[ccp4bb] Generate high resolution pirctures in pymol
Hi all, Can somebody please help me to generate high resolution movie files for secondary structure of proteins? After I ray a model with high resolution in pymol and then save it as movie frames, the high resolution and ray seem lost. I have tried the command likes ray 2000,2000 and it does work for a single frame, but can anybody tell me how it could be extended to say 40 or 80 frames of a movie? Your suggestions are highly appreciated. Thanks in advance!
Re: [ccp4bb] Generate high resolution pirctures in pymol
Hi, There are detailed instructions on the net but as far as I can remember all you need before starting to generate the frames is the following command: set ray_trace_frames, 1 Also, why do you need such a high resolution. I know that computers have a lot of power to burn but if you want to use animation in the presentation later on say 320x240 is more then enough! Remember that nowadays beamers seldom can do more then 1024x768. Andrzej yang li wrote: Hi all, Can somebody please help me to generate high resolution movie files for secondary structure of proteins? After I ray a model with high resolution in pymol and then save it as movie frames, the high resolution and ray seem lost. I have tried the command likes ray 2000,2000 and it does work for a single frame, but can anybody tell me how it could be extended to say 40 or 80 frames of a movie? Your suggestions are highly appreciated. Thanks in advance!
Re: [ccp4bb] Progresss with Stereo 3D under Mac OS X Leopard
Hi Warren CCP4ers, first of all, it is great that at least one application, MacPyMOL, works again in stereo under Leopard! It is good if developers like you and users like us tell Apple how important a working stereo 3D is. Personally, I consider stereo 3D as VERY important and would like to see Tiger's X11 stereo capabilities also under Leopard. I think, I've made this point clear in a couple of e-mails to Apple's X11 users list, and from the responses, it seems, that Apple is willing to spend time and money for solving this issue. However, until X11 stereo has been fixed under Leopard, I stick to Tiger on my MacPro and use Leopard on my laptop, only. Best regards, Dirk. Am 17.09.2008 um 02:26 schrieb Warren DeLano: CCP4bb, Some graphics news: Full operating-system support for stereo 3D has at last been restored on Mac OS X Leopard, but NOT in Leopard's X11 just yet (the Xquartz open-source community will hopefully soon remedy this...). While today's fix is great for native Mac OpenGL applications like MacPyMOL, my fear is that other critical applications will still be unable to support stereo 3D under Leopard because of a reliance upon X11/GLX for OpenGL. While Qt-based programs may now work fine in stereo 3D, X11-based apps such as open-source PyMOL are definitely still mono 3D-only under Leopard 10.5.5. Perhaps some of the other software developers can chime in soon regarding their support for stereo 3D under Mac OS X Leopard 10.5.5? At the very least, I am thinking of: ccp4mg, O, coot, and VIDA/AFITT, as well as perhaps Chimera, VMD, and MOE. Apologies if I left out something important! Along those lines, what other go to molecular graphics apps are crystallographers using on Macs these days? In other words, who else should we/Apple lean on? Also, do crystallographers still consider stereo 3D to be a high-priority or must-have feature in a graphics workstation? Cheers, Warren [EMAIL PROTECTED] *** Dirk Kostrewa Gene Center, A 5.07 Ludwig-Maximilians-University Feodor-Lynen-Str. 25 81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: [EMAIL PROTECTED] ***
Re: [ccp4bb] Rotation Function of MOLREP
ALMN can plot the rotation function as a map - although I challenge anyone to make much sense of it! More or less the same methodology as MOLREP. More useful - it lists all peaks generated by the symmetry operators in Eulerian, and polar angles and gives the direct cosines of the rotation axes - you can then check which is related to which by trigonometry. Eleanor To repeat: Hmm - this is tricky. 1) Presumably the size of your cell and your molecule determine how many molecules you expect in an asymmetric unit. THE asym. unit for I4(1)22 is half that of I4(1) if the cell dimensions are the same so it is reasonable to have 2 mols in I41 which generate a tetramer using the crystallographic 2-fold -x,-y,z and 1 mol in I4122 which generates a tetramer using the 2 perpendicular crystallographic 2 folds of I4(1)22, -x,-y,z and y,x,-z. 2) A rotation function is not a Patterson - it is a function of intensities, and can be visualised as an integration of the product of overlapping patterson function within a spherical volume, but it cannot be simpler plotted as a map. ALMN ( an old MR program) did output a map of these values along the Eulerian angles alpha, beta, gamma, but it is not very useful for visualisation. 3) peak heights for the rotation function are not very reliable - and without having the values I cant comment. You often get shoulders of existing symmetry related peaks. Did you search with the monomer alone? The solution usually comes out of the translation search. Eleanor Rajan Pillai wrote: Hi All, I want to plot the rotation function that MOLREP uses. I cannot find any output of rotation function in the logfile or in moIrep.doc. I want to locate the peaks of the rotation function, that are shortlisted as solutions, which would help me in understanding the following problem. My protein is a tetramer with 222 point group symmetry. In I4(1) space group Molrep gives two molecules in the asymmetric unit with top two RF peak heights 10 sigma and 6 sigma. The final solution is obtained from these two peaks after TF search. Moreover in case of another protein with the same tetrameric assembly and quite the same unit cell parameters, but in space group I4(1)22, Molrep gives 1 molecule in the asymmetric unit; however, in this case the peaks from the RF are 14 and 12 sigmas and the solution is obtained from the first peak after TF search. In the input file I did not mention the number of monomers to be searched. It detects that based on Matthews coefficient. I am a bit confused as to why in space group I4(1) the RF values are so different. I would have expected them to be closer in values as they are dimer. And also, in case of I4(1)22, the RF values also should be closer. I was wondering if plotting the RF can help in understanding the relation of the peaks and their values based on their location. I believe MOLREP calculates RF over the whole unit cell, instead of the asymmetric unit. Thanks, Rajan
Re: [ccp4bb] Generate high resolution pirctures in pymol
Remember, there's a whole mailing list wiki dedicated to PyMOL, so no need to clutter up CCP4bb with PyMOL-specific questions! https://lists.sourceforge.net/lists/listinfo/pymol-users http://pymolwiki.org More complete answer: # assuming that movie has already been defined in PyMOL # (such that it already plays interactively), you can then issue: viewport 2000,2000 set ray_trace_frames mpng mov/img # resulting images will be mov/img0001.png, mov/img0002.png, etc. Also note that it may be necessary to run the above as a script in command-line only mode (-c launch option) if your screen is less than 2000 pixels high and if the operating system doesn't permit windows larger than the screen size. Cheers, Warren -Original Message- From: CCP4 bulletin board on behalf of Andrzej Lyskowski Sent: Wed 9/17/2008 12:54 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Generate high resolution pirctures in pymol Hi, There are detailed instructions on the net but as far as I can remember all you need before starting to generate the frames is the following command: set ray_trace_frames, 1 Also, why do you need such a high resolution. I know that computers have a lot of power to burn but if you want to use animation in the presentation later on say 320x240 is more then enough! Remember that nowadays beamers seldom can do more then 1024x768. Andrzej yang li wrote: Hi all, Can somebody please help me to generate high resolution movie files for secondary structure of proteins? After I ray a model with high resolution in pymol and then save it as movie frames, the high resolution and ray seem lost. I have tried the command likes ray 2000,2000 and it does work for a single frame, but can anybody tell me how it could be extended to say 40 or 80 frames of a movie? Your suggestions are highly appreciated. Thanks in advance!
[ccp4bb] Topp fails: TOP: Open failed: File: /people/...../myfile.pdb
Hi all, Using the 6.0.2 distribution of CCP4, the top program keeps failing because it just can't see the pdb files. The files can be accessed by the text viewer of CCP4. (the button VIEW) I have tried to put them in other directories to make the path string shorter, etc. None of those helped. I have tried moving to various Linux versions (64bit,32bit, var. levels of Fedora or RHEL) Any ideas? Jan Dohnalek -- == Mr. Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Laboratory of Structural Analysis of Molecules Heyrovskeho nam. 2 16206 Prague 6 Tel: +420 296809205 Fax: +420 296809410 http://protein.awardspace.com/ ==
Re: [ccp4bb] Topp fails: TOP: Open failed: File: /people/...../myfile.pdb
Hi Jan We had this problem, I think it's because the character strings used to store pathnames are only 80 chars long, so if you have a long pathname (you didn't show your full pathname!) then it has a problem. You can either fix the program, or do as we did make a soft link in the current directory. Cheers -- Ian -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Jan Dohnalek Sent: 17 September 2008 10:02 To: ccp4bb Subject: Topp fails: TOP: Open failed: File: /people/./myfile.pdb Hi all, Using the 6.0.2 distribution of CCP4, the top program keeps failing because it just can't see the pdb files. The files can be accessed by the text viewer of CCP4. (the button VIEW) I have tried to put them in other directories to make the path string shorter, etc. None of those helped. I have tried moving to various Linux versions (64bit,32bit, var. levels of Fedora or RHEL) Any ideas? Jan Dohnalek -- == Mr. Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Laboratory of Structural Analysis of Molecules Heyrovskeho nam. 2 16206 Prague 6 Tel: +420 296809205 Fax: +420 296809410 http://protein.awardspace.com/ == Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
[ccp4bb] Non-integer epsilons for rotation axes.
All - I've been trying to track down a paper (or papers) where it was shown that the epsilon values (symmetry factors) for space groups with pure rotation axes are not integers as is usually assumed (but still integers for screw axes). It's almost certainly in Acta Cryst., probably in the 60's or 70's and I think it was by Main and/or Woolfson and/or Rogers (but I could be completely wrong about that part), and it might just be in an Appendix. I tried the obvious searches on the IUCr website with no luck (I was rather surprised to find that searching for 'symmetry' or 'space group' by 'Main' and/or 'Woolfson' yielded no hits - I find that very hard to believe!). If anyone knows the reference I'd be eternally grateful! Cheers -- Ian Ian J. Tickle, DPhil. Director of X-ray Technology Astex Therapeutics Ltd 436 Cambridge Science Park Milton Road, Cambridge CB4 0QA, UK Tel: +44(0)1223 226214 Fax: +44(0)1223 226201 www.astex-therapeutics.com Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
Re: [ccp4bb] Topp fails: TOP: Open failed: File: /people/...../myfile.pdb
Sorry I should have copied this to the BB as it may be of general interest: -Original Message- From: Ian Tickle Sent: 17 September 2008 11:05 To: 'Jan Dohnalek' Subject: RE: [ccp4bb] Topp fails: TOP: Open failed: File: /people/./myfile.pdb OK try this one: looking at the program I see that it searches for the string 'pdb' in the pathname and uses the name up to that point: IF (INP(1:4).EQ.'MOL1') THEN ISP = INDEX(INP,' ') indpdb=INDEX(INP,'pdb') i=isp do i=isp,indpdb if(inp(i:i).ne.' ') goto 2255 enddo 2255 continue FILE1=INP(i:indpdb+2) So if your file is called say 'junk.pdb' it's fine, if it's called junkpdb.pdb it will try to open 'junkpdb'!! Your pathname doesn't have the string 'pdb' somewhere in it (except at the end) by any chance? -- Ian -Original Message- From: Jan Dohnalek [mailto:[EMAIL PROTECTED] Sent: 17 September 2008 10:33 To: Ian Tickle Subject: Re: [ccp4bb] Topp fails: TOP: Open failed: File: /people/./myfile.pdb Dear Ian, I have done this exercise even before I sent my original e-mail (as you may notice in my original e-mail). The shortest path length was 33 characters. I know this normally fixes many of these problems. This time it does not ... Jan Ian Tickle wrote: Hi Jan We had this problem, I think it's because the character strings used to store pathnames are only 80 chars long, so if you have a long pathname (you didn't show your full pathname!) then it has a problem. You can either fix the program, or do as we did make a soft link in the current directory. Cheers -- Ian -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Jan Dohnalek Sent: 17 September 2008 10:02 To: ccp4bb Subject: Topp fails: TOP: Open failed: File: /people/./myfile.pdb Hi all, Using the 6.0.2 distribution of CCP4, the top program keeps failing because it just can't see the pdb files. The files can be accessed by the text viewer of CCP4. (the button VIEW) I have tried to put them in other directories to make the path string shorter, etc. None of those helped. I have tried moving to various Linux versions (64bit,32bit, var. levels of Fedora or RHEL) Any ideas? Jan Dohnalek -- == Mr. Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Laboratory of Structural Analysis of Molecules Heyrovskeho nam. 2 16206 Prague 6 Tel: +420 296809205 Fax: +420 296809410 http://protein.awardspace.com/ == Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674 -- == Mr. Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Laboratory of Structural Analysis of Molecules Heyrovskeho nam. 2 16206 Prague 6 Tel: +420 296809205 Fax: +420 296809410 http://protein.awardspace.com/ == Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this
Re: [ccp4bb] Non-integer epsilons for rotation axes.
I think that you are looking for A.J.C. Wilson, Acta Cryst. 17 (1964) 1591-2. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Wed, 17 Sep 2008, Ian Tickle wrote: All - I've been trying to track down a paper (or papers) where it was shown that the epsilon values (symmetry factors) for space groups with pure rotation axes are not integers as is usually assumed (but still integers for screw axes). It's almost certainly in Acta Cryst., probably in the 60's or 70's and I think it was by Main and/or Woolfson and/or Rogers (but I could be completely wrong about that part), and it might just be in an Appendix. I tried the obvious searches on the IUCr website with no luck (I was rather surprised to find that searching for 'symmetry' or 'space group' by 'Main' and/or 'Woolfson' yielded no hits - I find that very hard to believe!). If anyone knows the reference I'd be eternally grateful! Cheers -- Ian Ian J. Tickle, DPhil. Director of X-ray Technology Astex Therapeutics Ltd 436 Cambridge Science Park Milton Road, Cambridge CB4 0QA, UK Tel: +44(0)1223 226214 Fax: +44(0)1223 226201 www.astex-therapeutics.com Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
Re: [ccp4bb] Progresss with Stereo 3D under Mac OS X Leopard
On Sep 16, 2008, at 5:26 PM, Warren DeLano wrote: Also, do crystallographers still consider stereo 3D to be a high-priority or must-have feature in a graphics workstation? Hi Warren: I'd put lack of stereo 3D in the same categories as lack of grant support or involuntary celibacy. I'm still hoping for LCD stereo some day. (I am also hoping my grant will get renewed, world peace, stable economy, ...). Thank you very much for advocating for this on all of our behalf. Bill
Re: [ccp4bb] Progresss with Stereo 3D under Mac OS X Leopard
On Sep 16, 2008, at 5:26 PM, Warren DeLano wrote: Also, do crystallographers still consider stereo 3D to be a high-priority or must-have feature in a graphics workstation? Yes, I do. Really, how can you do without? As for LCD stereo: yes, please!
[ccp4bb] Error while compiling ccp4-6.0.99e from source
Dear CCP4ers, I am compiling ccp4-6.0.99e from source and get the errors listed below when the compilation gets to lib/ccif/libccif.a. I re-ran configure with the --with-rxdispencer option as recommended but the error persists. My system is a Fedora Core 8 Linux xtal2.itqb.unl.pt 2.6.23.1-42.fc8 #1 SMP Tue Oct 30 13:55:12 EDT 2007 i686 i686 i386 GNU/Linux What can I do to overcome this error ? Is there any system component missing, or did I miss something obvious? Thanks in advance, Pedro. rxdispencer routines being added to library make[1]: *** No rule to make target `/home/xtal/ccp4-6.0.99e/lib/data/cif_mm.dic', needed by `cif_mmdic.lib'. Stop. make[1]: Leaving directory `/home/xtal/software/ccp4-6.1/temp-install/ccp4-6.0.99e/lib/ccif' make[1]: Entering directory `/home/xtal/software/ccp4-6.1/temp-install/ccp4-6.0.99e/lib/ccif' if test -f /home/xtal/software/ccp4-6.1/temp-install/ccp4-6.0.99e/lib/rxdispencer/rx/librx.a; then \ rm -rf rx.dir; mkdir rx.dir; \ echo 'rxdispencer routines being added to library'; \ cp /home/xtal/software/ccp4-6.1/temp-install/ccp4-6.0.99e/lib/rxdispencer/rx/librx.a rx.dir; cd rx.dir; \ ar -x librx.a; cd ..; \ ar r libccif.a rx.dir/*.o; \ ranlib libccif.a; rm -rf rx.dir; \ fi rxdispencer routines being added to library gcc -O -w -DGFORTRAN -DPROTOTYPE -I/home/xtal/software/ccp4-6.1/temp-install/ccp4-6.0.99e/lib/rxdispencer/rx -DHAVE_SIGNAL_H=1 -DHAVE_TIME_H=1 -DHAVE_ASSERT_H=1 -DUPDATE_WARN=1 -DUSER_ZZMODE_STACK=1 -D_XOPEN_SOURCE=500 -D_XOPEN_SOURCE_EXTENDED=1 -DHAVE_MMAP=1 -I/home/xtal/software/ccp4-6.1/temp-install/ccp4-6.0.99e/lib/ccif -o cifdic_to_symtab cifdic_to_symtab.o -lm -L`pwd` -lccif -lm -L/home/xtal/software/ccp4-6.1/temp-install/ccp4-6.0.99e/lib/rxdispencer/rx -lrx make[1]: *** No rule to make target `/home/xtal/ccp4-6.0.99e/lib/data/cif_mm.dic', needed by `cif_mmdic.lib'. Stop. make[1]: Leaving directory `/home/xtal/software/ccp4-6.1/temp-install/ccp4-6.0.99e/lib/ccif' make: *** [cciflib] Error 2 Industry and Medicine Applied Crystallography Macromolecular Crystallography Unit ___ Phones : (351-21) 446-9100 Ext. 1669 (351-21) 446-9669 (direct) Fax : (351-21) 441-1277 or 443-3644 email : [EMAIL PROTECTED] http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit Mailing address : Instituto de Tecnologia Quimica e Biologica Apartado 127 2781-901 OEIRAS Portugal
[ccp4bb] MrBump Installation ccp4
Hi all, We' ve just encountered a problem concerning the installation of MrBump on our Linux machine. MrBump needs Fasta35 for operation, but during installation does not recognise the already installed Fasta35, even if Fasta35 is placed in the ccp4i bin. Under the same location the recognition of ClustalW did not oppose a problem. Can anybody help us? Where do we have to put Fasta35 in order to continue the installation of MrBump? Or is something possibly wrong with the permissions (global or local)? If anyone has an idea, please let us know! Thanks a lot in advance! Daniel Daniel Wohlwend GZMB Abt. für molekulare Strukturbiologie Georg-August-Universitaet Goettingen Justus-von-Liebig-Weg 11 37077 Goettingen phone: 0551-39-14074 e-mail: [EMAIL PROTECTED]
Re: [ccp4bb] MrBump Installation ccp4
Hi Daniel, Sorry to hear about your problem with mrbump. You say that you put the Fasta35 executable in the ccp4i bin directory(note the i). This directory is probably not in your system PATH. I would recommend that you put it into the $CCP4/bin which should be in your system path provided that CCP4 is set up correctly. Kind regards, Ronan Daniel Wohlwend wrote: Hi all, We' ve just encountered a problem concerning the installation of MrBump on our Linux machine. MrBump needs Fasta35 for operation, but during installation does not recognise the already installed Fasta35, even if Fasta35 is placed in the ccp4i bin. Under the same location the recognition of ClustalW did not oppose a problem. Can anybody help us? Where do we have to put Fasta35 in order to continue the installation of MrBump? Or is something possibly wrong with the permissions (global or local)? If anyone has an idea, please let us know! Thanks a lot in advance! Daniel Daniel Wohlwend GZMB Abt. für molekulare Strukturbiologie Georg-August-Universitaet Goettingen Justus-von-Liebig-Weg 11 37077 Goettingen phone: 0551-39-14074 e-mail: [EMAIL PROTECTED]
Re: [ccp4bb] Progresss with Stereo 3D under Mac OS X Leopard
Very well phrased Steve, and I do agree - however stereo is helpful e.g. looking at binding pockets etc. I think it depends very much on your workflow what you are actually doing if you really need lots of stereo. In my case I run everything on my MacbookPro but I occasionally walk over to our stereo linux box to visualize things in stereo. How often does this happen is the question - I'd say 2-5% of my model building / analysis time. And a workaround e.g. at home is crosseyed in Pymol it's weird but it works - at least for me. I'd love to have the option to use stereo on Leopard or hopefully Snow Leopard. Jürgen On 17 Sep 2008, at 08:02, Steve Lane wrote: Warren et al.: The following is based largely on a survey conducted here about 6 months ago (the survey questions are at the bottom of this msg). Among the older generation of PIs, there is a strong perception that stereo and SGI dials are very important to users. This perception is not at all borne out among users themselves (20+ grad students and postdocs, plus one or two junior faculty) - no one uses the dials (see below for why), and stereo is used very infrequently to never. The consensus among the users regarding stereo seems to be some version of the following: if it's available, I might use it occasionally for a particularly difficult part of a molecule, but not otherwise; if it's not available, that's fine. Reasons for not using it seem to be based primarily on: inconvenience (we use StereoGraphics glasses and emitters - in spite of having many pairs available, and efforts by the admins here to keep them functional, it can be difficult for a user to find a pair that works, either because of dead batteries or because they're just broken); discomfort (wearing the glasses themselves is a pain, people complain of headaches, and the ambient lighting situation can make using them difficult under some circumstances and cause eye strain); and lack of need. No one uses the dials because no one in our environment is building with O, and this is the only piece of software we have that supports the dials (we have a Linux-only environment). *Everyone* here builds with Coot. I believe (based on somewhat anecdotal evidence) that if Coot supported the dials people would use them more, but they seem quite happy without them; they are certainly not enough reason for people to learn to use O (or go back to using it). The above perception vs reality dichotomy seems to stem largely from a generation gap: users who learned to build using SGIs running O are firm believers in the need for stereo and dials (even though, for the most part, they are no longer actively building); users who learned to build on Linux boxes using Coot simply don't see the need, for the most part. Note that these are, for the most part, users who have never used O, but who *do* actively build, spending hours and days at a time sitting in front of the workstation doing so. In addition, many/most users these days do alot of their building using their own laptops (many/most of which are Macs running OS X), often but not always in conjunction with an external flat panel display. When doing so, they don't use stereo or dials, and again, this doesn't seem to be a huge loss to them, especially given the convenience of being able to work where they want (i.e. at home, in coffee shops libraries, outdoors, etc.) Users also like to be able to sit in front of a flat-panel display to do their work. This seems to be a combination of two factors: the extra space available on the work surface that isn't taken up by a huge CRT; and the absence of the huge, heavy, space-hogging CRT sitting in front of them all day (i.e. a psychological lightness provided by a flat- panel display - this seems hard to quantify, but I experienced it myself when switching from a CRT to a flat-panel, and others I have talked to have reported similar feelings). Obviously, if a reasonably-priced flat- panel stereo solution were to become available this would influence decisions about stereo. I've included our survey questions below my .sig - please feel free to use or adapt them as you like. -- Steve Lane System, Network and Security Administrator Doudna Lab Biomolecular Structure and Mechanism Group UC Berkeley == Greetings. This is a semi-informal survey of recent crystallography workstation users. Please take a minute to respond. Your answers will help us improve the crystallography computing environment. 1) Have you recently (past few months) used a crystallography workstation for molecular model building and/or visualization? YES NO Answer: 2) If yes to (1), which model building software did you use (list all that apply)? COOT O OTHER - please specify Answer: 3) When model building, do you use the dial box? ALWAYS OFTEN SOMETIMES RARELY NEVER Answer: 4)
Re: [ccp4bb] Progresss with Stereo 3D under Mac OS X Leopard
I would agree with this statement, my preference is VERY STRONG. We mostly
work on Nucleosome and Nucleosome-nuclear protein complexes. By definition
these are low-resolution structures. They are very difficult to interpret, even
with stereo and I could not imagine even trying to work on things like this
without stereo. And yes, I am old - I learned O on SGIs with dials (which we
have kept as a momento, but nobody uses them anymore) and yes, most of us have
changed to Coot.
This reminds me: it would REALLY be nice to have a program that is better at
fitting ('non-standard') DNA in electron density. Any suggestions?
Mark
-Original Message-
From: Patrick Loll [EMAIL PROTECTED]
To: CCP4BB@JISCMAIL.AC.UK
Sent: Wed, 17 Sep 2008 6:01 am
Subject: Re: [ccp4bb] Progresss with Stereo 3D under Mac OS X Leopard
People's feelings about using stereo seem to be highly idiosyncratic, but for
many of us who are pro-stereo, the preference is VERY STRONG.
Pat
On Sep 16, 2008, at 8:26 PM, Warren DeLano wrote:
CCP4bb,
Some graphics news:? Full operating-system support for stereo 3D has at
last been restored on Mac OS X Leopard, but NOT in Leopard's X11 just
yet (the Xquartz open-source community will hopefully soon remedy
this...).
While today's fix is great for native Mac OpenGL applications like
MacPyMOL, my fear is that other critical applications will still be
unable to support stereo 3D under Leopard because of a reliance upon
X11/GLX for OpenGL. ?
While Qt-based programs may now work fine in stereo 3D, X11-based apps
such as open-source PyMOL are definitely still mono 3D-only under
Leopard 10.5.5.
Perhaps some of the other software developers can chime in soon
regarding their support for stereo 3D under Mac OS X Leopard 10.5.5?? At
the very least, I am thinking of: ?
ccp4mg, O, coot, and VIDA/AFITT, as well as perhaps Chimera, VMD, and
MOE.
Apologies if I left out something important!? Along those lines, what
other go to molecular graphics apps are crystallographers using on
Macs these days?? In other words, who else should we/Apple lean on?
Also, do crystallographers still consider stereo 3D to be a
high-priority or must-have feature in a graphics workstation? ?
Cheers,
Warren
[EMAIL PROTECTED]
-
Patrick J. Loll, Ph. D.?? ? ? ? ? ? ? ? ?
Professor?of Biochemistry Molecular Biology
Director, Biochemistry Graduate Program
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St., Mailstop 497
Philadelphia, PA??19102-1192??USA
(215) 762-7706
[EMAIL PROTECTED]
=
[ccp4bb] OS X 10.5.5 update and X11
Hi folks: My apologies to those who will find this irrelevant, but hopefully they didn't read beyond the subject line. I've gotten many questions about this, so ... After the update to 10.5.5, you have to update (again) X11, preferably to 2.3.1. Why Apple didn't include this in the 10.5.5 is anyone's guess, but there is an official update available here: http://xquartz.macosforge.org/trac/wiki This is the real thing, made by the real Apple X11 developer. I installed it and everything is working as well as ever. Except stereo in X11, but we can keep hoping... Bill Scott
Re: [ccp4bb] Progresss with Stereo 3D under Mac OS X Leopard
Just to put my two cents in on this as I would fall into that new generation so to speak: I started out with the SGI and linux systems with stereo, O, and dials about eight years ago. Never used the dials and rarely seen anyone else use them. Over the past few years I have transition to coot, pc, and now have a MAC. The freedom of not having a bulky system that I have to build on is a huge plus for many of the reasons you described. However, My colleagues and I I DO WANT STEREO. I have nearly perfected building without IT not out of choice but mostly out of lack of one. I feel as many of my colleagues do, that if we had the stereo option on our flat panels we most undoubtedly would use it. We just don't those type of options right know. As a result, I wholeheartedly support anyone trying to get us this added capability. Scott Steve Lane wrote: Warren et al.: The following is based largely on a survey conducted here about 6 months ago (the survey questions are at the bottom of this msg). Among the older generation of PIs, there is a strong perception that stereo and SGI dials are very important to users. This perception is not at all borne out among users themselves (20+ grad students and postdocs, plus one or two junior faculty) - no one uses the dials (see below for why), and stereo is used very infrequently to never. The consensus among the users regarding stereo seems to be some version of the following: if it's available, I might use it occasionally for a particularly difficult part of a molecule, but not otherwise; if it's not available, that's fine. Reasons for not using it seem to be based primarily on: inconvenience (we use StereoGraphics glasses and emitters - in spite of having many pairs available, and efforts by the admins here to keep them functional, it can be difficult for a user to find a pair that works, either because of dead batteries or because they're just broken); discomfort (wearing the glasses themselves is a pain, people complain of headaches, and the ambient lighting situation can make using them difficult under some circumstances and cause eye strain); and lack of need. No one uses the dials because no one in our environment is building with O, and this is the only piece of software we have that supports the dials (we have a Linux-only environment). *Everyone* here builds with Coot. I believe (based on somewhat anecdotal evidence) that if Coot supported the dials people would use them more, but they seem quite happy without them; they are certainly not enough reason for people to learn to use O (or go back to using it). The above perception vs reality dichotomy seems to stem largely from a generation gap: users who learned to build using SGIs running O are firm believers in the need for stereo and dials (even though, for the most part, they are no longer actively building); users who learned to build on Linux boxes using Coot simply don't see the need, for the most part. Note that these are, for the most part, users who have never used O, but who *do* actively build, spending hours and days at a time sitting in front of the workstation doing so. In addition, many/most users these days do alot of their building using their own laptops (many/most of which are Macs running OS X), often but not always in conjunction with an external flat panel display. When doing so, they don't use stereo or dials, and again, this doesn't seem to be a huge loss to them, especially given the convenience of being able to work where they want (i.e. at home, in coffee shops libraries, outdoors, etc.) Users also like to be able to sit in front of a flat-panel display to do their work. This seems to be a combination of two factors: the extra space available on the work surface that isn't taken up by a huge CRT; and the absence of the huge, heavy, space-hogging CRT sitting in front of them all day (i.e. a psychological lightness provided by a flat-panel display - this seems hard to quantify, but I experienced it myself when switching from a CRT to a flat-panel, and others I have talked to have reported similar feelings). Obviously, if a reasonably-priced flat-panel stereo solution were to become available this would influence decisions about stereo. I've included our survey questions below my .sig - please feel free to use or adapt them as you like. -- Steve Lane System, Network and Security Administrator Doudna Lab Biomolecular Structure and Mechanism Group UC Berkeley == Greetings. This is a semi-informal survey of recent crystallography workstation users. Please take a minute to respond. Your answers will help us improve the crystallography computing environment. 1) Have you recently (past few months) used a crystallography workstation for molecular model building and/or visualization? YES NO Answer: 2) If yes to (1), which model building software did you use
Re: [ccp4bb] Progresss with Stereo 3D under Mac OS X Leopard
I find that depth-cue/fog is a sufficient cue for me to determine the 3-dimensionality of what I am viewing on my 2-dimensional monitor, and I find that most 3D systems tend to give me a headache long before I would get one without them. Even when the depth-cue/fog isn't enough, simply rotating the view slightly with the mouse often makes the 3D arrangement very obvious. For those of us who drink too much coffee, this is already a constant process. When I've tried to use 3D stereo in the past, I found myself reflexively spinning the molecules around anyway. Fake 3D is no substitute for multiple perspectives, IMHO. (And I can't even interpret the cross-eyed stereo images in older crystallography papers.) Since I was one of Steve's survey-takers, I can confirm that this is almost entirely a generational difference (and .One factor he left out is that those of us who came of age (technologically speaking) in an era of ubiquitous bright, high-contrast (and increasingly massive) LCD screens can't bear to look at a CRT display any more. Using a Linux workstation with a CRT increasingly feels like stepping back in time; imagine how much worse this felt around 2004, before we got rid of the Octanes. Thanks to other software and hardware improvements, many of us aren't used to routinely building entire models from scratch either, so in theory we don't have to spend as much time squinting at electron density. (Disclaimer: I don't work on RNA or nucleosomes or low-resolution structures, so I'm spoiled.) Even the P.I.s who swear by stereo for building usually end up doing much of the paper preparation on their Macs anyway. I haven't seen any evidence to support the idea that stereo is necessary (the way use of R-free is necessary) for good crystallography or paper-writing except as a matter of personal preference. I'm also inclined to think that the superiority of the Mac vs. Linux in nearly every other aspect - and the convenience of laptops, of course - more than compensates for the lack of stereo. I do think we'd benefit from better input devices - I like the Griffin Powermate, but it's too simple to be a complete solution. If Apple ever introduces tablets or iMacs with iPhone-like multi-touch screens, I'll be in heaven. -Nat
Re: [ccp4bb] Progresss with Stereo 3D under Mac OS X Leopard
My use goes back to Evans and Sutherland workstations, FRODO, SGI's with O, Duncan's graphics program suite, and COOT, on multiple platforms. I don't use dials at all, and multiple uses with a three-button mouse are far more favorable. I still prefer O to COOT for a number of reasons. The main reason is that the graphics isn't as good on most PC/linux/mac boxes, the screen isn't as large, and the color range isn't as good. I rarely, if ever, use stereo options, even when available. You can in 3D fine without it, and you need a system that has a fast enough refresh rate and no shadowing. When users learn by building without stereo, they don't see the advantages of it later on. Bernie Santarsiero = Greetings. This is a semi-informal survey of recent crystallography workstation users. Please take a minute to respond. Your answers will help us improve the crystallography computing environment. 1) Have you recently (past few months) used a crystallography workstation for molecular model building and/or visualization? YES NO Answer: YES 2) If yes to (1), which model building software did you use (list all that apply)? COOT O OTHER - please specify Answer: O 3) When model building, do you use the dial box? ALWAYS OFTEN SOMETIMES RARELY NEVER Answer: NEVER 4) When model building, do you use 3D stereo visualization (i.e. stereo glasses)? ALWAYS OFTEN SOMETIMES RARELY NEVER Answer: RARELY to NEVER 5) If yes to (1), which molecular visualization software did you use (list all that apply)? COOT O CHIMERA PYMOL OTHER - please specify Answer: PYMOL, O, RASMOL, INSIGHT 6) When visualizing molecular models, do you use the dial box? ALWAYS OFTEN SOMETIMES RARELY NEVER Answer: NEVER 7) When visualizing molecular models, do you use 3D stereo visualization (i.e. stereo glasses)? ALWAYS OFTEN SOMETIMES RARELY NEVER Answer: NEVER 8) Is there any software you would like to have available in the computing environment to assist you in molecular model building and/or visualization that is not currently available? Answer: NO Thank you for your time. -- Dr. Jeroen R. Mesters Gruppenleiter Strukturelle Neurobiologie und Kristallogenese Institut für Biochemie, Universität zu Lübeck Zentrum für Medizinische Struktur- und Zellbiologie Ratzeburger Allee 160, D-23538 Lübeck Tel: +49-451-5004070, Fax: +49-451-5004068 Http://www.biochem.uni-luebeck.de Http://www.iobcr.org Http://www.selfish-brain.org Http://www.opticryst.org -- If you can look into the seeds of time and say which grain will grow and which will not - speak then to me (Macbeth) -- -- Scott D. Pegan, Ph.D. Senior Research Specialist Center for Pharmaceutical Biotechnology University of Illinois at Chicago
Re: [ccp4bb] Progresss with Stereo 3D under Mac OS X Leopard
Hi Nat: On Sep 17, 2008, at 11:14 AM, Nathaniel Echols wrote: those of us who came of age (technologically speaking) in an era of ubiquitous bright, high-contrast (and increasingly massive) LCD screens can't bear to look at a CRT display any more. The day I stopped using CRTs in the presence of fluorescent lighting was the day I stopped getting cracking headaches (except those that are induced by other people). The stereo glasses that flicker made it 100 times worse, but there are alternatives to that. I also find the latest generation LCD screens too bright, and the trend toward shiny glass (latest iMacs and laptops) annoying. Stereo makes it easier for people unfamiliar with your molecule to see what is going on. However, judicious color choice and depth cuing can often be as effective. I hope Apple will choose to offer it as an option, even though the preference for it is not universal. Bill
[ccp4bb] available Stereo 3D LCD monitors / Linux compatibility
Dear all, I would like to continue the discussion on the availability of 3D-LCD monitors that work with Linux or Mac (started in the discussion Progresss with Stereo 3D under Mac OS X Leopard). (We do have a running stereo capable system with Linux-PC SGI-CTR-monitor CrystalEyes.) Now we are seeking a 3D-LCD monitor that work with Linux (or Mac). Is there anyone using a good, affordable 3D-LCD monitor? Here's what I've found so far: dti3d.com 19 3D LCD (3,695 US$) works officially with linux, pymol, coot. (I'm in contact with a Munich based salesman, I'll keep you updated) Cheaper but apparently not working with Linux /Mac (?) (designed for 3d computer games): Newsight.com 17 (500 EUROs) and 24 (1300 EUROs) no glasses required Drawback: * Windows XP (for additional controller program) required + Nvidia Geforce graphics card http://www.newsight.com/3d-products/displays.html Zalman ZM-M220W: a 22 3D-TFT, simple plarized glasses are required. Drawbacks: * optimal viewing angle for 3D seems to be rather small. Price: 500 EUROs * Windows Vista (for additional controller program) required + Nvidia Geforce graphics card http://www.zalman.co.kr/ENG/product/CategorySecond_Pic.asp?categoryname=MonitorscategorySecond= iZ3D 22 3D LCD Flat Panel Computer Gaming Monitor, works with simple polarized glasses, available on amazon.com, not shipped to Germany. Anybody knows anything about it? == someone has good connections to Nvidia? Shouldn't be too difficult for them to add the 3D-support directly to the driver (which would make the additional controller program unnecessary) [Note that there is already support for SeeReal digital flat panel and Sharp3D digital flat panel in the Nvidia Quadro * linux driver, but SeeReal and Sharp are not selling 3D LCDs any more (I asked SeeReal and Sharp:http://www.superwarehouse.com/Sharp_LL1513D_15_Black_LCD_Monitor/LL1513D/p/1481235 ...) Further I have contacted and am waiting for their reply: dimen / miracube.net tridelity.de spatialview.com Many companies I got from this page: http://www.stereo3d.com/displays.htm Anyone knows if Philips, Sanyo, Sharp, VIEWSONIC, 3dis.co.kr etc. are selling 3D displays? (there is some info on the web that these are working on this technology). Thank you for any contribution to this topic, Christian Rausch Dr. Christian Rausch [EMAIL PROTECTED] Lehrstuhl f. Biologische Chemie Phone: +49 (0)8161 71-4050 Technische Universitaet MuenchenFax: -4352 85350 Freising-Weihenstephan Germany http://www.wzw.tum.de/bc __ Do You Yahoo!? Sie sind Spam leid? Yahoo! Mail verfügt über einen herausragenden Schutz gegen Massenmails. http://mail.yahoo.com
Re: [ccp4bb] Progresss with Stereo 3D under Mac OS X Leopard
Dear all, following this discussion and enjoying AGAIN 3D on a Mac - at least in Pymol -, I'd like to add my two cent opinion. Whether or not stereo is important in research might be a matter of debate, true! But, we are focussing on membrane proteins and normally these structures are at medium resolution. Here, stereo is absolutely a plus and no depth-cue or whatsoever is an alternative. This is why we still keep some old SGI somehow running, although everything else is done on the Mac. But I agree that this might be a personal taste or age-question. Although I do not think that I am really that old - no offense to anybody out there :-) However, I like to add another flavor to the discussion. Have you ever seen the eyes of students when they see their first 3D structure of a protein? It happened to me today that I showed a stereo representation of a protein to an old emeritus professor in pymol. And suddenly he understood the enzyme, he was working on for a really long time. True, he is not a student anymore but this example was an eye-opener for me. Thus, research is one thing and a lot of personal taste is involved, but do students not deserve the best we can offer? And 3D beamers are one thing, but stereo is for sure a must! The alternative is to switch to LInux, true again, but at least at German universities we hardly have the man power to keep up and running X-ray generators, computers, protein purification, etc. I am not complaining here, I simply like to make the point that Apple might miss a big opportunity in not fixing stereo in Leopard. Cheers Lutz Am 17.09.2008 um 20:14 schrieb Nathaniel Echols: I find that depth-cue/fog is a sufficient cue for me to determine the 3-dimensionality of what I am viewing on my 2-dimensional monitor, and I find that most 3D systems tend to give me a headache long before I would get one without them. Even when the depth-cue/fog isn't enough, simply rotating the view slightly with the mouse often makes the 3D arrangement very obvious. For those of us who drink too much coffee, this is already a constant process. When I've tried to use 3D stereo in the past, I found myself reflexively spinning the molecules around anyway. Fake 3D is no substitute for multiple perspectives, IMHO. (And I can't even interpret the cross-eyed stereo images in older crystallography papers.) Since I was one of Steve's survey-takers, I can confirm that this is almost entirely a generational difference (and .One factor he left out is that those of us who came of age (technologically speaking) in an era of ubiquitous bright, high-contrast (and increasingly massive) LCD screens can't bear to look at a CRT display any more. Using a Linux workstation with a CRT increasingly feels like stepping back in time; imagine how much worse this felt around 2004, before we got rid of the Octanes. Thanks to other software and hardware improvements, many of us aren't used to routinely building entire models from scratch either, so in theory we don't have to spend as much time squinting at electron density. (Disclaimer: I don't work on RNA or nucleosomes or low-resolution structures, so I'm spoiled.) Even the P.I.s who swear by stereo for building usually end up doing much of the paper preparation on their Macs anyway. I haven't seen any evidence to support the idea that stereo is necessary (the way use of R-free is necessary) for good crystallography or paper-writing except as a matter of personal preference. I'm also inclined to think that the superiority of the Mac vs. Linux in nearly every other aspect - and the convenience of laptops, of course - more than compensates for the lack of stereo. I do think we'd benefit from better input devices - I like the Griffin Powermate, but it's too simple to be a complete solution. If Apple ever introduces tablets or iMacs with iPhone-like multi- touch screens, I'll be in heaven. -Nat
[ccp4bb] Classic density map drawing!
Hi All, I am trying to make a quite classic demonstration of electron density map sliced and contoured as (smoothed) isoheight curves. The sliced section is random and NOT along any main cell axes. I am curious if there is any crystallographic software can handle this, which will save me from writing and debugging codes. Thanks a lot! Lijun Liu, PhD Institute of Molecular Biology HHMI Department of Physics University of Oregon Eugene, OR 97403 541-346-4080
Re: [ccp4bb] Progresss with Stereo 3D under Mac OS X Leopard
if you have bad/poor experimental phases and you are building de novo/ from scratch by hand, in my opinion stereo is very handy and makes map interpretation much easier. -tommi On Sep 17, 2008, at 6:02 PM, Steve Lane wrote: Warren et al.: The following is based largely on a survey conducted here about 6 months ago (the survey questions are at the bottom of this msg). Among the older generation of PIs, there is a strong perception that stereo and SGI dials are very important to users. This perception is not at all borne out among users themselves (20+ grad students and postdocs, plus one or two junior faculty) - no one uses the dials (see below for why), and stereo is used very infrequently to never. The consensus among the users regarding stereo seems to be some version of the following: if it's available, I might use it occasionally for a particularly difficult part of a molecule, but not otherwise; if it's not available, that's fine. Reasons for not using it seem to be based primarily on: inconvenience (we use StereoGraphics glasses and emitters - in spite of having many pairs available, and efforts by the admins here to keep them functional, it can be difficult for a user to find a pair that works, either because of dead batteries or because they're just broken); discomfort (wearing the glasses themselves is a pain, people complain of headaches, and the ambient lighting situation can make using them difficult under some circumstances and cause eye strain); and lack of need. No one uses the dials because no one in our environment is building with O, and this is the only piece of software we have that supports the dials (we have a Linux-only environment). *Everyone* here builds with Coot. I believe (based on somewhat anecdotal evidence) that if Coot supported the dials people would use them more, but they seem quite happy without them; they are certainly not enough reason for people to learn to use O (or go back to using it). The above perception vs reality dichotomy seems to stem largely from a generation gap: users who learned to build using SGIs running O are firm believers in the need for stereo and dials (even though, for the most part, they are no longer actively building); users who learned to build on Linux boxes using Coot simply don't see the need, for the most part. Note that these are, for the most part, users who have never used O, but who *do* actively build, spending hours and days at a time sitting in front of the workstation doing so. In addition, many/most users these days do alot of their building using their own laptops (many/most of which are Macs running OS X), often but not always in conjunction with an external flat panel display. When doing so, they don't use stereo or dials, and again, this doesn't seem to be a huge loss to them, especially given the convenience of being able to work where they want (i.e. at home, in coffee shops libraries, outdoors, etc.) Users also like to be able to sit in front of a flat-panel display to do their work. This seems to be a combination of two factors: the extra space available on the work surface that isn't taken up by a huge CRT; and the absence of the huge, heavy, space-hogging CRT sitting in front of them all day (i.e. a psychological lightness provided by a flat- panel display - this seems hard to quantify, but I experienced it myself when switching from a CRT to a flat-panel, and others I have talked to have reported similar feelings). Obviously, if a reasonably-priced flat- panel stereo solution were to become available this would influence decisions about stereo. I've included our survey questions below my .sig - please feel free to use or adapt them as you like. -- Steve Lane System, Network and Security Administrator Doudna Lab Biomolecular Structure and Mechanism Group UC Berkeley == Greetings. This is a semi-informal survey of recent crystallography workstation users. Please take a minute to respond. Your answers will help us improve the crystallography computing environment. 1) Have you recently (past few months) used a crystallography workstation for molecular model building and/or visualization? YES NO Answer: 2) If yes to (1), which model building software did you use (list all that apply)? COOT O OTHER - please specify Answer: 3) When model building, do you use the dial box? ALWAYS OFTEN SOMETIMES RARELY NEVER Answer: 4) When model building, do you use 3D stereo visualization (i.e. stereo glasses)? ALWAYS OFTEN SOMETIMES RARELY NEVER Answer: 5) If yes to (1), which molecular visualization software did you use (list all that apply)? COOT O CHIMERA PYMOL OTHER - please specify Answer: 6) When visualizing molecular models, do you use the dial box? ALWAYS OFTEN SOMETIMES RARELY NEVER Answer: 7) When visualizing molecular models, do
Re: [ccp4bb] Progresss with Stereo 3D under Mac OS X Leopard
Dear Steve, despite your survey/perception, bottom line is, comes paper writing time, nothing beats stereo viewing of the molecules or the packing of them in the crystal lattice: facts become apparent that are otherwise easily overseen in two dimensions! Stereo-free macromolecular crystallography? Not really a good practice/idea! Jeroen. Steve Lane wrote: Warren et al.: The following is based largely on a survey conducted here about 6 months ago (the survey questions are at the bottom of this msg). Among the older generation of PIs, there is a strong perception that stereo and SGI dials are very important to users. This perception is not at all borne out among users themselves (20+ grad students and postdocs, plus one or two junior faculty) - no one uses the dials (see below for why), and stereo is used very infrequently to never. The consensus among the users regarding stereo seems to be some version of the following: if it's available, I might use it occasionally for a particularly difficult part of a molecule, but not otherwise; if it's not available, that's fine. Reasons for not using it seem to be based primarily on: inconvenience (we use StereoGraphics glasses and emitters - in spite of having many pairs available, and efforts by the admins here to keep them functional, it can be difficult for a user to find a pair that works, either because of dead batteries or because they're just broken); discomfort (wearing the glasses themselves is a pain, people complain of headaches, and the ambient lighting situation can make using them difficult under some circumstances and cause eye strain); and lack of need. No one uses the dials because no one in our environment is building with O, and this is the only piece of software we have that supports the dials (we have a Linux-only environment). *Everyone* here builds with Coot. I believe (based on somewhat anecdotal evidence) that if Coot supported the dials people would use them more, but they seem quite happy without them; they are certainly not enough reason for people to learn to use O (or go back to using it). The above perception vs reality dichotomy seems to stem largely from a generation gap: users who learned to build using SGIs running O are firm believers in the need for stereo and dials (even though, for the most part, they are no longer actively building); users who learned to build on Linux boxes using Coot simply don't see the need, for the most part. Note that these are, for the most part, users who have never used O, but who *do* actively build, spending hours and days at a time sitting in front of the workstation doing so. In addition, many/most users these days do alot of their building using their own laptops (many/most of which are Macs running OS X), often but not always in conjunction with an external flat panel display. When doing so, they don't use stereo or dials, and again, this doesn't seem to be a huge loss to them, especially given the convenience of being able to work where they want (i.e. at home, in coffee shops libraries, outdoors, etc.) Users also like to be able to sit in front of a flat-panel display to do their work. This seems to be a combination of two factors: the extra space available on the work surface that isn't taken up by a huge CRT; and the absence of the huge, heavy, space-hogging CRT sitting in front of them all day (i.e. a psychological lightness provided by a flat-panel display - this seems hard to quantify, but I experienced it myself when switching from a CRT to a flat-panel, and others I have talked to have reported similar feelings). Obviously, if a reasonably-priced flat-panel stereo solution were to become available this would influence decisions about stereo. I've included our survey questions below my .sig - please feel free to use or adapt them as you like. -- Steve Lane System, Network and Security Administrator Doudna Lab Biomolecular Structure and Mechanism Group UC Berkeley == Greetings. This is a semi-informal survey of recent crystallography workstation users. Please take a minute to respond. Your answers will help us improve the crystallography computing environment. 1) Have you recently (past few months) used a crystallography workstation for molecular model building and/or visualization? YES NO Answer: 2) If yes to (1), which model building software did you use (list all that apply)? COOT O OTHER - please specify Answer: 3) When model building, do you use the dial box? ALWAYS OFTEN SOMETIMES RARELY NEVER Answer: 4) When model building, do you use 3D stereo visualization (i.e. stereo glasses)? ALWAYS OFTEN SOMETIMES RARELY NEVER Answer: 5) If yes to (1), which molecular visualization software did you use (list all that apply)? COOT O CHIMERA PYMOL OTHER - please specify Answer: 6) When visualizing molecular models, do you use the dial box? ALWAYS OFTEN SOMETIMES
Re: [ccp4bb] available Stereo 3D LCD monitors / Linux compatibility
Christian, I think it would be great to continue this discussion on CCP4bb, especially as we learn more about all the new stereo-capable display products now hitting the market. It would be even more wonderful if a few volunteers could monitor this discusson and then summarize their distilled knowledge to a community web page specifically geared toward stereo 3D display options for molecular visualization. Although www.stereo3d.com exists, it is too general, cluttered, and overwhelming... So in order to make this as painless and likely to succeed as possible, I have just created a Stereo 3D Display Options page on the public PyMOL Wiki, and seeded with some headings and links: http://pymolwiki.org/index.php/Stereo_3D_Display_Options Note that to edit the page, you will need a PyMOLWiki account which can be obtained via the link below: http://pymolwiki.org/index.php?title=Special:Userlogintype=signup Cheers, Warren -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Christian RAUSCH Sent: Wednesday, September 17, 2008 12:14 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] available Stereo 3D LCD monitors / Linux compatibility Dear all, I would like to continue the discussion on the availability of 3D-LCD monitors that work with Linux or Mac (started in the discussion Progresss with Stereo 3D under Mac OS X Leopard). (We do have a running stereo capable system with Linux-PC SGI-CTR- monitor CrystalEyes.) Now we are seeking a 3D-LCD monitor that work with Linux (or Mac). Is there anyone using a good, affordable 3D-LCD monitor? Here's what I've found so far: dti3d.com 19 3D LCD (3,695 US$) works officially with linux, pymol, coot. (I'm in contact with a Munich based salesman, I'll keep you updated) Cheaper but apparently not working with Linux /Mac (?) (designed for 3d computer games): Newsight.com 17 (500 EUROs) and 24 (1300 EUROs) no glasses required Drawback: * Windows XP (for additional controller program) required + Nvidia Geforce graphics card http://www.newsight.com/3d-products/displays.html Zalman ZM-M220W: a 22 3D-TFT, simple plarized glasses are required. Drawbacks: * optimal viewing angle for 3D seems to be rather small. Price: 500 EUROs * Windows Vista (for additional controller program) required + Nvidia Geforce graphics card http://www.zalman.co.kr/ENG/product/CategorySecond_Pic.asp?categoryname=Mo nitorscategorySecond= iZ3D 22 3D LCD Flat Panel Computer Gaming Monitor, works with simple polarized glasses, available on amazon.com, not shipped to Germany. Anybody knows anything about it? == someone has good connections to Nvidia? Shouldn't be too difficult for them to add the 3D-support directly to the driver (which would make the additional controller program unnecessary) [Note that there is already support for SeeReal digital flat panel and Sharp3D digital flat panel in the Nvidia Quadro * linux driver, but SeeReal and Sharp are not selling 3D LCDs any more (I asked SeeReal and Sharp:http://www.superwarehouse.com/Sharp_LL1513D_15_Black_LCD_Monitor/LL1 513D/p/1481235 ...) Further I have contacted and am waiting for their reply: dimen / miracube.net tridelity.de spatialview.com Many companies I got from this page: http://www.stereo3d.com/displays.htm Anyone knows if Philips, Sanyo, Sharp, VIEWSONIC, 3dis.co.kr etc. are selling 3D displays? (there is some info on the web that these are working on this technology). Thank you for any contribution to this topic, Christian Rausch Dr. Christian Rausch [EMAIL PROTECTED] Lehrstuhl f. Biologische Chemie Phone: +49 (0)8161 71-4050 Technische Universitaet MuenchenFax: -4352 85350 Freising-Weihenstephan Germany http://www.wzw.tum.de/bc __ Do You Yahoo!? Sie sind Spam leid? Yahoo! Mail verfügt über einen herausragenden Schutz gegen Massenmails. http://mail.yahoo.com
Re: [ccp4bb] Progresss with Stereo 3D under Mac OS X Leopard
From another member of the new generation... I could not agree more with Scott. Stereo is not essential, my lab of thirteen crystallographers does not even have the capability, and noone has ever asked for it (including our older PI). And I have refined and built in one year one 3.9 A and one 3.8 A model, and someone else just built a 3.5A de novo phased model on a small Mac screen with coot (I think that was heroic). We have to do without stereo, but only if there was an easy way to set it up and use it, I would have it. And we should have it (hear that Apple). It's just not worth the lack of freedom and limitations right now. As a grad student we had access to stereo, I did not use it much. I have to say I do not know why new students would be swayed just by them. As a young grad student, I was amazed by chemistry in action (and I still am), and did not need stereo to think about charge, coordination, pi-pi packing and hydrogen bonding, and not the cool 3D (I see the attraction to middle or high school students). Rotating models with depth cues was sufficient. Engin Scott Pegan wrote: Just to put my two cents in on this as I would fall into that new generation so to speak: I started out with the SGI and linux systems with stereo, O, and dials about eight years ago. Never used the dials and rarely seen anyone else use them. Over the past few years I have transition to coot, pc, and now have a MAC. The freedom of not having a bulky system that I have to build on is a huge plus for many of the reasons you described. However, My colleagues and I I DO WANT STEREO. I have nearly perfected building without IT not out of choice but mostly out of lack of one. I feel as many of my colleagues do, that if we had the stereo option on our flat panels we most undoubtedly would use it. We just don't those type of options right know. As a result, I wholeheartedly support anyone trying to get us this added capability. Scott Steve Lane wrote: Warren et al.: The following is based largely on a survey conducted here about 6 months ago (the survey questions are at the bottom of this msg). Among the older generation of PIs, there is a strong perception that stereo and SGI dials are very important to users. This perception is not at all borne out among users themselves (20+ grad students and postdocs, plus one or two junior faculty) - no one uses the dials (see below for why), and stereo is used very infrequently to never. The consensus among the users regarding stereo seems to be some version of the following: if it's available, I might use it occasionally for a particularly difficult part of a molecule, but not otherwise; if it's not available, that's fine. Reasons for not using it seem to be based primarily on: inconvenience (we use StereoGraphics glasses and emitters - in spite of having many pairs available, and efforts by the admins here to keep them functional, it can be difficult for a user to find a pair that works, either because of dead batteries or because they're just broken); discomfort (wearing the glasses themselves is a pain, people complain of headaches, and the ambient lighting situation can make using them difficult under some circumstances and cause eye strain); and lack of need. No one uses the dials because no one in our environment is building with O, and this is the only piece of software we have that supports the dials (we have a Linux-only environment). *Everyone* here builds with Coot. I believe (based on somewhat anecdotal evidence) that if Coot supported the dials people would use them more, but they seem quite happy without them; they are certainly not enough reason for people to learn to use O (or go back to using it). The above perception vs reality dichotomy seems to stem largely from a generation gap: users who learned to build using SGIs running O are firm believers in the need for stereo and dials (even though, for the most part, they are no longer actively building); users who learned to build on Linux boxes using Coot simply don't see the need, for the most part. Note that these are, for the most part, users who have never used O, but who *do* actively build, spending hours and days at a time sitting in front of the workstation doing so. In addition, many/most users these days do alot of their building using their own laptops (many/most of which are Macs running OS X), often but
Re: [ccp4bb] Progresss with Stereo 3D under Mac OS X Leopard
An advantage with stereo viewing is that you can increase the slab in a crowed active site and still make sense of it. In my experiance, valuable for understanding structure function relationships in flexible proteins. Paula Lario On 17-Sep-08, at 8:21 PM, Engin Ozkan [EMAIL PROTECTED] wrote: From another member of the new generation... I could not agree more with Scott. Stereo is not essential, my lab of thirteen crystallographers does not even have the capability, and noone has ever asked for it (including our older PI). And I have refined and built in one year one 3.9 A and one 3.8 A model, and someone else just built a 3.5A de novo phased model on a small Mac screen with coot (I think that was heroic). We have to do without stereo, but only if there was an easy way to set it up and use it, I would have it. And we should have it (hear that Apple). It's just not worth the lack of freedom and limitations right now. As a grad student we had access to stereo, I did not use it much. I have to say I do not know why new students would be swayed just by them. As a young grad student, I was amazed by chemistry in action (and I still am), and did not need stereo to think about charge, coordination, pi-pi packing and hydrogen bonding, and not the cool 3D (I see the attraction to middle or high school students). Rotating models with depth cues was sufficient. Engin Scott Pegan wrote: Just to put my two cents in on this as I would fall into that new generation so to speak: I started out with the SGI and linux systems with stereo, O, and dials about eight years ago. Never used the dials and rarely seen anyone else use them. Over the past few years I have transition to coot, pc, and now have a MAC. The freedom of not having a bulky system that I have to build on is a huge plus for many of the reasons you described. However, My colleagues and I I DO WANT STEREO. I have nearly perfected building without IT not out of choice but mostly out of lack of one. I feel as many of my colleagues do, that if we had the stereo option on our flat panels we most undoubtedly would use it. We just don't those type of options right know. As a result, I wholeheartedly support anyone trying to get us this added capability. Scott Steve Lane wrote: Warren et al.: The following is based largely on a survey conducted here about 6 months ago (the survey questions are at the bottom of this msg). Among the older generation of PIs, there is a strong perception that stereo and SGI dials are very important to users. This perception is not at all borne out among users themselves (20+ grad students and postdocs, plus one or two junior faculty) - no one uses the dials (see below for why), and stereo is used very infrequently to never. The consensus among the users regarding stereo seems to be some version of the following: if it's available, I might use it occasionally for a particularly difficult part of a molecule, but not otherwise; if it's not available, that's fine. Reasons for not using it seem to be based primarily on: inconvenience (we use StereoGraphics glasses and emitters - in spite of having many pairs available, and efforts by the admins here to keep them functional, it can be difficult for a user to find a pair that works, either because of dead batteries or because they're just broken); discomfort (wearing the glasses themselves is a pain, people complain of headaches, and the ambient lighting situation can make using them difficult under some circumstances and cause eye strain); and lack of need. No one uses the dials because no one in our environment is building with O, and this is the only piece of software we have that supports the dials (we have a Linux-only environment). *Everyone* here builds with Coot. I believe (based on somewhat anecdotal evidence) that if Coot supported the dials people would use them more, but they seem quite happy without them; they are certainly not enough reason for people to learn to use O (or go back to using it). The above perception vs reality dichotomy seems to stem largely from a generation gap: users who learned to build using SGIs running O are firm believers in the need for stereo and dials (even though, for the most part, they are no longer actively building); users who learned to build on Linux boxes using Coot simply don't see the need, for the most part. Note that these are, for the most part, users who have never used O, but who *do* actively build,
[ccp4bb] Clarification of MOLREP logfile
Hi All, In the portion of the MOREP logfile where it lists the RF peaks, what does Rf and Rf/sigma mean? Is Rf - peak height and Rf/sigma - peak heights measured as deviations from mean? Looking into the CCP4 tutorial on MOLREP (http://www.ccp4.ac.uk/dist/examples/tutorial/html/mr-tutorial.html) this is mentioned as R factor. Please explain. Rajan.
Re: [ccp4bb] Progresss with Stereo 3D under Mac OS X Leopard
Ironically as this stereo discussion ensues, it seems NVidia is pushing 3d glasses once again (http://tech.slashdot.org/tech/08/09/17/1530202.shtml ) . Those 120Hz LCD's are welcome reprieve from the bulky SGI monitors in our x-ray core now. More on topic, however, as a 'newer' generation (4th year grad) and after building several structures, I have no problem with not having stereo. One particular case it might be helpful in my experience is building into experimental density maps (the worse the map the more helpful the stereo). However, with automated building programs available (even secondary structure building is quite good), I find this to be a non issue anymore. As for normal building, at least in coot, a simple movement of the model/monomer into the density (using simple translations) and then real space refine usually takes care of the job. More of my opinion, I use software that I can run on minimal hardware / low cost (it surprises me how much the Quad FX card for a Mac Pro costs!). My 0.02 FR On Sep 17, 2008, at 9:21 PM, Engin Ozkan wrote: From another member of the new generation... I could not agree more with Scott. Stereo is not essential, my lab of thirteen crystallographers does not even have the capability, and noone has ever asked for it (including our older PI). And I have refined and built in one year one 3.9 A and one 3.8 A model, and someone else just built a 3.5A de novo phased model on a small Mac screen with coot (I think that was heroic). We have to do without stereo, but only if there was an easy way to set it up and use it, I would have it. And we should have it (hear that Apple). It's just not worth the lack of freedom and limitations right now. As a grad student we had access to stereo, I did not use it much. I have to say I do not know why new students would be swayed just by them. As a young grad student, I was amazed by chemistry in action (and I still am), and did not need stereo to think about charge, coordination, pi-pi packing and hydrogen bonding, and not the cool 3D (I see the attraction to middle or high school students). Rotating models with depth cues was sufficient. Engin Scott Pegan wrote: Just to put my two cents in on this as I would fall into that new generation so to speak: I started out with the SGI and linux systems with stereo, O, and dials about eight years ago. Never used the dials and rarely seen anyone else use them. Over the past few years I have transition to coot, pc, and now have a MAC. The freedom of not having a bulky system that I have to build on is a huge plus for many of the reasons you described. However, My colleagues and I I DO WANT STEREO. I have nearly perfected building without IT not out of choice but mostly out of lack of one. I feel as many of my colleagues do, that if we had the stereo option on our flat panels we most undoubtedly would use it. We just don't those type of options right know. As a result, I wholeheartedly support anyone trying to get us this added capability. Scott Steve Lane wrote: Warren et al.: The following is based largely on a survey conducted here about 6 months ago (the survey questions are at the bottom of this msg). Among the older generation of PIs, there is a strong perception that stereo and SGI dials are very important to users. This perception is not at all borne out among users themselves (20+ grad students and postdocs, plus one or two junior faculty) - no one uses the dials (see below for why), and stereo is used very infrequently to never. The consensus among the users regarding stereo seems to be some version of the following: if it's available, I might use it occasionally for a particularly difficult part of a molecule, but not otherwise; if it's not available, that's fine. Reasons for not using it seem to be based primarily on: inconvenience (we use StereoGraphics glasses and emitters - in spite of having many pairs available, and efforts by the admins here to keep them functional, it can be difficult for a user to find a pair that works, either because of dead batteries or because they're just broken); discomfort (wearing the glasses themselves is a pain, people complain of headaches, and the ambient lighting situation can make using them difficult under some circumstances and cause eye strain); and lack of need. No one uses the dials because no one in our environment is building with O, and this is the only piece of software we have that supports the dials (we have a Linux-only environment). *Everyone* here builds with Coot. I believe (based on somewhat
Re: [ccp4bb] Progresss with Stereo 3D under Mac OS X Leopard
On Sep 17, 2008, at 8:21 PM, Engin Ozkan wrote: As a grad student we had access to stereo, I did not use it much. I have to say I do not know why new students would be swayed just by them. As a young grad student, I was amazed by chemistry in action (and I still am), and did not need stereo to think about charge, coordination, pi-pi packing and hydrogen bonding, and not the cool 3D (I see the attraction to middle or high school students). Rotating models with depth cues was sufficient. One thing I have learned in 11 years of teaching chemistry is that no one approach works for everyone. When it comes to spatial visualization, this is especially the case, which is why, for example, organic chemistry is so difficult to teach effectively (and often to learn). Hence I think having as few limitations in place as possible is a good thing, and having stereo hardware available to those (young or old) who could benefit is crucial. For me, I tend to think very abstractly, so it was quantum mechanics and group theory that really sunk the hook into me. But my first introduction to group theory was in my first year of college. I had just learned organic chemistry and was fascinated by the Woodward- Hoffmann rules and how with simply the symmetry of the orbitals alone, one could predict with almost metaphysical certitude the outcome of a complicated pericyclic reaction for which solving the Schrödinger equation accurately would be completely hopeless. So I spent a very long night in the library with a friend of mine going through every group theory book that she and I could find. One of these had stereo glasses in the back (along with those ubiquitous character tables) that made it possible for me, for the first time, to really see in 3D the stereographic projections of various point groups. It was an absolutely stunning revelation, and probably had a lot to do with me later pursuing crystallography. We were completely transfixed by this for hours, (which admittedly may have had something to do with dropping acid earlier that day), but nonetheless it was far better than simply rotating models with depth cueing (which I since learned to do in my mind's eye). Hardware stereo isn't for everyone, but I certainly think everyone benefits from having it as an option on as many platforms as possible. So keep it legal.
