[ccp4bb] Align linux version
Dear CCP4 users, We are trying to align two different structures. It would be helpful for us if anybody has linux compiled align version? Regards, Mintu Chandra
Re: [ccp4bb] Align linux version
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Mintu Chandra, Do you mean by 'has linux compiled align version', that 'align' is a program you use for the alignment? I wonder because I have not heard of it. If you would be happy with any alignment software, you could use coot (graphical) or lsqkab (command line). Both programs areavailable once you installed ccp4. Regards, Tim Gruene On 11/10/2013 01:30 PM, Mintu Chandra wrote: > Dear CCP4 users, > > We are trying to align two different structures. It would be > helpful for us if anybody has linux compiled align version? > > Regards, > > Mintu Chandra > - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.15 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFSf/YeUxlJ7aRr7hoRAvhHAJ4+LUkvSIMPWjbTkKdw3+6LMtztfQCgztjN lG+aflDaFBmC8kBvJYA4WoE= =Vpsr -END PGP SIGNATURE-
Re: [ccp4bb] Align linux version
Mintu Chandra, align is gerson cohen's program. Unless you talk about another align. I googled "align for linux Gerson Cohen" and here is what I found -- the linux version http://software.compbio.washington.edu/ramp/ramp/src/other_source/align.save.f Test it and see if it works. If not, there is a superpose server as well that you can use in the internet. just google superpose. Also coot. Phenix has some option as I recall I have seen it. lsqman does the job as well. jackie vitali On Sun, Nov 10, 2013 at 4:09 PM, Tim Gruene wrote: > -BEGIN PGP SIGNED MESSAGE- > Hash: SHA1 > > Dear Mintu Chandra, > > Do you mean by 'has linux compiled align version', that 'align' is a > program you use for the alignment? I wonder because I have not heard > of it. > > If you would be happy with any alignment software, you could use coot > (graphical) or lsqkab (command line). Both programs areavailable once > you installed ccp4. > > Regards, > Tim Gruene > > On 11/10/2013 01:30 PM, Mintu Chandra wrote: > > Dear CCP4 users, > > > > We are trying to align two different structures. It would be > > helpful for us if anybody has linux compiled align version? > > > > Regards, > > > > Mintu Chandra > > > > - -- > Dr Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > -BEGIN PGP SIGNATURE- > Version: GnuPG v1.4.15 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ > > iD8DBQFSf/YeUxlJ7aRr7hoRAvhHAJ4+LUkvSIMPWjbTkKdw3+6LMtztfQCgztjN > lG+aflDaFBmC8kBvJYA4WoE= > =Vpsr > -END PGP SIGNATURE- >
Re: [ccp4bb] Align linux version
Back in 2003 I wrote an email to Gerson Cohen concerning ALIGN and he told me to contact Boaz Shaanan. Boaz was so kind to send me his linuxified fortran code of the align program (reading of a prealigment could not be implemented) that is still working on our linux machines! We use it a lot, great program. Ask Boaz (but not all at once please :-) )!! - J. - Am 10.11.13 22:09, schrieb Tim Gruene: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Mintu Chandra, Do you mean by 'has linux compiled align version', that 'align' is a program you use for the alignment? I wonder because I have not heard of it. If you would be happy with any alignment software, you could use coot (graphical) or lsqkab (command line). Both programs areavailable once you installed ccp4. Regards, Tim Gruene -- 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: +49-451-5004065 Fax: +49-451-5004068 Http://www.biochem.uni-luebeck.de Http://www.iobcr.org Http://www.selfish-brain.org Http://www.opticryst.org -- Any intelligent fool can make things bigger and more complex. It takes a lot of genius and a lot of courage to move in the opposite direction (Albert Einstein, 1879-1955) Ifyou can look into the seeds of time and say which grain will grow and which will not - speak then to me(Macbeth) -- Disclaimer * Employees of the Institute are expressly required not to make defamatory statements and not to infringe or authorize any infringement of copyright or any other legal right by email communications. Any such communication is contrary to Institute policy and outside the scope of the employment of the individual concerned. The Institute will not accept any liability in respect of such communication, and the employee responsible will be personally liable for any damages or other liability arising. Employees who receive such an email must notify their supervisor immediately. * This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. * E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission. If verification is required please request a hard-copy version. Please send us by fax any message containing deadlines as incoming e-mails are not screened for response deadlines. --
Re: [ccp4bb] Align linux version
Please correct me if I'm wrong, but I think lsqman implements G. Cohen's operator improvement in DP_improve. Assuming of course if that was the reason why someone wanted to use align. Fred [32m*** Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular BiologyFax: 301-496-0201 DHHS/NIH/NIDDK e-mail:fred.d...@nih.gov Bldg. 5. Room 303 Bethesda, MD 20892-0560 URGENT message e-mail: 2022476...@mms.att.net Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred ***[m
Re: [ccp4bb] Spam:Re: [ccp4bb] Align linux version
Hi Jeroen, Indeed, I did write to the original poster about this, asking him if he really meant Gerson Cohen's align program in his post, in which case I would be happy to send it to him. I still have the linux version but, as others have pointed out, there are new kids on the block that do the job. In fact, I myself don't use align these days, nor am I sure that the version I have will handle the v3 pdb's properly. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of mesters [mest...@biochem.uni-luebeck.de] Sent: Monday, November 11, 2013 11:19 AM To: בעז שאנן Subject: Spam:Re: [ccp4bb] Align linux version Back in 2003 I wrote an email to Gerson Cohen concerning ALIGN and he told me to contact Boaz Shaanan. Boaz was so kind to send me his linuxified fortran code of the align program (reading of a prealigment could not be implemented) that is still working on our linux machines! We use it a lot, great program. Ask Boaz (but not all at once please :-) )!! - J. - Am 10.11.13 22:09, schrieb Tim Gruene: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Mintu Chandra, Do you mean by 'has linux compiled align version', that 'align' is a program you use for the alignment? I wonder because I have not heard of it. If you would be happy with any alignment software, you could use coot (graphical) or lsqkab (command line). Both programs areavailable once you installed ccp4. Regards, Tim Gruene -- 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: +49-451-5004065 Fax: +49-451-5004068 Http://www.biochem.uni-luebeck.de Http://www.iobcr.org Http://www.selfish-brain.org Http://www.opticryst.org -- Any intelligent fool can make things bigger and more complex. It takes a lot of genius and a lot of courage to move in the opposite direction (Albert Einstein, 1879-1955) If you can look into the seeds of time and say which grain will grow and which will not - speak then to me (Macbeth) -- Disclaimer * Employees of the Institute are expressly required not to make defamatory statements and not to infringe or authorize any infringement of copyright or any other legal right by email communications. Any such communication is contrary to Institute policy and outside the scope of the employment of the individual concerned. The Institute will not accept any liability in respect of such communication, and the employee responsible will be personally liable for any damages or other liability arising. Employees who receive such an email must notify their supervisor immediately. * This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. * E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission. If verification is required please request a hard-copy version. Please send us by fax any message containing deadlines as incoming e-mails are not screened for response deadlines. --
