[ccp4bb] Fwd: [ccp4bb] pdbset
-- Forwarded message -- From: Swastik Phulera swastik.phul...@gmail.com Date: Tue, Jun 11, 2013 at 1:51 PM Subject: Re: [ccp4bb] pdbset To: Tim Gruene t...@shelx.uni-ac.gwdg.de Dear Tim, Miguel Thanks for your suggestions, the program does work now, but it seems that it cant handle AnsioU s . It gives an error: PDBSET: *** AnisoU present: cannot reset B *** Is there any other program which would set minimum bfactors for me. Also I am looking for a program that would set the maximum occupancy to a desired value (It seems that pdbset can only play with the minimum values).. On Tue, Jun 11, 2013 at 12:11 PM, Tim Gruene t...@shelx.uni-ac.gwdg.dewrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Swastik Phulera, after the word 'output.pdb' you must first hit the Enter-key which takes you into the program pdbset. Then you type B_reset Minimum 0 END and the program runs. If you wish to do it without interaction, e.g. in a script, you can use the shell construct '': pdbset XYZIN input.pdb XYZOUT output.pdb eof B_reset MINIMUM 0 eof Best, Tim On 06/11/2013 08:15 AM, Swastik Phulera wrote: Dear All, I am trying to use pdbset from the terminal and am constantly getting an error: [XYZ@NCCS3 110613]$ pdbset XYZIN input.pdb XYZOUT output.pdb B_reset MINIMUM 0 CCP4 library signal ccp4_general:Use: logical name file name (Error) raised in ccp4fyp pdbset: Use: logical name file name pdbset: Use: logical name file name Times: User: 0.0s System:0.0s Elapsed: 0:00 Does any one have any idea what's wrong here? Swastik Phulera - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFRtsaJUxlJ7aRr7hoRAiAsAKCuDDip6GFczecze/Y18+YaD4+SqACdGnSU fG1/zzDml0ynkX8uOBN7S+o= =2I5+ -END PGP SIGNATURE- -- -- स्वस्तिक फुलेरा वरिष्ठ अनुसंधान कर्ता संरचनात्मक जीवविज्ञान प्रयोगशाला डी. एन. ए. फिंगरप्रिंटिंग एवं निदान केंद्र हैदराबाद, ५००, ००१ और राष्ट्रीय कोशिका विज्ञान केंद्र पुणे विश्वविद्यालय परिसर, गणेशखिंड पुना, ४११,००७ -- -- स्वस्तिक फुलेरा वरिष्ठ अनुसंधान कर्ता संरचनात्मक जीवविज्ञान प्रयोगशाला डी. एन. ए. फिंगरप्रिंटिंग एवं निदान केंद्र हैदराबाद, ५००, ००१ और राष्ट्रीय कोशिका विज्ञान केंद्र पुणे विश्वविद्यालय परिसर, गणेशखिंड पुना, ४११,००७
Re: [ccp4bb] Fwd: [ccp4bb] pdbset
What about getting rid of the ANISOU records before processing the pdb file, with grep -v ANISOU input.pdb output.pdb ? If a program complains about ANISOU records then you use the isotropic approximation... That's what I would do as a quick and dirty fix. Fred. On 11/06/13 10:22, Swastik Phulera wrote: -- Forwarded message -- From: *Swastik Phulera* swastik.phul...@gmail.com mailto:swastik.phul...@gmail.com Date: Tue, Jun 11, 2013 at 1:51 PM Subject: Re: [ccp4bb] pdbset To: Tim Gruene t...@shelx.uni-ac.gwdg.de mailto:t...@shelx.uni-ac.gwdg.de Dear Tim, Miguel Thanks for your suggestions, the program does work now, but it seems that it cant handle AnsioU s . It gives an error: PDBSET: *** AnisoU present: cannot reset B *** Is there any other program which would set minimum bfactors for me. Also I am looking for a program that would set the maximum occupancy to a desired value (It seems that pdbset can only play with the minimum values).. On Tue, Jun 11, 2013 at 12:11 PM, Tim Gruene t...@shelx.uni-ac.gwdg.de mailto:t...@shelx.uni-ac.gwdg.de wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Swastik Phulera, after the word 'output.pdb' you must first hit the Enter-key which takes you into the program pdbset. Then you type B_reset Minimum 0 END and the program runs. If you wish to do it without interaction, e.g. in a script, you can use the shell construct '': pdbset XYZIN input.pdb XYZOUT output.pdb eof B_reset MINIMUM 0 eof Best, Tim On 06/11/2013 08:15 AM, Swastik Phulera wrote: Dear All, I am trying to use pdbset from the terminal and am constantly getting an error: [XYZ@NCCS3 110613]$ pdbset XYZIN input.pdb XYZOUT output.pdb B_reset MINIMUM 0 CCP4 library signal ccp4_general:Use: logical name file name (Error) raised in ccp4fyp pdbset: Use: logical name file name pdbset: Use: logical name file name Times: User: 0.0s System:0.0s Elapsed: 0:00 Does any one have any idea what's wrong here? Swastik Phulera - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFRtsaJUxlJ7aRr7hoRAiAsAKCuDDip6GFczecze/Y18+YaD4+SqACdGnSU fG1/zzDml0ynkX8uOBN7S+o= =2I5+ -END PGP SIGNATURE- -- -- स्वस्तिक फुलेरा वरिष्ठ अनुसंधान कर्ता संरचनात्मक जीवविज्ञान प्रयोगशाला डी. एन. ए. फिंगरप्रिंटिंग एवं निदान केंद्र हैदराबाद, ५००, ००१ और राष्ट्रीय कोशिका विज्ञान केंद्र पुणे विश्वविद्यालय परिसर, गणेशखिंड पुना, ४११,००७ -- -- स्वस्तिक फुलेरा वरिष्ठ अनुसंधान कर्ता संरचनात्मक जीवविज्ञान प्रयोगशाला डी. एन. ए. फिंगरप्रिंटिंग एवं निदान केंद्र हैदराबाद, ५००, ००१ और राष्ट्रीय कोशिका विज्ञान केंद्र पुणे विश्वविद्यालय परिसर, गणेशखिंड पुना, ४११,००७ -- Fred. Vellieux (B.Sc., Ph.D., hdr) ouvrier de la recherche IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494
Re: [ccp4bb] Fwd: [ccp4bb] pdbset
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Swastik Phulera, unless you need the ANISOU cards, you can first remove them with e.g. grep -v ^ANISOU youfile.pdb yournewfile.pdb before running pdbset. (I hope you don't work on a Windows machine, then you would probably first find a way to install 'grep', a command common on unixoid operating systems). By the way: how did you get negative B-values into your PDB-file? Best, Tim On 06/11/2013 10:22 AM, Swastik Phulera wrote: -- Forwarded message -- From: Swastik Phulera swastik.phul...@gmail.com Date: Tue, Jun 11, 2013 at 1:51 PM Subject: Re: [ccp4bb] pdbset To: Tim Gruene t...@shelx.uni-ac.gwdg.de Dear Tim, Miguel Thanks for your suggestions, the program does work now, but it seems that it cant handle AnsioU s . It gives an error: PDBSET: *** AnisoU present: cannot reset B *** Is there any other program which would set minimum bfactors for me. Also I am looking for a program that would set the maximum occupancy to a desired value (It seems that pdbset can only play with the minimum values).. On Tue, Jun 11, 2013 at 12:11 PM, Tim Gruene t...@shelx.uni-ac.gwdg.dewrote: Dear Swastik Phulera, after the word 'output.pdb' you must first hit the Enter-key which takes you into the program pdbset. Then you type B_reset Minimum 0 END and the program runs. If you wish to do it without interaction, e.g. in a script, you can use the shell construct '': pdbset XYZIN input.pdb XYZOUT output.pdb eof B_reset MINIMUM 0 eof Best, Tim On 06/11/2013 08:15 AM, Swastik Phulera wrote: Dear All, I am trying to use pdbset from the terminal and am constantly getting an error: [XYZ@NCCS3 110613]$ pdbset XYZIN input.pdb XYZOUT output.pdb B_reset MINIMUM 0 CCP4 library signal ccp4_general:Use: logical name file name (Error) raised in ccp4fyp pdbset: Use: logical name file name pdbset: Use: logical name file name Times: User: 0.0s System:0.0s Elapsed: 0:00 Does any one have any idea what's wrong here? Swastik Phulera - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFRtuJQUxlJ7aRr7hoRAhcWAKDGPXBS3iJhzzbaYBK4GnJGjijyngCgqYZI B26VKBDFO5FQNJJQd6plsc8= =mDut -END PGP SIGNATURE-
Re: [ccp4bb] Fwd: [ccp4bb] pdbset
In Windows: findstr /b /v ANISOU input.pdb output.pdb Cheers, Robbie -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim Gruene Sent: Tuesday, June 11, 2013 10:40 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fwd: [ccp4bb] pdbset -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Swastik Phulera, unless you need the ANISOU cards, you can first remove them with e.g. grep -v ^ANISOU youfile.pdb yournewfile.pdb before running pdbset. (I hope you don't work on a Windows machine, then you would probably first find a way to install 'grep', a command common on unixoid operating systems). By the way: how did you get negative B-values into your PDB-file? Best, Tim On 06/11/2013 10:22 AM, Swastik Phulera wrote: -- Forwarded message -- From: Swastik Phulera swastik.phul...@gmail.com Date: Tue, Jun 11, 2013 at 1:51 PM Subject: Re: [ccp4bb] pdbset To: Tim Gruene t...@shelx.uni-ac.gwdg.de Dear Tim, Miguel Thanks for your suggestions, the program does work now, but it seems that it cant handle AnsioU s . It gives an error: PDBSET: *** AnisoU present: cannot reset B *** Is there any other program which would set minimum bfactors for me. Also I am looking for a program that would set the maximum occupancy to a desired value (It seems that pdbset can only play with the minimum values).. On Tue, Jun 11, 2013 at 12:11 PM, Tim Gruene t...@shelx.uni-ac.gwdg.dewrote: Dear Swastik Phulera, after the word 'output.pdb' you must first hit the Enter-key which takes you into the program pdbset. Then you type B_reset Minimum 0 END and the program runs. If you wish to do it without interaction, e.g. in a script, you can use the shell construct '': pdbset XYZIN input.pdb XYZOUT output.pdb eof B_reset MINIMUM 0 eof Best, Tim On 06/11/2013 08:15 AM, Swastik Phulera wrote: Dear All, I am trying to use pdbset from the terminal and am constantly getting an error: [XYZ@NCCS3 110613]$ pdbset XYZIN input.pdb XYZOUT output.pdb B_reset MINIMUM 0 CCP4 library signal ccp4_general:Use: logical name file name (Error) raised in ccp4fyp pdbset: Use: logical name file name pdbset: Use: logical name file name Times: User: 0.0s System:0.0s Elapsed: 0:00 Does any one have any idea what's wrong here? Swastik Phulera - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFRtuJQUxlJ7aRr7hoRAhcWAKDGPXBS3iJhzzbaYBK4GnJGjijyngCgqYZI B26VKBDFO5FQNJJQd6plsc8= =mDut -END PGP SIGNATURE-
Re: [ccp4bb] Fwd: [ccp4bb] pdbset
Dear Tim,Fred Negative B factors and occupancies higher than one came in from shelxl, Also getting rid of Ansiou at first would lead me to an additional step of placing them in their right place later on (is there a short cut that I may take). On Tue, Jun 11, 2013 at 2:09 PM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Swastik Phulera, unless you need the ANISOU cards, you can first remove them with e.g. grep -v ^ANISOU youfile.pdb yournewfile.pdb before running pdbset. (I hope you don't work on a Windows machine, then you would probably first find a way to install 'grep', a command common on unixoid operating systems). By the way: how did you get negative B-values into your PDB-file? Best, Tim On 06/11/2013 10:22 AM, Swastik Phulera wrote: -- Forwarded message -- From: Swastik Phulera swastik.phul...@gmail.com Date: Tue, Jun 11, 2013 at 1:51 PM Subject: Re: [ccp4bb] pdbset To: Tim Gruene t...@shelx.uni-ac.gwdg.de Dear Tim, Miguel Thanks for your suggestions, the program does work now, but it seems that it cant handle AnsioU s . It gives an error: PDBSET: *** AnisoU present: cannot reset B *** Is there any other program which would set minimum bfactors for me. Also I am looking for a program that would set the maximum occupancy to a desired value (It seems that pdbset can only play with the minimum values).. On Tue, Jun 11, 2013 at 12:11 PM, Tim Gruene t...@shelx.uni-ac.gwdg.dewrote: Dear Swastik Phulera, after the word 'output.pdb' you must first hit the Enter-key which takes you into the program pdbset. Then you type B_reset Minimum 0 END and the program runs. If you wish to do it without interaction, e.g. in a script, you can use the shell construct '': pdbset XYZIN input.pdb XYZOUT output.pdb eof B_reset MINIMUM 0 eof Best, Tim On 06/11/2013 08:15 AM, Swastik Phulera wrote: Dear All, I am trying to use pdbset from the terminal and am constantly getting an error: [XYZ@NCCS3 110613]$ pdbset XYZIN input.pdb XYZOUT output.pdb B_reset MINIMUM 0 CCP4 library signal ccp4_general:Use: logical name file name (Error) raised in ccp4fyp pdbset: Use: logical name file name pdbset: Use: logical name file name Times: User: 0.0s System:0.0s Elapsed: 0:00 Does any one have any idea what's wrong here? Swastik Phulera - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFRtuJQUxlJ7aRr7hoRAhcWAKDGPXBS3iJhzzbaYBK4GnJGjijyngCgqYZI B26VKBDFO5FQNJJQd6plsc8= =mDut -END PGP SIGNATURE- -- -- स्वस्तिक फुलेरा वरिष्ठ अनुसंधान कर्ता संरचनात्मक जीवविज्ञान प्रयोगशाला डी. एन. ए. फिंगरप्रिंटिंग एवं निदान केंद्र हैदराबाद, ५००, ००१ और राष्ट्रीय कोशिका विज्ञान केंद्र पुणे विश्वविद्यालय परिसर, गणेशखिंड पुना, ४११,००७
Re: [ccp4bb] Fwd: [ccp4bb] pdbset
If you are resetting B factors you must recalculate the AniosUs later But if you are getting negative B values something in your procedure is less than optimal! Are you refining aniso Us with too limited data? You need high resolution data to attempt this. Are you trying to refine B factors and occupancies at the same time? You need superb data to do this, and as a rule it isnt recommended. (Maybe for metal atoms, or some special ligand, but not a good general practice..) Or have you set occupancies too low, and the B factor is trying to compensate for that? Eleanor On 11 June 2013 10:42, Swastik Phulera swastik.phul...@gmail.com wrote: Dear Tim,Fred Negative B factors and occupancies higher than one came in from shelxl, Also getting rid of Ansiou at first would lead me to an additional step of placing them in their right place later on (is there a short cut that I may take). On Tue, Jun 11, 2013 at 2:09 PM, Tim Gruene t...@shelx.uni-ac.gwdg.dewrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Swastik Phulera, unless you need the ANISOU cards, you can first remove them with e.g. grep -v ^ANISOU youfile.pdb yournewfile.pdb before running pdbset. (I hope you don't work on a Windows machine, then you would probably first find a way to install 'grep', a command common on unixoid operating systems). By the way: how did you get negative B-values into your PDB-file? Best, Tim On 06/11/2013 10:22 AM, Swastik Phulera wrote: -- Forwarded message -- From: Swastik Phulera swastik.phul...@gmail.com Date: Tue, Jun 11, 2013 at 1:51 PM Subject: Re: [ccp4bb] pdbset To: Tim Gruene t...@shelx.uni-ac.gwdg.de Dear Tim, Miguel Thanks for your suggestions, the program does work now, but it seems that it cant handle AnsioU s . It gives an error: PDBSET: *** AnisoU present: cannot reset B *** Is there any other program which would set minimum bfactors for me. Also I am looking for a program that would set the maximum occupancy to a desired value (It seems that pdbset can only play with the minimum values).. On Tue, Jun 11, 2013 at 12:11 PM, Tim Gruene t...@shelx.uni-ac.gwdg.dewrote: Dear Swastik Phulera, after the word 'output.pdb' you must first hit the Enter-key which takes you into the program pdbset. Then you type B_reset Minimum 0 END and the program runs. If you wish to do it without interaction, e.g. in a script, you can use the shell construct '': pdbset XYZIN input.pdb XYZOUT output.pdb eof B_reset MINIMUM 0 eof Best, Tim On 06/11/2013 08:15 AM, Swastik Phulera wrote: Dear All, I am trying to use pdbset from the terminal and am constantly getting an error: [XYZ@NCCS3 110613]$ pdbset XYZIN input.pdb XYZOUT output.pdb B_reset MINIMUM 0 CCP4 library signal ccp4_general:Use: logical name file name (Error) raised in ccp4fyp pdbset: Use: logical name file name pdbset: Use: logical name file name Times: User: 0.0s System:0.0s Elapsed: 0:00 Does any one have any idea what's wrong here? Swastik Phulera - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFRtuJQUxlJ7aRr7hoRAhcWAKDGPXBS3iJhzzbaYBK4GnJGjijyngCgqYZI B26VKBDFO5FQNJJQd6plsc8= =mDut -END PGP SIGNATURE- -- -- स्वस्तिक फुलेरा वरिष्ठ अनुसंधान कर्ता संरचनात्मक जीवविज्ञान प्रयोगशाला डी. एन. ए. फिंगरप्रिंटिंग एवं निदान केंद्र हैदराबाद, ५००, ००१ और राष्ट्रीय कोशिका विज्ञान केंद्र पुणे विश्वविद्यालय परिसर, गणेशखिंड पुना, ४११,००७
Re: [ccp4bb] Fwd: [ccp4bb] pdbset
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Swastik Phulera, if your res-file sports negative U-values, your model has room for improvement. You really should go back to the ins-file and make the appropriate modifications in order to get rid of negative U-values (the do not make chemical sense!). Do you use RIGU? It might overcome your problem. Negative B-values (of waters) could also mean that you placed an oxygen instead of a heavier ion. Best, Tim On 06/11/2013 11:42 AM, Swastik Phulera wrote: Dear Tim,Fred Negative B factors and occupancies higher than one came in from shelxl, Also getting rid of Ansiou at first would lead me to an additional step of placing them in their right place later on (is there a short cut that I may take). On Tue, Jun 11, 2013 at 2:09 PM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: Dear Swastik Phulera, unless you need the ANISOU cards, you can first remove them with e.g. grep -v ^ANISOU youfile.pdb yournewfile.pdb before running pdbset. (I hope you don't work on a Windows machine, then you would probably first find a way to install 'grep', a command common on unixoid operating systems). By the way: how did you get negative B-values into your PDB-file? Best, Tim On 06/11/2013 10:22 AM, Swastik Phulera wrote: -- Forwarded message -- From: Swastik Phulera swastik.phul...@gmail.com Date: Tue, Jun 11, 2013 at 1:51 PM Subject: Re: [ccp4bb] pdbset To: Tim Gruene t...@shelx.uni-ac.gwdg.de Dear Tim, Miguel Thanks for your suggestions, the program does work now, but it seems that it cant handle AnsioU s . It gives an error: PDBSET: *** AnisoU present: cannot reset B *** Is there any other program which would set minimum bfactors for me. Also I am looking for a program that would set the maximum occupancy to a desired value (It seems that pdbset can only play with the minimum values).. On Tue, Jun 11, 2013 at 12:11 PM, Tim Gruene t...@shelx.uni-ac.gwdg.dewrote: Dear Swastik Phulera, after the word 'output.pdb' you must first hit the Enter-key which takes you into the program pdbset. Then you type B_reset Minimum 0 END and the program runs. If you wish to do it without interaction, e.g. in a script, you can use the shell construct '': pdbset XYZIN input.pdb XYZOUT output.pdb eof B_reset MINIMUM 0 eof Best, Tim On 06/11/2013 08:15 AM, Swastik Phulera wrote: Dear All, I am trying to use pdbset from the terminal and am constantly getting an error: [XYZ@NCCS3 110613]$ pdbset XYZIN input.pdb XYZOUT output.pdb B_reset MINIMUM 0 CCP4 library signal ccp4_general:Use: logical name file name (Error) raised in ccp4fyp pdbset: Use: logical name file name pdbset: Use: logical name file name Times: User: 0.0s System:0.0s Elapsed: 0:00 Does any one have any idea what's wrong here? Swastik Phulera - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFRtwdfUxlJ7aRr7hoRAsy/AKCI1LfMVm9XM8HQfYacV91pRqK/3ACgtcSY LT/zS9Igbt0Q/EghhpU4LDw= =MCpu -END PGP SIGNATURE-
