Re: [PyMOL] Orientation
Dear Folmer, Thanks a lot for your comment. Thats exactly what I was looking for and works perfectly. Thank you heaps. Regards Nagesh Folmer Fredslund wrote: Dear Nagesh Just a short comment. If you want the orientation you can write get_view and the orientation will be printed to the GUI. Then all you have to do is put it at the end of your script Best regards, Folmer Nagesh Chakka wrote: Dear Joel, Thanks for you email. I now installed version 0.99 and my problem is solved. Regards Nagesh Joel Tyndall wrote: Dear Nagesh, If you upgrade to the latest version (0.99) there is an option do display the disulfides under the show menu J Nagesh Chakka wrote: Hi Jerome, Thanks for the mail. The web address you gave is about obtaining information about Cys involved in bond formation. In my case, I do know which pair of Cys are involved in it and this information is also provided in the PDB file but I am unable to display the bridge in the PyMOL viewer. Also I need to display the structure in a particular orientation. Can this information be be added in my script. Thanks Nagesh Jerome Pansanel wrote: Hello, You can find some documentation about sulfur bonds on this page: http://www.pymolwiki.org/index.php/Process_All_Files_In_Directory If you are not successfull by using this resource, don't hesitate to post again. Cheers, Jerome Pansanel Selon Nagesh Chakka nagesh.cha...@anu.edu.au: Hello everyone, I am unable to display disulphide bonds using PyMOL (version 0.97). My understanding is that PyMOL can connect Cys that are within bonding distance. The PDB file (ID 1AG2) defines residues involved in the SSBond formation. I also tried to use the command bond to connect the residues but without any success. I am not sure if I am doing anything wrong. Any suggestion in this regard is appreciated. Thanks Nagesh Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users Mail sent through IMP: http://horde.org/imp/ Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] APBS - libreadline
I'm trying to install APBS on a LINUX (IBM T43P) box running SuSE 9.3 Professional. I've successfully installed maloc, but the apbs install gives: error: Failed dependencies libreadline.so.4 is needed by apbs-0.4.0-1 What to do? Thanks, Joe Becker Merck Research Labs -- Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp Dohme or MSD and in Japan, as Banyu) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. --
Re: [PyMOL] APBS - libreadline
This is using the binary distributions of APBS? Becker, Joseph W wrote: I'm trying to install APBS on a LINUX (IBM T43P) box running SuSE 9.3 Professional. I've successfully installed maloc, but the apbs install gives: error: Failed dependencies libreadline.so.4 is needed by apbs-0.4.0-1 What to do? Thanks, Joe Becker Merck Research Labs
[PyMOL] FW: APBS - libreadline
Yes, apbs-0.4.0-1.i386.rpm Joe -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Sabuj Pattanayek Sent: Friday, June 23, 2006 11:02 AM To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] APBS - libreadline This is using the binary distributions of APBS? Becker, Joseph W wrote: I'm trying to install APBS on a LINUX (IBM T43P) box running SuSE 9.3 Professional. I've successfully installed maloc, but the apbs install gives: error: Failed dependencies libreadline.so.4 is needed by apbs-0.4.0-1 What to do? Thanks, Joe Becker Merck Research Labs Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp Dohme or MSD and in Japan, as Banyu) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. --
Re: [PyMOL] FW: APBS - libreadline
I just installed the binary -i686 (not -i386), x86_64, and ia64 versions of apbs and apbs tools for some redhat machines and tested them all yesterday. None of the machines return anything when I do rpm -qa | grep maloc . Do you actually need maloc if you're not compiling from source? Becker, Joseph W wrote: Yes, apbs-0.4.0-1.i386.rpm Joe
Re: [PyMOL] FW: APBS - libreadline
I have these versions installed on i686 RH boxes: readline-4.3-13 readline-devel-4.3-13 At http://rpmfind.net/linux/rpm2html/search.php?query=readlinesubmit=Search+... it shows that SuSE 9.3 uses readline-5.0-7.2.i586.rpm . I don't know if that is going to be a problem. You may have to re-compile. venkataraman kabaleeswaran wrote: Hi I had the same problem while installing the apbs, I contacted the apbs-users mailing list , they adviced me to install readline, I did but still didnot work , after installation I got the same error. check and see if your system as readline library if not install that and try againg, good luck. Try post your problem at apbs-us...@lists.sourceforge.net. cheers vk
Re: [PyMOL] FW: APBS - libreadline
The fix on SuSE is to download the readline4.3 compatibility patch, and after installing that the install seems to go just fine: The file is attached, or find at http://rpmfind.net/linux/rpm2html/search.php?query=libreadline.so.4 Make sure to get the compat-readline4-4.3-3.i586.rpm for SuSE 9.3 Steve -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Sabuj Pattanayek Sent: Friday, June 23, 2006 12:23 PM To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] FW: APBS - libreadline I have these versions installed on i686 RH boxes: readline-4.3-13 readline-devel-4.3-13 At http://rpmfind.net/linux/rpm2html/search.php?query=readlinesubmit=Search+.. . it shows that SuSE 9.3 uses readline-5.0-7.2.i586.rpm . I don't know if that is going to be a problem. You may have to re-compile. venkataraman kabaleeswaran wrote: Hi I had the same problem while installing the apbs, I contacted the apbs-users mailing list , they adviced me to install readline, I did but still didnot work , after installation I got the same error. check and see if your system as readline library if not install that and try againg, good luck. Try post your problem at apbs-us...@lists.sourceforge.net. cheers vk Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp Dohme or MSD and in Japan, as Banyu) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. --
