loaded from. I made some slight modifications to that set of commands reflecting a newer PyMOL build (1.3r1); you should be able to copy/paste this: # 1. Fetch PDB file fetch 1w2i, async=0 # 2. Fetch 2fofc map if on EDS server fetch 1w2i, type=2fofc, async=0 # 3. Zoom in the active site select active, (resi 14-20,38) and chain A zoom active hide all show stick, active # 4. Locate and Display the active site water select active_water, ( (resi 38 and name ND2 and chain A) around 3.5) and (resn HOH) show spheres, active_water alter active_water, vdw=0.5 rebuild # 5. Display the electron density around the active site atoms at sigma level=1.0 isomesh mesh1, 1w2i_2fofc, 1.0, active, carve=1.6 Cheers, -- Jason On Tue, Oct 19, 2010 at 5:56 PM, Rakesh Joshi rjo...@purdue.edu wrote: Hi all, I am trying to get a model-density figure made where selected residues are shown with their densities whereas the nearby unmodeled densities are removed. I tried the isomesh mesh command as suggested by the tutorial: 1. Loading PDB file File - Open - 1w2i.pdb 2. Load the map file File - Open - 2fofc.map.xplor It takes a while to load the map file. 3. Zoom in the active site PyMOL select active, (resi 14-20,38) and chain A PyMOL zoom active PyMOL hide all PyMOL show stick, active 4. Locate and Display the active site water We know that the amide group of Asn38 is h-bond to an active water. PyMOL select active_water, ( (resi 38 and name ND2 and chain A) around 3.5) and (resn HOH) The above command select any water molecules that is/are around 3.5A of the ND2 atom of resi 38 in chain A PyMOL show spheres, active_water Well the Oxygen atom is now shown in its vdw radius. We can reduce the size of the sphere to 0.5A by: PyMOL alter active_water, vdw=0.5 PyMOL rebuild 5. Display the electron density around the active site atoms at sigma level=1.0 PyMOL isomesh mesh1, 2fofc.map, 1.0, (resi 14-20,38 and chain A), carve=1.6 Because the residue atoms were previously defined as active, you can simply type: PyMOL isomesh mesh1, 2fofc.map, 1.0, active, carve=1.6 On doing this, I get an error message that reads map or brick objectname of my file not found. I can however open the entire density which tells me i have the file loaded correctly. My map file is a .ccp4 file. I do put in .map suffix when typing in the command. Any help will be welcome. Thanks in advance Rakesh -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120
Re: [ccp4bb] Graphics for notebook
Hi Eric, I wanted to know which type of graphics card is more suitable for a notebook which is going to be used for structural biology. Integrated or dedicated? ATI or NVIDIA? At the moment I have to choose between an integrated Intel HD Graphics or a dedicated NVIDIA NVS 3100M Graphics. Any suggestions are highly appreciated. These responses are in line with what I'd recommend. First, NVidia presently has the drivers with fewest number of PyMOL bugs (then ATI, then Intel) across all platforms. Their Linux support, has for years, outstripped the competition. Next, if you're doing anything graphics related, I'd highly suggest moving away from integrated boards. Last, the integrated mobile boards are the worst offenders--I'm looking at you Intel GM945!--so if you can help it, stay away from them. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120
Re: [ccp4bb] pyMol--set up view through one axis of the unit cell
Hi Jerry, If you wanted the mathematically exact axis, you _should_ be able to just make two pseudoatoms, position them at the proper position at the end of your axis and then use the orient command: pseudoatom axisMin, pos=[x1, y1, z1] pseudoatom axisMax, pos=[x2, y2, z2] orient axis* But, there is a bug with 'orient' on pseudoatoms: it's orienting the pseudoatoms along their 2nd principal axis, not the first. So, after you type those three command, follow up with: turn z, 90 and that should do it. Hope this helps, -- Jason On Tue, Sep 7, 2010 at 1:37 PM, Sampson, Jared jared.samp...@nyumc.org wrote: Hi Jerry, If your protein has an NCS symmetry axis parallel to a cell edge, you can try using the “orient” command. http://www.pymolwiki.org/index.php/Orient Best, Jared On 9/3/10 7:31 PM, James Stroud xtald...@gmail.com wrote: On Sep 3, 2010, at 4:03 PM, Jerry McCully wrote: It is a Pymol question. How can I set up the view through one axis of the unit cell? By eye. Use orthoscopic view to help. Show the unit cell as a guide: http://www.pymolwiki.org/index.php/Cell James -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center New York, NY 10016 (212) 263-7898 This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. = -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120
Re: [ccp4bb] local copy of wiki
Tim, In general, the best way to go is to contact the owner and ask for an SQL dump. It'll save far more time and frustration than scraping the wiki. You can then use mysqlimport to import the dump into your system. After that, copy the media files over and you should be set. Make sure you install any necessary extensions (like the math writer for rendering LaTeX). Heavily compressed, the PyMOLWiki dump with media is about 650 MB, so we won't make a habit of giving them away. Cheers, -- Jason On Fri, Aug 20, 2010 at 5:52 AM, Roger Dodd roger.d...@gmail.com wrote: (just forwarding this to the list...) Dear Tim, I think it may be possible, though rather long-winded to do. First of all, you'll need a working installation of mediawiki. My suggestion to get this would be to download one of the self-contained installations available from bitnami: http://bitnami.org/stack/mediawiki . That way, if anything goes wrong you can just wipe it without affecting the rest of your system. The more difficult bit will be downloading the wiki's information and inserting it into the database of your installation. If you contact the admin for the pymolwiki, they may be able to provide you with an sql dump that would make your life a lot easier. There is good documentation on the mediawiki website for importing these sql backups. The other, much more convoluted method, would be to use this page - http://pymolwiki.org/index.php/Special:Export - to export the pages. You need to supply this with a list of pages (one page per line) and it will give you an xml file containing them all that you can then import into your wiki. You can get a list of all the pages on the pymolwiki here: http://pymolwiki.org/index.php/Special:AllPages . The more difficult thing will be to get hold of all the images, though you could scrape them from this page: http://pymolwiki.org/index.php/Special:ListFiles and copy them to your installation's images folder. Good luck and hope that helps, Cheers, Roger On 20 August 2010 10:06, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: Dear all, is there a simple way for a local installation of a wiki (in particular the pymol wiki)? Our working network is physically separated from the internet and going back and forth between computers just to look up a single command is rather time consuming. Thanks a lot, Tim P.S.: I am aware of wget and curl but consider them as a last resort because it's difficult to set the correct level of recursion. -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.9 (GNU/Linux) iD8DBQFMbkWEUxlJ7aRr7hoRAhm2AJ0akHmmT8mUJUhF+Ivap1Ae32LhfgCgpezU osMfrFB+I8/teK2u+w4wQuw= =sj7e -END PGP SIGNATURE- -- Roger B. Dodd, PhD. Cambridge Institute for Medical Research Wellcome Trust/MRC Building Hills Road Cambridge CB2 0XY UK -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120
Re: [ccp4bb] CONE built-in in pymol
Hi Tim, CGO objects are sparsely documented in PyMOL. Aside from the old PyMOL Manual and the content on the wiki, there's not much else. The parameters for a CGO cone object in PyMOL are: (1) CONE the keyword (2-4) x, y, z position of the base of the cone (3-5) x, y, z position of the tip of the cone (6) radius of the base (7) radius of the tip (doesn't have to be 0) (8-10) r, g, b color specification for the base of the cone (11-13) r, g, b color specification for the tip of the cone (14) if 1 the base of the cone is filled in and colored; if 0 the base of the cone is open (15) if 1 the tip of the cone is filled in and colored; if 0 the tip of the cone is open Last, you can find more info here (http://pymol.sourceforge.net/newman/user/S0500cgo.html#14) on CGOs in PyMOL. Hope this helps, -- Jason On Thu, Aug 19, 2010 at 6:59 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: Hello, according to the pymol wiki http://www.pymolwiki.org/index.php/Arrows, pymol 1.1 has a CONE built-in. While the code of the API is quite nicely readable and I can guess the meanings of most of the parameters, I was wondering whether anyone could point me to documentation of that command - I couldn't find it on the wiki. Thanks a lot, Tim P.S.: I am aware that there is a pymol mailing list. -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.9 (GNU/Linux) iD8DBQFMbQ6ZUxlJ7aRr7hoRAoxnAKC900VnP+FAVmL89jWtNB6xosFD5ACeJx4C XioMtnyCI2F6D7VOsQI07V8= =GFYk -END PGP SIGNATURE- -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120
Re: [ccp4bb] merging Pymol sessions ? Non-CCP4 question
Jürgen, PyMOL sessions are essentially pickled Python dictionaries. At this point I'm not aware of a way to easily merge the contents of two sessions. This would be a nice new feature; I've added it to my list of features enhancement requests. Thanks, -- Jason On Sun, Apr 18, 2010 at 6:36 PM, Jürgen Bosch jubo...@jhsph.edu wrote: Dear CCP4bb, I'm running into some difficulties with Pymol, in particular I want to visualize via APBS the electrostatic surface of the protein, a protein peptide and an inhibitor molecule. I can render the electrostatic surfaces for each of them separately but I fail to show individual surfaces for each of the items in question. Since the .pse files are in binary format I was unable to find a way how to merge the individual .pse files in a meaningful manner (only the first file will be interpreted when all files are cated) If anybody has some suggestions I would be very glad to try them out. Thanks, Jürgen - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120
Re: [ccp4bb] How to show the ligand in my protein as sticks....???
Hussain, You can do a couple things. (1) At the PyMOL command line type: as sticks, organic (2) Create an organic selection using the mouse via the object menu, A Generate Selection Organic. PyMOL makes a new selection for you (if there is at least one organic small molecule). Then, from the new selection select S As Sticks. By the way, A Generate Selection means select A for your protein of choice, then from that menu select Generate then Selection, ... and so on. Hope this helps, -- Jason On Mon, Apr 12, 2010 at 2:15 PM, Hussain Bhukyagps hsn...@yahoo.com wrote: Dear all i'm trying to show ligand which is in the pdb of my protein as sticks, but it is showing the folowing message in the pymol Tcl/Tk GUI. You clicked /1204//X/TL1`0/C10 Selector: selection sele defined with 45 atoms. but it not responding to that command. can any one help..?? thank you. Send free SMS to your Friends on Mobile from your Yahoo! Messenger. Download Now! http://messenger.yahoo.com/download.php -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120
Re: [ccp4bb] How to show the ligand in my protein as sticks....???
Hussain, Spheres, dots, non-bonded spheres are for atoms. Sticks and lines show bonds. This indicates that your metal isn't bound to anything. If you like, feel free to send me the file or a snippet of it and I'll take a look. PyMOL does have some weirdness when it comes to figuring out proper bonding, especially in things like heme groups: you might have to do some bond-editing yourself. Good luck, -- Jason On Mon, Apr 12, 2010 at 3:14 PM, Hussain Bhukyagps hsn...@yahoo.com wrote: Dear Jason Vertrees, My ligand is a metal complex. i followed the way u suggested to me, but still i'm not able to solve it. it is working for spheres, dots, nb_spheres etc.. But not sticks and lines. By the way i'm able to generate thank U... Send free SMS to your Friends on Mobile from your Yahoo! Messenger. Download Now! http://messenger.yahoo.com/download.php -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120
Re: [ccp4bb] Zalman LCD availability
On Thu, Jan 14, 2010 at 3:57 PM, Andrew Ring ar...@berkeley.edu wrote: Hello All, Has anyone else noticed a lack of availability of Zalman 3-D LCD monitors? For at least a few weeks now, NewEgg and Dell are currently out of stock, as is every retailer that lists their inventory. I attempted to contact Zalman, but have not yet had a response. If you know of a retailer with them in stock could you send me a message? Does anyone have insight into Zalman's situation they can share? Thank you, Andrew -- === Andrew Ring System Administrator Kuriyan Laboratory http://jkweb.qb3.berkeley.edu/ Doudna Laboratory http://rna.berkeley.edu/ University of California, Berkeley Office: 542 Stanley Hall Shipping: 176 Stanley Hall, QB3 Berkeley, CA 94720-3220 tel: (510) 643 0166 fax: (510) 643 2352 Andrew, My Zalman Trimon is in the mail. It was ordered about a week ago, so no issues here. I am discussing 3D PyMOL development with Zalman support and can ask them about it if you like. -- Jason P.S. First post. :-) -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120
