Re: [PyMOL] Adding python modules
Finaly I succesfully installed the .NET framework, the Platform SDK, and so on... a lot o stuff indeed! I'm not clear on why you'd need the .NET framework (pymol/python stuff is generally compiled to machine code, not CLR bytecode). One thing to check is that you're using the correct compiler (MS has a dialect of c++ that compiles to CLR bytecode which would probably not work so well as a python module). [snip] _mysql.c C:\Program Files\DeLano Scientific\PyMOL\py24\include\Python.h(41) : fatal error C1083: Cannot open include file: 'unistd.h': No such file or directory Now I don't have the faintest idea, where should I get unistd.h from... what it is after all? As far as I know, unistd.h is a POSIX (unix) header file. I don't know this is available on windows natively (I believe some versions of windows are supposed to be POSIX compliant, but I'm not sure how compilant they are); possibly the pre-processer definations are not being set correctly. I'd recommend either installing mingw or cywin at this point, and compiling pymol from source, then using the same compilers to build the mysql module. Actually, I'd recommend switching to linux or another unix varient (OS X, one of the bsd's, etc); but that may be more trouble than you're willing to go to for this problem. But possibly someone with more experience in windows programming than I am has a better suggestion. Good luck, Pete Pete Meyer Fu Lab BMCB grad student Cornell University
Re: [PyMOL] Adding python modules
I know that as well... what I don't know is how to install it under PyMOL. If I were using simply python, than that would be no big deal, I did that a 1000 times: setup.py --build; setup.py --intall Presently I'm using the windows version of PyMol, and installing a separate python interpreter, and installing MySQLdb module didn't help. When I tried to start PyMOL and enter into command line: run setup.py --build, it didn't work as well, as it wants to find the file setup.py --build. If I'm understanding the situation correctly, you're trying to get MySQLdb into the pymol python, not the seperate python installation. And if there's a seperate python.exe in the windows pymol install, you've probably tried that already (there may not be one with the windows pymol binary). When you try to run setup.py with arguments from the pymol python intpreter, it intprets the arguments as a filename. Have you tried re-setting sys.argv before running setup (aka sys.argv=['setup.py','--build'] ; run setup.py,local )? If I'm understanding the help for the pymol run command correctly, you'd want to use either local or module (so that the global namespace doesn't confuse things). This may do strange things to your pymol install, and might not work, but it seems like it would be worth a try. Good luck, Pete Pete Meyer Fu Lab BMCB grad student Cornell University
Re: [PyMOL] contour levels in pymol
a mystery to me. Why is there a difference bewteen contour levels of FFT electron density maps displayed in Xfit vs pymol? When using the command for example :isomesh mesh1, fo-fc, 1.0, etc..., in pymol what does 1.0 in terms of sigma level really mean. I was under the assumption that 1.0 sigma is equal to 1.0 sigma as defined by FFT, but then there would not be a difference in the two maps displayed at this value in the two programs, which there is. Can anyone help clarify this issue? I was confused about this myself a few months back. The sigma level comes from the rms deviation of the map, not the fft itself. So if the maps are different (different sizes, covering different regions, or calculated using different grid spacints), then the sigma levels won't necessariily be equivalent. If all of the map parameters are the same and you still get differences in the displayed maps for the two programs, then there's something else going on. Pete Pete Meyer Fu Lab BMCB grad student Cornell University
Re: [PyMOL] how do i unset a cmd.set_key() binding ?
Hi,
I have a problem with set_key() that appeared when I executed two scripts
sequentially. In both scripts I set the F1 key to do something different
(ok, not a very smart move...). I thought that the newest set_key() would
take precedence over the latest and overtake its adressing, but
unfortunately it does not. The binding is very persistent, because I need
to close pymol and reopen it altogether between the two scripts so that
the new binding can take place. The current workaround for me is to have 2
I'm not completely sure this would work, but you could try
cmd.set_key('F1',None) before the second binding. This should eliminate
the previously-bound function.
Good luck,
Pete
Pete Meyer
Fu Lab
BMCB grad student
Cornell University
Re: [PyMOL] OSx X11 Pymol Clicking problem
Scott, I have had this problem for the past few weeks, and it has been difficult to diagnose the cause. The problem is that in the X11 version of pymol run on my mactel osx laptop does not interpret my three button mouse click properly. When I click on a given atom in the UI, it selects something else, often far away from the the intended selection. This is more of an annoyance, since I can visualize molecule, but the wizards and click menus are basically non- functional. I've sees slightly similar problems (mouse selection with stereo enabled using the fglrx driver for ati firegl cards doesn't work; same selection with stereo off works fine). If anyone out there has any suggestions I would love to hear them. I don't have any solutions for you, but the graphics card driver (or X11 configuration) might be a good place to start poking around for troubleshooting. Good luck, Pete Pete Meyer Fu Lab BMCB grad student Cornell University
Re: [PyMOL] ImportError: No module named _cmd
You could also try to add sys.path.append(dllpath) to your python script, where dllpath is the full path to the location of the pymol dll's. Of course, this approach might run into problems with different python versions; but depending on what you're trying to do it might be worth a shot (if there's a python.exe that ships with the precompiled pymol windows builds, then running your python script with that would be probably be the easiest way). Pete Yun, Precompiled PyMOL builds for Windows run inside their own Python interpreter. Thus, to access PyMOL from Python, you need to run your script from within PyMOL. An easy way to do this is to give your script a .pym extension. Cheers, DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info BLOCKED::mailto:del...@delsci.info Not yet a PyMOL Subscriber, but want to support the project? Email sa...@delsci.com to quote your lab, school, or employer. Thank you for sponsoring this open-source endeavor! -WLD _ From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Li, Yun Sent: Tuesday, January 30, 2007 11:09 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] ImportError: No module named _cmd Hi, I just installed the latest windows binary of PyMol on a PC. I tried to run PyMol from a Python script and run into the following error message: ImportError: No module named _cmd I remember running into the problem before. From somewhere I was able to find a _cmd.dll and solved the problem. But this time I could find a solution. Hope somebody could help me. Yun Li Assistant Professor of Chemistry Delaware Valley College 700 E. Butler Ave., Doylestown, PA 18901 (215) 489-2482 - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users Pete Meyer Fu Lab BMCB grad student Cornell University
Re: [PyMOL] pymol slow on linux PC
Warren, Right now, I would only buy a straight Linux desktop for ideological rather than practical reasons. If you instead buy a Mac Pro, you get the ability to run all three operating systems simultaneously, at native CPU speeds, and on an as-needed basis thanks to virtualization. Right now, Mac is the best way to go for desktop or for laptop. Does cost count as an ideological reason? I wouldn't argue that stereo on proprietary systems generally works with less trouble (at least for the sgi's and alpha's; haven't had a chance to play around with Mac's yet). For example, I am currently emailing from native Outlook 2003 running under Windows XP inside Parallels under Mac OS X Tiger on a Intel-based MacBook Pro, which also happily runs Vista and SUSE. Surreal! Slightly off-topic, but does parallels support OpenGL acceleration? I seem to remember hearing that there was work being done on this, but I'm not up to date on the virtualization stuff (you've definately got me beat for cool virtualization tricks...the only useful thing I've done w\ a vm is a svn server on a usb stick). Pete Pete Meyer Fu Lab BMCB grad student Cornell University
[PyMOL] suse 10.2/amd64 build notes and questions
Well, I've managed to get pymol-0.99rc6 (with ext-0_99rc1) almost working on suse 10.2/amd64 and figured I'd post my work-arounds so that next time someone searches the list archives they won't have to figure them out again (sorry if I'm duplicating things...I wasn't able to find anything); as well as one problem I'm stuck on currently. Building ext-0_99rc1 manually using linux shared lib targets: Numerous tcl/tk compile errors (which appear for static targets as well) which seem to end up in fstatfs argument incompatibilities. Compiling tcl/tk 8.5a5 with --prefix pointing to the ext target directory and removing the tck/tk 8.4.11 targets from build.com resolves this. Building pymol-0.99rc6: Update setup/Rules.make and setup/pymol.com.template for new tcl/tk versions (and python2.4 from ext-0_99 instead of python2.1). After these changes, pymol appears to function normally with the exception of isomesh. Using a pml script that loads a model and map normally on another system (with identical pymol and ext versions) displays the model with no problems; however the map isomesh is not displayed. Any suggestions for where I should start looking to fix this? Thanks, Pete Pete Meyer Fu Lab BMCB grad student Cornell University
Re: [PyMOL] Coloring structure by hydrophobicity
Is there a good way to calculate and color residues by hydrophobicity in pymol? A google search showed only a very simple script that was based entirely on a single-residue lookup table. I'm looking at a set of structure predictions, and it would be nice to easily see that a fold exposes a large patch of hydrophobic surface to solvent. Could you clarify what you're trying to do? I'd think that coloring residues by hydrophobicity, displaying the surface, and looking for whatever your favorite color for hydrophobic is would work fine. Why would a lookup table be inappropriate for what you're trying to do? Pete Pete Meyer Fu Lab BMCB grad student Cornell University
Re: [PyMOL] Installing pymol (again)
Terry, Method 1. - In the most straightforward effort, I download pymol-0_99rc6-src.tgz and run python setup.py install python setup2.py install ./pymol as instructed. The first two commands run fine. The ./pymol gets me Fatal Python error: Interpreter not initialized (version mismatch?) You've probably tried this already, but what happens if you give a full-path to a single python interpreter (aka /usr/local/bin/python24 instead of python below). Assuming that the pymol launch script is using the same python intpreter, and PYTHON_HOME/PYTHONPATH is set correctly, this might clear up the version mismatch (or at least lead to different errors). Method 2. - Can't help you here...maybe one of the OS X experts will chime in. Method 3: - Which freeglut target are you using (freeglut or freeglut-static)? You've probably tried the other build target, but if not it may be worth a shot. The command below looks like it's trying to build a static library while linking to a dynamic/shared one...there's probably a way to do this, but it seems like avoiding it might reduce possible sources of problems. Also, what happens when you set up LDFLAGS so that it tries using -bind_at_load? I tried to build completely from source (something I've done before). When building the ext packages, build.com fails building freeglut: gcc -g -O2 -o CallbackMaker CallbackMaker-CallbackMaker.o ../../../src/.libs/libglut.a -lm -L/usr/X11R6/lib -lGL -lGLU -lXext -lX11 -lXxf86vm /usr/bin/ld: warning multiple definitions of symbol _glPointParameteri /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib(gll_api.o) definition of _glPointParameteri /usr/X11R6/lib/libGL.dylib(dri_dispatch.o) definition of _glPointParameteri /usr/bin/ld: warning multiple definitions of symbol _glPointParameteriv /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib(gll_api.o) definition of _glPointParameteriv /usr/X11R6/lib/libGL.dylib(dri_dispatch.o) definition of _glPointParameteriv /usr/bin/ld: warning suggest use of -bind_at_load, as lazy binding may result in errors or different symbols being used /usr/bin/ld: Undefined symbols: _glutBitmapHelvetica12 _glutBitmap8By13 _glutBitmap9By15 _glutBitmapHelvetica10 _glutBitmapHelvetica18 _glutBitmapTimesRoman10 _glutBitmapTimesRoman24 _glutStrokeMonoRoman _glutStrokeRoman symbol _glPointParameteri used from dynamic library /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib(gll_api.o) not from earlier dynamic library /usr/X11R6/lib/libGL.1.dylib(dri_dispatch.o) symbol _glPointParameteriv used from dynamic library /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib(gll_api.o) not from earlier dynamic library /usr/X11R6/lib/libGL.1.dylib(dri_dispatch.o) Good luck, Pete Pete Meyer Fu Lab BMCB grad student Cornell University
Re: [PyMOL] Changing Fog Color
Albion, Is there any way in Pymol to change the color of the fog? I want dark fog on a white background. As far as I know, fog works by setting transparency based distance from the view center (clipping planes? I'm not sure of the specifics). You might be able to do this in a post-processing step in gimp or photoshop, but I don't think that it could be done in pymol without a lot of trouble. Good luck, Pete Pete Meyer Fu Lab BMCB grad student Cornell University
Re: [PyMOL] APBS and Pymol
Hi, parseInput self.parseLines(file.readlines()) File /usr/local/apbs-0.4.0/tools/manip/psize.py, line 116, in parseLines self.q = self.q + float(words[3]) ValueError: invalid literal for float(): 1.00119.63 Any clues ? It looks like it's reading from a pdb file when it's expecting a pqr file, and that the split statement didn't produce the expected input due to the B factor in the pdb file being too large. Possibly you have to generate a pqr file before setting the grid (I'm not farmilar enough with the apbs-pymol plugin to remember offhand). Good luck, Pete Pete Meyer Fu Lab BMCB grad student Cornell University
Re: [PyMOL] weird crashes inside /home/$USER
i install pymol via svn ebuild (attached). It crashes with a segfault but only if i am inside my home directory. If i am outside, everything works fine. Any ideas what this could be related to? This may be a long-shot, but do you have any python scripts in your home directory? If so, there's a possibility that import statements are getting confused. You could also try temporarilly removing (or renaming) ~/.pymolrc and ~/.python.rc and see if that helps any. It might also be worthwhile to check for any pwd statements in the main pymol launch script. Good luck, Pete Pete Meyer Fu Lab BMCB grad student Cornell University
Re: [PyMOL] how to add labels to a movie script
Hi Yehuda,
I'm doing a movie script and my boss wants me to add labels,
I know how to write the cmd command but i because i'm using cmd.mdo i
can't
add more ' ' then the one in begging and one on the end.
the line with the problem is:
cmd.mdo (691, hide spheres,ERYTHROMYCIN;show cartoon,rna_ery;set
label_size, 30; set label_postion,[ 1.0, 0.0, 1.75000 ]; label
(resi 2041 and name C4*,resi))
what can i write to make the labels appear
If I'm understanding what you're trying to do correctly, you need to
escape the quotations in the label string. In pymol (and python in
general), you can do this by either a backslash before the double quotes
for the label, or enclosing the label string in single quotes.
Since I probably didn't explain that very clearly, your example would
convert to (the quotes around the selection in the label command may not
be needed in this case):
1. cmd.mdo (691, hide spheres,ERYTHROMYCIN;show cartoon,rna_ery;set
label_size, 30; set label_postion,[ 1.0, 0.0, 1.75000 ]; label
(\resi 2041 and name C4*\,\resi\ ))
2. cmd.mdo (691, hide spheres,ERYTHROMYCIN;show cartoon,rna_ery;set
label_size, 30; set label_postion,[ 1.0, 0.0, 1.75000 ]; label
('resi 2041 and name C4*','resi' ))
Alternatively, you could generate your movie as a png series (one png for
each frame), and combine them with convert (part of ImageMagick), ffmpeg,
or mencoder.
Good luck,
Pete
Pete Meyer
Fu Lab
BMCB grad student
Cornell University
Re: [PyMOL] ray trace density
Hi, We are, for the first time, using pymol to make figures that show electron density in addition to the model. No problem making the figure, but when we go to ray-trace the image, pymol crashes. This only seems to happen when electron density is present in the figure. We are using ccp4 style maps and have tried this on our Macs, PCs and Linux boxes, all of which have failed to ray trace the figure. I've seen similar situations for both isomesh and isosurface objects that seemed to be due to the complexity of the scene requiring more memory than available for ray-tracing. Isomesh doesn't require quite as much memory as isosurface, but both are a big increase over just a model. There are a two ways to get around this. The easy one is to increase memory (either physical memory or swap space; although using swap space will dramatically increase ray-tracing time). The other way is to decrease the complixity of your scene, or otherwise reduce the amount of memory pymol needs. If it's a close up, use a map with an extent that just barely covers the physical region you're trying to display. Or calculate the map using fewer gridpoints (which will give you a coarser map, and may only be appropriate for overall views depending on the resolution of the map). One other trick is to make sure that you are not starting from a saved session file (*.pse). Loading a pse uses additional memory (there's more details on this in the list archives), loading the same objects from a pml script will allow for more memory available for ray-tracing. Good luck, Pete Pete Meyer Fu Lab BMCB grad student Cornell University
Re: [PyMOL] Suse 10 and PyMOL crashes
Hi, I have tried 0.99 rc6 and rc7, and the 1.00 beta 01 that is described as for testing on 64-bit linux, all with the same result. PyMOL appears to start normally Good troubleshooting procedureI've had no problems w\ 0.99rc9 on suse 10.0 (single cpu though...so smp/threading issues would be a place to look). One thing you don't mention is if you're using the binary or source version (trying both shouldn't make a difference, but is straightfoward enough that it's worth checking). But as soon any object (either ccp4 map or coordinates) is read in, the whole machine irretrievably crashes. Could you provide more details on how it crashes (exceptions, core dumps, x-windows freeze, machine catches fire)? Any suggestions would be much appreciated as we are stumped. We are about to try different OpenGL / nvidia driver combinations but I thought I'd see if anyone else had had similar experiences so far. I was having sporadic issues a few months back with pymol sporadically freezing the x-server (and ending up with a process that would refuse to stop, even when killed by root); is this what you mean by the whole machine crashing? If so, check the list archive for details (the short version is that it could be caused by issues w\ binary graphics card drivers, and a possible fix is to use the open source drivers). Good luck, Pete Pete Meyer Fu Lab BMCB grad student Cornell University
Re: [PyMOL] Suse 10 and PyMOL crashes
Thanks for the reply. Irretrievably crashing means that everything stops dead. The screen freezes, mouse/keyboard become unresponsive, the machine becomes unreachable (via ssh or even ping) from other workstations. Background processes instantaneously halt. A 'proper' crash in other words! It does sound like an impressive crash. One things that sometimes works for me in cases like that is to have an open ssh session running from another machine running top (you've probably tried this already). It won't fix anything, but occaisonally helps figure out what the problem is. One option would be to try running through a stack of live-cd's of different distributions (boot, try to launch pymol and see if it freezes, and repeat). Again, this is more to figure out where the problem is than to fix it. Most likely it's something with the graphics drivers, but if chimera works alright then I'd keep an open mind as to what could be causing the problem (presumably they're both using the same opengl and x-windows drivers). Your best bet is probably to try out the different driver versions you were talking about (my normal approach would be to keep recompiling with as many options disabled as possible...no smp, multi-threading, shared libraries; but that would take some patience when the system freezes every time you get it wrong). Good luck, Pete Pete Meyer Fu Lab BMCB grad student Cornell University
Re: [PyMOL] Map Oddities
Hi, Based on your mapman info, it looks like this map is centered on the origin of your unit cell. One possibly explaination is that your model is in the center of the unit cell, and that Chimera is using symmetry to generate density around the region you are centered on (I have never used Chimera, so I could be wrong about this...but this behavior is fairly common). Pymol (as far as I know) does not currently do symmetry expansion of the map; so you'd need to use your favorite map manipulation program to extract a region covering your model. Pete I am experiencing a strange phenomenon when I open maps in Pymol. I have a Chimera session with a PDB file docked into a CCP4 map. If I display the unit cell in Chimera the density is centered in the unit cell. If I open the exact same map and PDB file in Pymol, the model and map are no longer in agreement, and when I display the unit cell in Pymol the map is situated at the corner of the unit cell rather than in the center. I have found that if I translate the PDB model by _roughly_ half the unit cell length (in all dimensions) I arrive at where it is normally situated in Chimera. But even this is not exact, and it appears to be half the unit cell dimensions + ~10A. I am just trying to understand how this map is being interpreted by Pymol and what known ambiguities or assumptions are made when it is loaded that might cause this behavior. Thanks Albion Here is the maps info from MAPMAN Grid= 969696 Origin =-48 -48 -48 Extent = 969696 Cell=213.423 213.423 213.42390.00090.000 90.000 UVW = 1 2 3 Spcgrp = 1 Nr of points = 884736 Density min = -6.915E-01 Max = 2.397E+00 Average = 7.247E-11 Sigma= 2.290E-01 Variance= 5.243E-02 Mappage Prod= 8.257E+01 Plus = 57 Dyn. range = -6.903E-01 To = 2.398E+00 Cell vol. = 9.721E+06 Voxel vol. = 1.099E+01 Grid vol. = 9.721E+06 %Cell vol. = 100.00 Origin frac = -0.5 -0.5 -0.5 Origin Cart = -106.712 -106.712 -106.712 Top frac=0.48958 0.48958 0.48958 Top Cart=104.488 104.488 104.488 Spacing = 2.223 2.223 2.223 Top = 474747 Changes = F - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys -- and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users Pete Meyer Fu Lab BMCB grad student Cornell University
Re: [PyMOL] wrong symmetry for 2mol/AU
Hi, I want to align two structures (worked fine in pymol) then generate symmetry related molecules for each to compare crystal packing contacts (did not). Both structures are for same dna each with different ligand. One structure has one molecules/AU (generates symmetry fine). The other 2/AU (does not work; messed up symmetry whereby half of original is superimposed by half of symmetry related). The latter generates symmetry fine in coot. Problem with coot: can't align. Any ideas? If you align before generating symmetry-mates in your 2/AU structure, then you may be getting incorrect generated molecules, because the coordinates have changed but your symmetry operators have not (this is probably something you're already aware of, and are avoiding, but it could be an issue). On the other hand, you could have problems if you generate symmetry-mates before alignment, because you presumably only want to align the original models, not the packing mates (which again, you're probably aware of). One way to work around this would be to get the transformation matrix for the alignment of the original models, generate unaligned symmetry-mates in coot (or pdbset, or another program that doesn't give you problems...I havne't had any problems w\ symexp in pymol, but you may be using a different spacegroup), and apply the alignment matrix to the symmetry-mates. Good luck, Pete Pete Meyer Fu Lab BMCB grad student Cornell University
Re: [PyMOL] pymol crashes - segmentation fault - PLEASE HELP
Hi Noel, Which version of gcc are you using? A quick check of google for the unterminated argument list in macro error makes it look like that could be an issues (on my systems, it works for gcc-3.4.5 and 4.0.2; but that's using make instead of python distutils). It looks to me like a c preprocessor issue, rather than something in Crystal.c; specifically dealing with the PRINTF macro in Feedback.h (although it does seem a little strange seeing special characters in a logfile...). You could try 1. checking that you've got all of your development packages installed (you probably do, but it never hurts to check); 2. upgrading (or downgrading) gcc; or 3. customize setup/rules.generic for your system, and build with make (personal preference is for building ext dependencies from ext-0_99rc1-src.tgz as well, but this shouldn't make a difference). Good luck, Pete Hi all, As suggested by Peter, I tried compiling PyMol from src (pymol-0_99rc6-src.tgz). Unfortunately it fell over :( Attached is the output. The error occurs in layer0/Crystal.c. I've look at the file in vim and there does not seem to be anything untowards (weird characters etc...) in it. I tried to compile from pymol-0_99rc1-src.tgz and got the same error. Any pointers?? Many thanks Noel snip Pete Meyer Fu Lab BMCB grad student Cornell University
Re: [PyMOL] Paths to loaded objects
Ron, I'm not sure I fully understand your suggestion. It sounds to me like what you're saying is that I should add code (e.g. a dictionary) to the importing.py load() function which saves the file information of objects as they're loaded. But then instead of just distributing my plugin, I would have to get users to change their PyMOL source, as well (which I'm not willing to do). Am I understanding correctly? Well, I may have been misunderstanding you...I'd though you mentioned you were using a gui to load the pdb files, which would be the natural place to add additional code. I'd assumed the gui you were talking about was specific to your plugin (if this isn't the case, then my suggestion doesn't help that much). Any other ways around this problem? You could try turning on logging, and scan through the logfile looking for load events (on my system, using the standard gui menus to open a pdb, this stores the full path to the input pdb file; although it does not associate it with the object name). Of course then you're stuck with the problem of getting the name/path of the logfile... Good luck, Pete Pete Meyer Fu Lab BMCB grad student Cornell University
Re: [PyMOL] Paths to loaded objects
Hi, I'm working on a plugin that reads information appended to the end of PDB files to draw CGO objects. Right now, I have the user specify the filesystem path to the currently loaded objects through the plugin GUI so that I know where to go to find the file. For one object, this isn't so bad. But if users load multiple objects that are in different directories, I will have to change the GUI so that the user has to specify the path to each object loaded. This kind of situation would quickly become tedious. Does PyMOL store the paths for objects that are loaded somewhere? I know I can get the current working directory using getcwd(), so I'm hoping there's a way to get the path to the loaded objects as well. I don't know of a way to get file information from a pymol object, but you could work around this by using a python dictionary (when the pdb file is loaded, store the full path to the file in a dictionary using the pymol object name as the key). Of course the fact that I don't know how to get the full path from a pymol object doesn't mean that there isn't a way... Good luck, Pete Pete Meyer Fu Lab BMCB grad student Cornell University
Re: [PyMOL] ObjectMapLoadDXFile-Error: Unable to open file!
Hi, 'D:\Program' is not recognized as an internal or external command, operable program or batch file. ObjectMapLoadDXFile-Error: Unable to open file! - something wrong in assigning a correct path name. How to fix this error? I appreciate for your valuable suggestions to overcome this problem. You're correct about the source of the problem...pymol isn't happy with the spaces in the filenames. The easiest way to fix this would be to use a path without spaces (aka d:\workspace), or a shortcut to that (have d:\workspace as a shortcut to your real working directory). I suspect both of these would require admin permissions (to write to top level directories, but I'm not completely farmiliar with the windows file permissions or user permissions. If you don't have admin access, then things get more complicated...You'd need to quote the full path, and escape the quotation marks in the path. Or wait for someone more experience with window to chime in with an easier solution... Hope this helps, Pete -B. Padmanabhan. Email: pa...@gsc.riken.jp- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users Pete Meyer Fu Lab BMCB grad student Cornell University
Re: [PyMOL] PyMol question?
The easiest way I'm aware of to do this would be to use the ccp4 program pdbset, but there are numerous other ways/programs that will do this (if pymol has this capacity, I'm not aware of it; but someone else will correct me). Pete snip I've been looking through the PyMol reference and wiki page and I can't find a command for moving a molecule through a matrix, I would like to move one pdb onto the other using the info below. Is there such a command? ## MATRICES: UX+T is the least-squares superimposition of STRID2 (X) onto STRID1 NR. STRID1 STRID2 U(.,1)U(.,2)U(., 3) T(.) 1: 9506-A 1risU(1,.) -0.230692 -0.010007 -0.972975 50.701385 1: 9506-A 1risU(2,.) 0.443459 0.888979 -0.114287 31.716473 1: 9506-A 1risU(3,.) 0.866098 -0.457839 -0.200643 26.479412 Pete Meyer Fu Lab BMCB grad student Cornell University
Re: [PyMOL] MacPyMol plug-ins
2) filelist:
snip
get a kind of temporary script which would be run on each file in the list
when you opened it. A kind of frozen view (or a curried one?).
Maybe I should just make it. Then I wouldn't have to explain the idea.
Ok, I was confused on what you meant before. I've been in similar
situations, if you are going to try something like this you might want to
take a look at the script I use (attached on the off chance you don't have
something similar). It'll probably need some customization, seeing as I
use it for checking search results quickly (and don't deal w\ any gui
stuff).
4) sec struc elem:
I'm two for two on misunderstanding you today apparently...Thanks for
clearing it up.
Pete
Pete Meyer
Fu Lab
BMCB grad student
Cornell Universityfrom pymol import cmd
class ModelHolder:
#loop over pdb files named base_##.pdb (from ##=0 to 99)
#to use: run ModelHolder.py ; m=ModelHolder('base')
def __init__(self,base):
self.base=base
self.pos=0
self.show()
def makefname(self):
fname=self.name()+'.pdb'
return fname
def name(self):
name=self.base+'_'+str(self.pos)
return name
def clear(self):
name=self.name()
cmd.delete(name)
def show(self):
n=self.name()
cmd.load(self.makefname(),n)
cmd.hide('everything',n)
cmd.show('ribbon',n)
#color red for even or cyan for odd pos
if self.pos%2==0: cmd.color('red',n)
else: cmd.color('cyan',n)
def next(self):
self.clear()
self.pos=self.pos+1
if self.pos99:
self.pos=0
cmd.bg_color('grey80')
self.show()
def last(self):
self.clear()
self.pos=self.pos-1
if self.pos0:
self.pos=99
cmd.bg_color('grey80')
self.show()
def go(self,n):
pos=self.pos
self.clear()
if (n=0) and ( n=99):
self.pos=n
self.show()
else:
self.show()
Re: [PyMOL] That _cmd thing
which I already have anyway, and I want to have pymol for multiple
flavours
of UNIX in the same directory on a shared network file system if possible.
Now I'm hitting that famous bit:
$ ./pymol
Traceback (most recent call last):
File /{my PYMOL_PATH}/modules/pymol/__init__.py, line 109, in ?
import pymol
File /{my PYMOL_PATH}/modules/pymol/__init__.py, line 353, in ?
import _cmd
ImportError: No module named _cmd
Am I trying something that can't be accomplished?
Interesting idea...I don't see any reason it couldn't be done.
You'll probably have to build the c pymol modules seperately for each
system, and add a switch based on OS in the pymol launch script so that
PYMOL_PATH points to the correct directories for each unix version (as
well as the correct path to python, if that varies between your unix
flavors). It might also be necessary to check that PYMOL_PATH is getting
into sys.path correctly in __init__.py.
Hope this helps,
Pete
Pete Meyer
Fu Lab
BMCB grad student
Cornell University
RE: [PyMOL] pse/session files increase memory usage?
Warren, I did a bit of testing (memory figures from top VIRT column, after pymol had finished executing commands and was responsive to input): pymol set.pml (316MB) save test.pse (537MB) reinitialize ; load test.pse (539MB after load) reinitialize ; load test.pse (540MB after load) reinitialize ; load test.pse (542MB after load) quit pymol test.pse (532MB) It looks to me like there's a small memory leak when reloading the same session file, but that this is fairly minor compared to the difference between loading objects from a script and loading from a session file. Pete Pete, It is a PyMOL fact of life that session files take more memory, because all state information must transient exist in both Python and C while the session is being loading. However, we should get that memory back after the session is fully loaded. If not, then you may be right about a memory leak. A good way to test this is to see what happens if you load the same session over and over again without restarting PyMOL. Does memory usage consistently increase or does it level off? The most likely cause of this would be PyMOL failing to decrement the reference counts on certain session data. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-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 Peter Adrian Meyer Sent: Tuesday, April 25, 2006 3:15 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] pse/session files increase memory usage? Hi all, For complex scenes, I've noticed that pymol 0.99rc6 (with ext0.99rc1) on linux appears to use more memory when started from a pse file than it does when loading the models/maps manually or from a pml script (based on the fact that I get out of memory errors during ray-tracing after starting from a pse, but not after starting from pml scripts). The easy work-around is to use pml scripts instead of pse files, but I was curious if anyone else had run into this (or, for that matter if it's a known issue...my best guess would be that there's a memory leak somewhere, or that the configuration flags I used to build python were causing problems). Pete Pete Meyer Fu Lab BMCB grad student Cornell University --- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057; dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users Pete Meyer Fu Lab BMCB grad student Cornell University
Re: [PyMOL] a scaling question
Fei, The easiest way would be to use get_view/set_view. 1. Move your first frame pdb around until you're happy with the view 2. type get_view (pymol viewer window, or pymol gui window), and save the output in a new text file (I'd call it view.pml, but that's just me) 3. Load all of your frames in a script (which you're probably doing already), change load frame2.pdb to load frame2.pdb ; @view.pml for all of your frames (or change whatever loop structure you're using). This way all of your frames will be in the same scale, as well as orientation (which may not be what you're looking for). If you only want to control scale (not orientation), then you could probably work something up that only takes the scale parameters out of the orientation matrix. Hope this helps, Pete Hi!: I met a scaling problem. I created many pdb files along one trajectory of DNA movement. I loaded each pdb file in pymol to create a picture, that is, one frame of the trajectory. Pymol shows each molecule in an optimal size automatically according the general shape of the molecular. The shape of the molecule along trajectory kept changing so that the size of the molecule also kept changing. When I connected all the time frames together, I saw the funny effect that the molecule was jumping back and forth. How can I put the molecule in the different time frames in exactly the same size? Thanks! Fei --- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users Pete Meyer Fu Lab BMCB grad student Cornell University
Re: [PyMOL] Default directory and browsing
There are two ways to do this. Either start pymol from the command line
in your working directory, or use .pymolrc to automatically change to this
directory (something like os.chdir('~/working_directory') should do it).
Pete
Would it be possible to add setting to pymol for a default working
directory?
Along with this, perhaps a setting that, by default, ignores hidden
directories? As it now stands, whenever I fire up pymol on linux, I
have
to
navigate down a huge list of hidden directories to find the directory, then
the subdirectory, within which my pdbs and pses reside. Pymol doesn't
remember this so every time I start it, it is the same thing all over
again.
Pete Meyer
Fu Lab
BMCB grad student
Cornell University
Re: [PyMOL] PymOl INstallation PRoblems
Hi Nick, This sounds vaguely similar to the msvcr71.dll issues that were recently discussed on the list (searching the list archives will give you more info on this, but the quick fix is to search the hd for msvcr71.dll and copy it to the pymol install directory). If that doesn't resolve the problem, then some more details might be useful. Which version of pymol are you running (I'm assuming one of the recent win32 binary distributions)? Are there any error messages, and if so what do they say? Are you starting-up pymol by clicking the start menu icon (if so, try opening a dos window, going to the pymol directory, and starting from the dos prompt...this probably won't fix the problem, but will probably give more detailed error messages)? The quickest resolution (assuming msvcr71.dll isn't the problem) might be to install a slightly older version. Hope this helps, Pete Hi PyWorld, I have been trying to help a friend install PyMol on her laptop (Sony Vaio) that has Windows XP Home Edition. The installation runs smooth with no problem at all. But once we try to open the program, its seems to stall, then crashes, and Windows XP asks if we would like to send a error report??? I have searched the archives and online for answers, but with no luck. Therefore, I present to you, my PyFriends, our dilemma and seek a remedy to our problem. I give you my word, my good friends, that upon finding the solution, I will not take all the credit for solving this mysteryjust kidding, credit will be duly noted. Thanks in advance for any and all help! Cheers, Nick Pete Meyer Fu Lab BMCB grad student Cornell University
Re: [PyMOL] manual update
this little thread points nicely to the major problem that I have quite often with PyMol: it is a really powerful program, but the documentation is somewhere scattered between various incomplete sources (manual, reference list, wiki, bulletin board, user home pages, ...). This makes it very difficult for the average user like me to make full use of PyMol's capabilities. I would _really_ prefer to have a good and up-to-date documentation available, at least for the last official version, rather than more and more improvements with poor documentation. In my experience, pymol's build in help system is a very good guide. Most of the questions I get from local users, as well as my own questions, can be resolved that way. When that fails, it's generally because I'm trying to do something that isn't directly supported (so I fall back on grep -nir $whatever in the source directory or the mailing list/list archives). I completely agree that having good documentation is important; but I haven't found pymol to be significantly lacking in that regard. I wouldn't mind more comments in the source code (particularly the underlying c modules), but that's probably due to lack of experience with 3d graphics programming on my part than anything else. just my opinion... Pete Pete Meyer Fu Lab BMCB grad student Cornell University
[PyMOL] sporadic pymol/X-server freezes?
Hi everyone, Has anyone else run into cases where pymol will freeze the X-server (pymol doesn't repond to mouse or keyboard input; keyboard non-responsive to caps-lock on/off)? The system is still stable, I'm able to login remotely and see that pymol is running at 100% CPU. Killing pymol results in xorg running at 100% CPU (killing the xorg process as root doesn't do anything). I've only seen this while looking at several maps/masks (but that's most of what I use pymol for, so I'm not sure if that's the cause). I've seen this error on both suse 10.0 and kubuntu (3.10? whatever the lastest apt-get dist upgrade got me; two different machines) using source builds of pymol-0.98, and 0.99rc6 with ext-0.98,ext-0.99rc6, and ext-0.95. Any suggestions on how to fix this (or get debugging information out of pymol to narrow down the problem)? Thanks, Pete Pete Meyer Fu Lab BMCB grad student Cornell University
RE: [PyMOL] sporadic pymol/X-server freezes?
Warren, Thanks for getting back to me so quickly. It's good to hear that this problem has been seen before (it's been one of those weeks for strange computer issues). I guess it shouldn't supprise me that there are issues with proprietary OpenGL on linux (FYI the two machines I've seen this on are using ATI and intel graphics cards). I'll try out the options you mentioned. Your idea about known-working (and non-working) combinations of hardware seems like a very good thing to do. Pete Pete, We have been suffering this same exact symptom with our nVidia-base 64-bit RHEL workstation for over a year. I have spent enough time troubleshooting the issue to have convinced myself that the problem isn't PyMOL -- it is an inability of certain combinations of hardware, Linux kernels, and proprietary OpenGL drivers to handle the vast quantity of immediate mode rendering geometry that PyMOL generates. It seems to be either a sporadic buffer overflow or a race condition within the kernel layer. The proprietary nature of the OpenGL drivers prevents anyone other than the hardware vendor from being able to actually understand and solve the problem. Plus, the problem is sporadic -- most of the time everything works fine, but sometimes PyMOL hangs, sometimes all of X11 freezes, and sometimes the whole system comes crashing down. The intractable nature of these Linux stability problems is one of the primary reasons why I recommend Mac OS X over Linux for unix-based PyMOL visualization. Note that the settings nvidia_bugs and use_display_lists may reduce the frequency of the problem on your system. Other than that, my suggestion would be to try different Linux kernels and OpenGL driver versions. The combinatorial matrix of possibilities is huge, but maybe we should create a table on the Wiki for people to post working and non-working combinations of Linux kernels, cpu and graphics hardware, and opengl drivers? That's how we used to do things in the old days. I suspect only 5-10% of configurations are truly unworkable, and once enough data is collected from enough people, meaningful patterns would likely emerge. Cheers Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-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 Peter Adrian Meyer Sent: Thursday, March 23, 2006 9:32 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] sporadic pymol/X-server freezes? Hi everyone, Has anyone else run into cases where pymol will freeze the X-server (pymol doesn't repond to mouse or keyboard input; keyboard non-responsive to caps-lock on/off)? The system is still stable, I'm able to login remotely and see that pymol is running at 100% CPU. Killing pymol results in xorg running at 100% CPU (killing the xorg process as root doesn't do anything). I've only seen this while looking at several maps/masks (but that's most of what I use pymol for, so I'm not sure if that's the cause). I've seen this error on both suse 10.0 and kubuntu (3.10? whatever the lastest apt-get dist upgrade got me; two different machines) using source builds of pymol-0.98, and 0.99rc6 with ext-0.98,ext-0.99rc6, and ext-0.95. Any suggestions on how to fix this (or get debugging information out of pymol to narrow down the problem)? Thanks, Pete Pete Meyer Fu Lab BMCB grad student Cornell University --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnkkid=110944bid=241720; dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users Pete Meyer Fu Lab BMCB grad student Cornell University
Re: [PyMOL] sporadic pymol/X-server freezes?
same here, how big are your map files in MB, how much ram and swap space do you have? ~5MB/map, 512MB RAM, ~2GB swap. I'd expect a segfault (or an exception at least) if I was overloading the memory/swap, and CPU would drop if it was running out of physical RAM and swapping too much. I haven't the slightest clue. Does this happen immediately after loading the map or while rotating or what? But I can tell you that I'm running gentoo, w/vanilla sources 2.6.15 running in x86_64 mode (straight from kernel.org), 1.0.8178 nvidia drivers on a quadro4 980xgl video card. No consistent pattern. Both machines are x86, non-nvidia graphics cards (which probably isn't helping). But, score at least one working setup (yours) as a fully functional combination. You might try as was suggested to upgrade your kernel. You can get 2.6.16 from kernel.org, copy your current .config into the root of the source directory, run make oldconfig, hit enter a bunch of times, then compile the kernel with make make modules_install. You will have to recompile the nvidia drivers for the new kernel too. It might come to that, but it'll be a last resort. I'm reluctant to make major modifications to a system that I'm using to do research in the middle of a project (I've had 2 independent backups fail me at the same time). Particularly for a problem that isn't predictably reproducable, so I wouldn't know if an upgraded kernel/module had actually fixed the problem or not (it could be done w\ testing livecd distributions or within a vm, or trying to get a debug build of pymol talking happily to a debugger, but at a certain point it becomes more trouble to track down and fix the bug than it does to deal with it). Thanks for the suggestions, Pete Pete Meyer Fu Lab BMCB grad student Cornell University
Re: [PyMOL] manipulate standard error ?
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 ? Create a new script (pymol.bash) containing these lines: #!/usr/bin/env bash pymol.com 2/dev/null This could probably be done within pymol.com itself as well, but someone else will have to point out how to do that (aka I don't know how). As a side question, why have a csh script with a .com extension? Pete Pete Meyer Fu Lab BMCB grad student Cornell University
[PyMOL] load_png doesn't support alpha (transparency)?
Hi all, I noticed today that when reading a png file using load_png, the alpha channel does not appear to be respected (regions of the png that should be transparent are not transparent but show up as white). Does anyone know if this by design, a bug, or something I'm doing incorrectly setting my alpha channel in the png file? If you're wondering why I'm trying to do this; I'm attempting to generate two aligned figures from models that are in crystallographic origins. The end goal is to have maps in each of these figures also aligned for comparison, so I can't just transform the models to get them aligned (use of the align command is out for similar reasons; unless there's a way to get the transformation matrix generated by model alignment and apply it to a map that I'm not aware of). Thanks, Pete Pete Meyer Fu Lab BMCB grad student Cornell University
Re: [PyMOL] installation problem on XP laptop
Daniel, I just tried to install the latest version of Pymol on a XP laptop. The installation completes but when I try to launch the program I get Are you trying the latest release version or one of the betas? In any event, it might be possible to install an older version (although this may not work, if it fails in the same way it could help you to isolate the problem). This application has failed to start because MSVCR71.dll was not found. MSVCR71.dll appears to a a windows c++ runtime library (probably required for some c stuff, as last time I checked there wasn't any c++ in pymol). Either the file isn't present (try searching for it), or the executable can't find this (on unix, you'd fix this with LD_LIBRARY_PATH... for windows, I believe this is done by registering the dll ; google or msdn should have more information on this. If I rememeber correctly, regsvr MSVCR77.dll should work, but as always check things carefully before messing around with the windows registry). Hope this helps (at least until somebody with more experience with windows than me can chime in). Pete Pete Meyer Fu Lab BMCB grad student Cornell University
[PyMOL] reinitialize fails to clear PyMOL Viewer
Hi all, I've run into a small glitch that I was wondering if anyone else had seen (or knew of a way to fix). At somewhat unpredicatable intervals, the reinitialize command doesn't actually clear the viewer display (objects show as deleted, but are still visible). Any ideas? Pete Pete Meyer Fu Lab BMCB grad student Cornell University
Re: [PyMOL] Saving Images
Hi everyone, Each time I try to save images, Pymol writes 640x480 pixel image to the file. I wonder if there is a way to save images (png format) other than 640X480 pixel that is default. Any help will be appreciated. Thanks. Images are saved as either the size of the viewer window, or the ray traced size. The easiest way to get a larger image is to maximize the viewer window, and then save. To get an arbritray size, use the ray-tracer (ray 1024,768 ; png BigImage.png). Pete Pete Meyer Fu Lab BMCB grad student Cornell University
Re: [PyMOL] saving multiple object in one pdb file
My question is: how to save multiple objects from pymol as one nice pdb file, for instance with each object with different chain name? alter SymgenObject,chain 'X' and repeat as needed for all objects (changing the chain as needed). Then use all of your objects as the selection for save (aka save AllObjects.pdb,(original,sym1,sym2) ) Pete Pete Meyer Fu Lab BMCB grad student Cornell University
Re: [PyMOL] Viewing cavities?
Hi Marcus, The surface rendering in PyMOL is quite nice, but I cannot separate the branches of the surface. That is, I would like to view a large cavity inside of a protein independently from the outer, solvent accessible surface. Is anyone aware of a means to do this? The easiest way I'm aware of is to select the residues involved on the surface of your cavity, and then do show surface, [selection]. Pete Pete Meyer Fu Lab BMCB grad student Cornell University
[PyMOL] displaying solvent mask?
Hi pymol users, Has anyone had any sucess in loading and displaying solvent masks in pymol? Checking the list archives and wiki didn't result in anything; neither did google. help mask within pymol seems to be talking about selection stuff. It seems like the best way would be to modify the ccp4 map loading/normalizing stuff so that it deals with the mask maptype; but if there's an easier way I'd greatly appreciate it if someone could let me know. Thanks, Pete Pete Meyer Fu Lab BMCB grad student Cornell University
Re: [PyMOL] displaying solvent mask? (solution)
Should anyone else ever need to try this, there turns out to be a very easy way to do it, assuming that your solvent mask is in ccp4 mask format. 1. use mapmask mskin $MASKFILE mapout $CONVERTED_FILE 2. load $CONVERTED_FILE into pymol, treating it as a normal map. Contouring at 1.0 will display the solvent mask correctly. Of course, it would be better if this had occured to me before spending a few hours in the depths of layer2/ObjectMask.c ; but that's Mondays for you. Pete Pete Meyer Fu Lab BMCB grad student Cornell University
Re: [PyMOL] how to increase the box size of electron density map
hi, In pymol how to increase the box size of electron density map. By default it is opening with an square box of some value. I want to increase the size. How to do that? Thank you for your help in advance! sidhu By default, pymol shows the entire map range. The easiest way to increase this is to increase the range that your map covers (how you do this will depend on which programs you used to calculate your map. There may be a way to use your symmetry operators to expand the map range within pymol, but if so I'm not farmiliar with it. Pete Pete Meyer Fu Lab BMCB grad student Cornell University
Re: [PyMOL] question about ray after alter and rebuild
multiple structura alignment. I pointed out three structures for further processing within all 12 structures. However, when I try to ray the structural resolution (only 3 of all 12 structures) to 2000x2000 with 'ray 2000, 2000', I always received a low resolution (as screen resolution only) result. How could I do? Thanks a lot! Pymol can't display a ray-traced image to higher resolution than your screen can show, but it can write it to a png file at that resolution (I'm assuming you're talking about pixel resolution, not diffraction resolution here). ray 2000,2000 ; png HighRes.png Pete Pete Meyer Fu Lab BMCB grad student Cornell University
Re: [PyMOL] question about ray after alter and rebuild
Or you can dump to povray and render at whatever resolution you want, but the image will not resemble exactly what is seen in the pymol viewer window. I've noticed problems with the clipping planes (z axis) whenever I've tried this. Specifically, the near clipping plane is apparently not respected in pov-ray conversion (particularly for maps/isomeshes). I don't know if this has been fixed or not as of yet, but I wasn't able to find a way to work around this. Your milage may vary... Pete Pete Meyer Fu Lab BMCB grad student Cornell University
Re: [PyMOL] Using a seperate python installation
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\\' If I'm understanding you correctly, you'd like to use a currently installed python with a newer version of pymol. It sounds like you may need to re-install the new pymol (possibly rebuild, with the new python paths (include/lib) set to your system version of python). There's always the standard sys.path workaround (start new version of pymol, add system python lib directory to sys.path, import your other modules and check them to make sure they still give the same results)...but that may cause version conflicts between pymol/system python module imports (it might not too, I've never tried it). Hopefully somebody more farmiliar (sp?) with python/pymol on windows (I'm assuming you're using that from the c:\python24 reference) has a better solution than this. Pete Pete Meyer Fu Lab BMCB grad student Cornell University
Re: [PyMOL] From scenes to movies?
Hi Dirk, a protein structure. Is there a way in PyMOL to export the individual frames for a movie from scenes? If not, this would be my most desired missing feature in PyMOL! Yes. What I do is to use a script to step through each frame of the movie (rotation by 1 degree, zoom in slightly, change transparency slightly, etc), ray-trace (optional), and dump the png. From there, ffmpeg will combine all of these into a single movie file (memcoder is supposed to do this as well). I'm not entirely sure what you mean by frames from scenes, though. Hope this helps, Pete Pete Meyer Fu Lab BMCB grad student Cornell University
Re: [PyMOL] cctbx woe's, continued
Simon,
I then tried to follow Peter Myers instructions by adding the cctbx
Meyer, not Myers (not that it matters much).
directory to the sys.path, however as I have two directories called
cctbx_build and cctbx_sources was not sure which should be added?
Probably cctbx_build. If in doubt, add both. It'll be a directory with
*.pyd, *.dll, *.py, or *.pyc files in it.
Incidently this issue with getting cctbx running properly has been
plaguing everyone in my lab for the last year. In the past we have just
jumped to alternative software packages. Is there any way cctbx can be
packaged with a pymol installation in the same way as python has been?
Other peoples experience may vary, but building/packaging software on/for
windows is problematic. This is particularly the case for software with
multiple dependencies (aka if it can't be done within a single IDE,
windows makes you jump through lots of hoops to get things working).
**
Since I didn't foward my last response to the list (oops), here's the
short version. ImportError means that the python interpeter can't find
the needed modules. Adding the directories these modules are installed in
to the system path lets the intepreter know where they are, and allows
them to be imported. To add directories to the system path, at the pymol
prompt:
sys.path.append('c:\cctbx_build')
sys.path.append('c:\cctbx_sources')
The sources line may not be (probably isn't needed). Both assume that
cctbx is installed in the listed directories (which probably isn't, but I
haven't set up a windows cctbx install).
Possibly this could be added to the pymolrc file (if it resolves the
problem). This is more a work-around than a fix.
Pete
Pete Meyer
Fu Lab
BMCB grad student
Cornell University
[PyMOL] Java extension? (was question about _cmd.pyd)
Why don't we? Because we do most PyMOL development on Mac OS and Linux, using free or open-source tools, such as GCC, GDB, and Apple's wonderful XCode, with CHUD and OpenGL profilers. Even on Windows, we are now bypassing Microsoft Visual Tools altogether and using MingW and GCC to build our native Java extension. native Java extension? Is this something new, something I didn't notice before, or a typo? Pete Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-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 wenming hu Sent: Wednesday, August 24, 2005 6:29 PM To: Warren DeLano; pymol-users@lists.sourceforge.net Subject: [PyMOL] Reï¼ RE: [PyMOL] question about _cmd.pyd I see. thank you for your answer. and i'm wondering, how do u develop python modules like _cmd.pyd? only via setup.py, and type python setup.py build to compile it? how do u debug it on the procudure of development? for me, it's not easy to develop _cmd.pyd only via setup.py script, i think, there must have some other way to debug python extend modules. thank you. Warren DeLano war...@delsci.com Wen, The only form of end-user PyMOL compilation we support on Windows is via Python's distutils facility. Assuming that your system paths are set up correctly, distutils compilations will work fine with msvc6 -- no Makefile is required. Your own c/c++ code should be built as a standalone DLL -- separate from _cmd.*, and you should use the Python interpreter to bring all of the native components together at runtime. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com DO YOU YAHOO!? é èå è´¹Gé®ç®±ï¼No.1çé²æ¯é²åå¾è¶ 大é®ç®± http://cn.mail.yahoo.com Pete Meyer Fu Lab BMCB grad student Cornell University
[PyMOL] Building pymol for Tru64.
Hi All,
In case anyone was interested, I was recently able to install pymol on
tru64 and figured I'd post how I did it.
This isn't as straightfoward as a linux build, but most of the difficulty
comes from building the extensions. For ext-0.95 and pymol-0.97, follow
the generic instructions, except for the following changes.
1. In build.com, add setenv PYTHONHOME ${BUILD} before the EXT_TARGETS line.
2. Use 2 EXT_TARGETS lines: tcl tk zlib python ; numpy pmw png-irix
glut-linux
3. Change setenv MAKE make to setenv MAKE gmake
4. Uncomment the tcl tk zlib python and run build.com
5. Change the installed version of pyconfig.h to define XOPEN 400.
6. Change src/patches/libpng/makefile.sgi to use the correct version of
zlib (zlib-1.2.1 is included in ext-0.95, but this makefile tries to use
zlib-1.1.4).
7. Comment out the first EXT_TARGETS line in build.com, and uncomment the
second.
8. run build.com again to build final set of dependencies. That's it for
ext.
9. In Rules.make, change CCOPT2 to remove gcc specific optimizations
(don't use -funroll-loops -fomit-frame-pointer).
And that's it. This is more of a work-around than an actual fix; probably
the changes to pyconfig.h should be done during python configuration, but
I wasn't able to make that work (for that matter, I'm not exactly clear on
what XOPEN does, but leaving it at the configure-generated value of 600
causes problems with sys/time.h and sys/stat.h). The zlib version for
libpng-sgi appears to be a bug in this ext version.
Pete
Pete Meyer
Fu Lab
BMCB grad student
Cornell University
