[PyMOL] Color menus off?
Hi all, I just upgraded to the pymol 1.2b2. The install works perfectly etc. I have a strange phenomenon though, all the colors in the menu on the right side of the graphics windows have disappeared as well as the colors in the sequence panel. Any hint what it might be? I have not change my configuration (environment variables): System: Windows XP sp3 Path containing C:\Program Files\Delano Scientific\Pymol PYMOLPATH defined to C:\Program Files\Delano Scientific\Pymol PYTHONPATH defined to C:\Python25 (I use python for other things...). Other than that, everything works perfectly (as far as I have tested) Gilles begin:vcard fn:Gilles Truan n:Truan;Gilles org;quoted-printable:CNRS;Centre de G=C3=A9n=C3=A9tique Mol=C3=A9culaire adr:;;1 Av. de la Terrasse;Gif-sur-Yvette Cedex;;91198;France email;internet:gilles.tr...@cgm.cnrs-gif.fr title;quoted-printable:Charg=C3=A9 de Recherches tel;work:33-(0)1 69 82 36 65 tel;fax:33-(0)1 69 82 36 82 tel;home:33-(0)1 64 92 09 15 tel;cell:33-(0)6 28 06 67 84 url:http://www.cgm.cnrs-gif.fr/pompon/index.html version:2.1 end:vcard
Re: [PyMOL] [Apbs-users] Strange behaviour with APBS
Thank you Tom! Well, I can change my APBS script to remove all alternate conformations from b to d or e!!! Thank you again for pulling out the information. Gilles Thomas Stout a écrit : To follow up on one of Gilles least important questions: I was convinced that the PDB must contain structures for which there are more than two alternate conformations. I downloaded all structures with resolutions between 0.5 and 1.0A and with a bit of regexp grepping, quickly found the following set of examples with at least three alternate conformers (I didn't find any with more than four, and the few that had four looked suspicious): 1BXO, 1BYI, 1CBN, 1CEX, 1DY5, 1EB6, 1EJG, 1EM0, 1EN8, 1EN9, 1ENE, 1ENN, 1ET1, 1EXR, 1F9Y, 1FN8, 1FY4, 1FY5, 1GCI, 1GDN, 1GWE, 1IX9, 1IXB, 1JFB, 1JXT, 1JXU, 1JXW, 1JXX, 1JXY, 1KTH, 1M40, 1MSO, 1MUW, 1MWQ, 1MXT, 1N1P, 1N4U, 1N4V, 1N4W, 1N55, 1N9B, 1OD3, 1PJX, 1PQ5, 1PQ8, 1R6J, 1S5M, 1S5N, 1SSX, 1TG0, 1US0, 1UZV, 1V0L, 1V6P, 1VB0, 1W0N, 1X6X, 1X6Z, 1XG0, 1XVO, 1YK4, 2AT0, 2BV4, 2BW4, 2CNQ, 2CWS, 2DDX, 2E4T, 2FWH, 2GEW, 2GG2, 2H5C, 2H5D, 2I16, 2I17, 2IXT, 2IZQ, 2NLS, 2NMZ, 2NRL, 2O7A, 2P74, 2PEV, 2PF8, 2PFH, 2PPP, 2PWA, 2PYA, 2QCP, 2QXW, 2RH2, 2V8B, 2VB1, 2Z6W, 3AL1, 3B3R, 3C78, 3CNJ, 3D1P, 8A3H Cheers! -Tom -Original Message- From: Gilles Truan [mailto:gilles.tr...@cgm.cnrs-gif.fr] Sent: Mon 9/22/2008 6:14 AM To: Nathan Baker Cc: David Gohara; apbs-us...@lists.sourceforge.net list; pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] [Apbs-users] Strange behaviour with APBS Dear all, Sorry for the late answer but I finally managed to find what the error is... First thing, I work on a Windows XP environment (nobody's perfect!!), and some of the problems were related to that. When I tried running everything from the command line (ie pdb2pqr and apbs) I did get the files 1CJC.pqr and the corresponding map pot.dx. I was able to read them with pymol and everything works. The problem arises only with the APBS pymol plugin. In the CJC file, residues with the alternate configuration A (and frankly I do not see the reason for that as the alt B is not present) existed and the handling of these alt conformations is different if pymol or pdb2pqr do the charge calculation. When the pdb file is transformed by pdb2pqr (command line version 1.3.0), the alternate sidechains conformations disappear. When Pymol transforms the file into a pqr one the alt field is still present and apbs does not understand the atom that looks something like NH1AARG. If I use the file generated by pdb2pqr (with the --apbs-input option) it works, apbs reads and does the calculation. The trick is the to remove alternate configurations (specially when no alt B exists!!!). I have done it on the CJC file and everything works perfectly from the apbs plugin and without the need to generate the pdb2pqr file. I was not able to pinpoint the problem with the pymol output when running APBS. I noticed that the error messages differ a bit if I run Pymol from a link (ie without a shell window) or from the pymol command in a DOS shell. In the Pymol command window the error message is : * APBS Tools: coarse grid: (301.633,318.546,307.146) APBS Tools: fine grid: (197.431,207.380,200.674) APBS Tools: center: (11.993,-11.506,14.548) APBS Tools: fine grid points (97,97,97) ObjectMapLoadDXFile-Error: Unable to open file! ObjectMapLoadDXFile: Does 'pymol-generated.dx' exist? * while in the cmd window the message is *Reading PQR-format atom data from pymol-generated.pqr. Valist_readPQR: Error parsing atom 3526! Error reading molecules! ObjectMapLoadDXFile-Error: Unable to open file! ObjectMapLoadDXFile: Does 'pymol-generated.dx' exist?* which of course is much more informative because it points directly to the error in the pqr file that I had not been able to find because the pqr looked ok to me (Unfortunately I did not jump to the 3526th atom that has the alt A conformation!!). Now the last problem: running the APBS plugin in WinXP generate path errors because of the spaces in the paths. *Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from **D:\Documents. VASSERT: ASSERTION FAILURE! filename vmem.c, line 241, ((num 0) (size 0)) This application has requested the Runtime to terminate it in an unusual way. Please contact the application's support team for more information. ObjectMapLoadDXFile-Error: Unable to open file! ObjectMapLoadDXFile: Does 'pymol-generated.dx' exist?* So the path is not complete (D:\Documents and Settings\Gilles\Mes Documents\blahblahblah\ is missing). Again, the error message in the pymol console was not complete: * APBS Tools: coarse grid: (103.210,121.009,109.487) APBS Tools: fine grid: (80.712,91.182,84.404) APBS Tools: center: (17.315,-2.473,13.671) APBS Tools: fine grid points (97,97,97) ObjectMapLoadDXFile-Error: Unable to open file! * Unfortunately I thought I had the same error while trying to run APBS
Re: [PyMOL] [Apbs-users] Strange behaviour with APBS
I think I found the problem with reading externally generated pqr files... When pymol generates by itself the pqr file, it puts it in the working directory, hence the pymol-generated.in used for apbs and the pqr file are in the same directory. In the pymol-generated.in the file name of the pqr is given directly without any path given. On the contrary, when an externally generated pqr file is given in apbs plugin, the pymol-generated.in puts the entire path of the file, and in my case the path has spaces in its directory name... The APBS manual is quite clear about that: /|path|/ The location of the molecular data file. This pathname should not include spaces. And therefore APBS cannot read the pqr file! Well, I think it really does not matter for now, as the different methods to work with the APBS plugin should work readilt. If for any reason some atoms are not assigned charges with pymo, I can still generated the pqr file, the apbs ini file and calculate the potential with apbs and read it with pymol Gilles Gilles Truan a écrit : Dear all, Sorry for the late answer but I finally managed to find what the error is... First thing, I work on a Windows XP environment (nobody's perfect!!), and some of the problems were related to that. When I tried running everything from the command line (ie pdb2pqr and apbs) I did get the files 1CJC.pqr and the corresponding map pot.dx. I was able to read them with pymol and everything works. The problem arises only with the APBS pymol plugin. In the CJC file, residues with the alternate configuration A (and frankly I do not see the reason for that as the alt B is not present) existed and the handling of these alt conformations is different if pymol or pdb2pqr do the charge calculation. When the pdb file is transformed by pdb2pqr (command line version 1.3.0), the alternate sidechains conformations disappear. When Pymol transforms the file into a pqr one the alt field is still present and apbs does not understand the atom that looks something like NH1AARG. If I use the file generated by pdb2pqr (with the --apbs-input option) it works, apbs reads and does the calculation. The trick is the to remove alternate configurations (specially when no alt B exists!!!). I have done it on the CJC file and everything works perfectly from the apbs plugin and without the need to generate the pdb2pqr file. I was not able to pinpoint the problem with the pymol output when running APBS. I noticed that the error messages differ a bit if I run Pymol from a link (ie without a shell window) or from the pymol command in a DOS shell. In the Pymol command window the error message is : * APBS Tools: coarse grid: (301.633,318.546,307.146) APBS Tools: fine grid: (197.431,207.380,200.674) APBS Tools: center: (11.993,-11.506,14.548) APBS Tools: fine grid points (97,97,97) ObjectMapLoadDXFile-Error: Unable to open file! ObjectMapLoadDXFile: Does 'pymol-generated.dx' exist? * while in the cmd window the message is *Reading PQR-format atom data from pymol-generated.pqr. Valist_readPQR: Error parsing atom 3526! Error reading molecules! ObjectMapLoadDXFile-Error: Unable to open file! ObjectMapLoadDXFile: Does 'pymol-generated.dx' exist?* which of course is much more informative because it points directly to the error in the pqr file that I had not been able to find because the pqr looked ok to me (Unfortunately I did not jump to the 3526th atom that has the alt A conformation!!). Now the last problem: running the APBS plugin in WinXP generate path errors because of the spaces in the paths. *Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from **D:\Documents. VASSERT: ASSERTION FAILURE! filename vmem.c, line 241, ((num 0) (size 0)) This application has requested the Runtime to terminate it in an unusual way. Please contact the application's support team for more information. ObjectMapLoadDXFile-Error: Unable to open file! ObjectMapLoadDXFile: Does 'pymol-generated.dx' exist?* So the path is not complete (D:\Documents and Settings\Gilles\Mes Documents\blahblahblah\ is missing). Again, the error message in the pymol console was not complete: * APBS Tools: coarse grid: (103.210,121.009,109.487) APBS Tools: fine grid: (80.712,91.182,84.404) APBS Tools: center: (17.315,-2.473,13.671) APBS Tools: fine grid points (97,97,97) ObjectMapLoadDXFile-Error: Unable to open file! * Unfortunately I thought I had the same error while trying to run APBS with the 1CJC file and using the pymol generated pqr (error with alt conformations) or using the pqr file generated independantly (PATH error with spaces in path names). It is all sorted out now. I can use the pdb2pqr web site to generate the pqr and apbs input files or directly pymol APBS plugin with the b factor and alternate conformation blanked out before use!!! I finally looked at the apbs.py file to see where the pqr calculation was and added a few commands
Re: [PyMOL] [Apbs-users] Strange behaviour with APBS
in common. For now, however, the workaround is to make sure no B-factors exceed 100. alter all, b=min(b,99.9) should about do it. Cheers, Warren -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Gilles Truan Sent: Wednesday, September 17, 2008 1:09 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Strange behaviour with APBS I have noticed a strange behaviour of the APBS module. I used it a lot recently and it works perfectly for 95% of the structures I analyzed. I usually fetch the pdb code, then remove waters, heteroatoms and so on. I also noticed that in some cases, when the b factor is quite big (over 100) APBS cannot work the pdb file because it mixes up the b factor and the number which is just before (occupancy). But I managed with that, I usually erase the b factor to 0 before doing the APBS calculation and everything works fine then. The other strange behavious is related to nothing I can pinpoint unfortunately. For some files (I always fetch them with the fetch command from Pymol), I can set the grid OK and when I launch APBS, I can see the file being processed (I see the select and hydrogens go on!) and then it stops with the following error message: ObjectMapLoadDXFile-Error: Unable to open file! ObjectMapLoadDXFile: Does 'pymol-generated.dx' exist? All the paths for APBS are correctly setup, the temp files are setup as well. If I then fetch a new file, APBS works, even for several files (one after another) and if I come back to the file I wanted to do first, it gives me the same error message (BTW, the pdb file is 1CJC). Any help would be greatly appreciated!!! -- --- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ apbs-users mailing list apbs-us...@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/apbs-users -- Associate Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ gilles_truan.vcf -- Associate Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ begin:vcard fn:Gilles Truan n:Truan;Gilles org;quoted-printable:CNRS;Centre de G=C3=A9n=C3=A9tique Mol=C3=A9culaire adr:;;1 Av. de la Terrasse;Gif-sur-Yvette Cedex;;91198;France email;internet:gilles.tr...@cgm.cnrs-gif.fr title;quoted-printable:Charg=C3=A9 de Recherches tel;work:33-(0)1 69 82 36 65 tel;fax:33-(0)1 69 82 36 82 tel;home:33-(0)1 64 92 09 15 tel;cell:33-(0)6 28 06 67 84 url:http://www.cgm.cnrs-gif.fr/pompon/index.html version:2.1 end:vcard
Re: [PyMOL] [Apbs-users] Strange behaviour with APBS
I installed APBS 0.4.0 and my pymol version is the latest build for windows, ie 1.1 r0, the apbs plugin is the latest also I believe. The b factor error is only visible when calculating the grid. I already use the b factor change (alter 1cjc, b=0), and the workaround works perfectly when the error message complains about strange numbers in the file (ValueError: invalid literal for float(): 1.00101.34). I also tried to do a pdb2pqr (via the web interface) before doing apbs, but I have never been able to read the pqr file through the APBS interface. In my hands, the pymol pdb to pqr conversion works quite well. My second problem is apparently not related to the b factor or the pqr file: it seems that for some pdb files, APBS cannot (or does not) see (or write) the pymol-generated.dx file... If I fetch 1EHB pdb file, I can calculate an APBS map (removing water and hem molecules). If I fetch 1CJC pdb file, I cannot (again removing water and fad molecules)!! If I fetch again 1EHB and redo the calculation, everything goes fine. Here is the output of the commands... PyMOLfetch 1ehb PyMOLremove resn hoh+hem APBS Tools: coarse grid: (61.146,53.431,62.444) APBS Tools: fine grid: (55.968,51.430,56.732) APBS Tools: center: (16.504,0.863,7.287) APBS Tools: fine grid points (97,97,97) DXStrToMap: Dimensions: 97 97 97 DXStrToMap: Origin -11.480 -24.852 -21.079 DXStrToMap: Grid0.5830.5360.591 DXStrToMap: 912673 data points. PyMOLdelete all PyMOLfetch 1cjc PyMOLremove resn hoh+fad Maximum number of grid points exceeded. Old grid dimensions were [129, 161, 161] Fine grid points rounded down from [91, 115, 115] New grid dimensions are [65, 97, 97] APBS Tools: coarse grid: (100.841,119.466,106.848) APBS Tools: fine grid: (79.318,90.274,82.852) APBS Tools: center: (17.545,-2.019,13.919) APBS Tools: fine grid points (65,97,97) ObjectMapLoadDXFile-Error: Unable to open file! ObjectMapLoadDXFile: Does 'pymol-generated.dx' exist? PyMOLdelete all PyMOLfetch 1ehb PyMOLremove resn hoh+hem APBS Tools: coarse grid: (61.146,53.431,62.444) APBS Tools: fine grid: (55.968,51.430,56.732) APBS Tools: center: (16.504,0.863,7.287) APBS Tools: fine grid points (97,97,97) DXStrToMap: Dimensions: 97 97 97 DXStrToMap: Origin -11.480 -24.852 -21.079 DXStrToMap: Grid0.5830.5360.591 DXStrToMap: 912673 data points. DeLano Scientific a écrit : Nathan, Strictly speaking, the issue may be with PDB2PQR itself, not APBS. Furthermore, we don't yet know whether a combined development version of all three packages would still reproduce the problem. As an aside, a good reason for PyMOL to see PQR files is for diagnostic visualization: to enable the user to inspect and modify or manipulate what is being fed directly into APBS. PyMOL can read write PQR directly, though we may have issues reading non-PDB-like PQR files. I would generally agree that use of PDB2PQR to convert PDBs to PQRs is the preferred route, since PyMOL doesn't do any checking or optimization. Anyway, based on reported symptoms alone, the problem appears to be that some component in the PyMOL-APBS pipeline assumes that the input PDBs are space-delimited rather than column-delimited. This guess is based on the observation that a B-factor of 100 or greater eliminates the space between the occupany and the B factor in spec-compliant PDB files, and the calculation fails. As a starting point for troubleshooting, I just pulled current pdb2pqr source from trunk and CANNOT reproduce the problem, so either this is already a solved problem with current code, or something else is going on. Gilles, what versions of PyMOL and APBS are you using? Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com -Original Message- From: Nathan Baker [mailto:nathanaba...@mac.com] Sent: Wednesday, September 17, 2008 6:28 PM To: DeLano Scientific Cc: gilles.tr...@cgm.cnrs-gif.fr; pymol-users@lists.sourceforge.net; apbs-us...@lists.sourceforge.net Subject: Re: [Apbs-users] [PyMOL] Strange behaviour with APBS Hi Warren -- The PQR format (which doesn't really have a standard) is basically just whitespace delimited. I'm curious, though -- why would a PyMOL APBS invocation ever see the PDB file? Wouldn't a user first convert it to PQR with PDB2PQR (ideally) or with PyMOL's built-in functionality? Thanks, Nathan On Sep 17, 2008, at 2:21 PM, DeLano Scientific wrote: Gilles, The PyMOL and APBS programs have differing views as to whether PDB PQR files are column-based or space-delimited, respectively. We must eventually sort this out, because it causes continued grief for our users in common. For now, however, the workaround is to make sure no B-factors exceed 100. alter all, b=min(b,99.9) should about do it. Cheers, Warren -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Gilles Truan Sent
[PyMOL] Strange behaviour with APBS
I have noticed a strange behaviour of the APBS module. I used it a lot recently and it works perfectly for 95% of the structures I analyzed. I usually fetch the pdb code, then remove waters, heteroatoms and so on. I also noticed that in some cases, when the b factor is quite big (over 100) APBS cannot work the pdb file because it mixes up the b factor and the number which is just before (occupancy). But I managed with that, I usually erase the b factor to 0 before doing the APBS calculation and everything works fine then. The other strange behavious is related to nothing I can pinpoint unfortunately. For some files (I always fetch them with the fetch command from Pymol), I can set the grid OK and when I launch APBS, I can see the file being processed (I see the select and hydrogens go on!) and then it stops with the following error message: ObjectMapLoadDXFile-Error: Unable to open file! ObjectMapLoadDXFile: Does 'pymol-generated.dx' exist? All the paths for APBS are correctly setup, the temp files are setup as well. If I then fetch a new file, APBS works, even for several files (one after another) and if I come back to the file I wanted to do first, it gives me the same error message (BTW, the pdb file is 1CJC). Any help would be greatly appreciated!!! begin:vcard fn:Gilles Truan n:Truan;Gilles org;quoted-printable:CNRS;Centre de G=C3=A9n=C3=A9tique Mol=C3=A9culaire adr:;;1 Av. de la Terrasse;Gif-sur-Yvette Cedex;;91198;France email;internet:gilles.tr...@cgm.cnrs-gif.fr title;quoted-printable:Charg=C3=A9 de Recherches tel;work:33-(0)1 69 82 36 65 tel;fax:33-(0)1 69 82 36 82 tel;home:33-(0)1 64 92 09 15 tel;cell:33-(0)6 28 06 67 84 url:http://www.cgm.cnrs-gif.fr/pompon/index.html version:2.1 end:vcard
[PyMOL] alter_state for y coordinates (2)?
Sorry for my first post, I just relaized it was kind of hard to read with all the funny tags I am reposting for clarity!!! I am trying to run a script to translate all pdb structures so that an atom of the protein gets the coordinate (0,0,0) I have written a small script for that: for i in pdb_names: stored.xyz = [] cmd.iterate_state(1,(%s and name fe %(i)),stored.xyz.append([x,y,z])) a=stored.xyz[0][0] b=stored.xyz[0][1] c=stored.xyz[0][2] cmd.alter_state (1,(%s %(i)),x=x-a) cmd.alter_state (1,(%s %(i)),y=y-b) cmd.alter_state (1,(%s %(i)),z=z-c) First, I have not been able to translate all the coordinates at once in the script with something like cmd.alter_state (1,(%s %(i)),((x,y,z)=(x-a,y-b,z-c))) I get this error message cmd.alter_state (1,(1AW3 and name fe),((x,y,z)=(x-a,y-b,z-c))) ^ SyntaxError: invalid syntax This was overcome by affecting each value separately. But then, when I check the coordinates of the fe atom that should be (0,0,0) all of them have zero values for x and z, but ot for y!! All the y values are unaffected!!! Is there something I am missing in the number format? When I check coordinates via the cmd.iterate_state, I can see that most of them are numbers with around 15 to 16 significative figures... where the pdb file has only three figures!! Is there something that is added by the iterate_state command, and might this could affect the calculation of the translation? Thanks in advance for your answers ;)
[PyMOL] TR : alter_state for y coordinates?
Yes, there definitely was an error in the quotes... And thank you for the insight in the parenthesis, actually it works without, I was not able to figure it out So the script for i in pdb_names: stored.xyz = [] cmd.iterate_state(1,(%s and name fe %(i)),stored.xyz.append([x,y,z])) a=stored.xyz[0][0] b=stored.xyz[0][1] c=stored.xyz[0][2] cmd.alter_state (1,(%s %(i)),x,y,z=x-a,y-b,z-c) cmd.alter_state (1,(%s-h %(i)),x,y,z=x-a,y-b,z-c) now works fine... But I still have the strange thing with the y displacement. If I run the script and I check the fe position (set as the reference one): PyMOLiterate_state 1,1AW3 and name fe,(x,y,z) (0.0, 9.5340003967285156, 0.0) So the y position has not change while the x and z have shifted Strange, no? Hi, Firstly, I can see why there is a syntax error for the alter_state command: cmd.alter_state (1,(1AW3 and name fe),((x,y,z)=(x-a,y-b,z-c))) has the quotes in the wrong place. I guess it should be: cmd.alter_state(1,(1AW3 and name fe),((x,y,z)=(x-a,y-b,z-c))) I can make every atom move by saying: cmd.alter_state(1, my_structure, x, y, z = x + 1, y + 1, z + 1) So, the x,y,z=x-a,y-b,z-c would probably work, too. I hadn't realised that variables in the current scope were accessible from the alter_state scope, too. gilleain On 6/19/07, Gilles Truan gtr...@cg... wrote: Sorry for my first post, I just relaized it was kind of hard to read with all the funny tags I am reposting for clarity!!! I am trying to run a script to translate all pdb structures so that an atom of the protein gets the coordinate (0,0,0) I have written a small script for that: for i in pdb_names: stored.xyz = [] cmd.iterate_state(1,(%s and name fe %(i)),stored.xyz.append([x,y,z])) a=stored.xyz[0][0] b=stored.xyz[0][1] c=stored.xyz[0][2] cmd.alter_state (1,(%s %(i)),x=x-a) cmd.alter_state (1,(%s %(i)),y=y-b) cmd.alter_state (1,(%s %(i)),z=z-c) First, I have not been able to translate all the coordinates at once in the script with something like cmd.alter_state (1,(%s %(i)),((x,y,z)=(x-a,y-b,z-c))) I get this error message cmd.alter_state (1,(1AW3 and name fe),((x,y,z)=(x-a,y-b,z-c))) ^ SyntaxError: invalid syntax This was overcome by affecting each value separately. But then, when I check the coordinates of the fe atom that should be (0,0,0) all of them have zero values for x and z, but ot for y!! All the y values are unaffected!!! Is there something I am missing in the number format? When I check coordinates via the cmd.iterate_state, I can see that most of them are numbers with around 15 to 16 significative figures... where the pdb file has only three figures!! Is there something that is added by the iterate_state command, and might this could affect the calculation of the translation? Thanks in advance for your answers ;)
[PyMOL] TR : TR : alter_state for y coordinates?
YES! Sometime you feel quite stupid It was considered as the b factor... So everything works fine now... I'll be careful with already used named variables. Thank you all for your help -Message d'origine- De : pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] De la part de lie...@ultr.vub.ac.be Envoyé : mardi 19 juin 2007 16:41 À : pymol-users@lists.sourceforge.net Objet : Re: [PyMOL] TR : alter_state for y coordinates? On Tuesday 19 June 2007 16:24, Gilles Truan wrote: cmd.alter_state (1,(%s %(i)),x,y,z=x-a,y-b,z-c) But I still have the strange thing with the y displacement. If I run the script and I check the fe position (set as the reference one): Maybe the problem is that the b is being interpreted as the B factor of the atom, while a and c have no special meaning. Try x0, y0 and z0 as the names for the variables for your displacement. -- Lieven Buts Laboratorium voor Ultrastructuur Vrije Universiteit Brussel - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
