Re: [ccp4bb] Dose anyone see this ligand before?

2013-07-18 Thread Wei Feng
Dear Dale Tronrud, Thanks for your advise. Initially, i focused on the shape of the density. As you suggest, i checked all possible biological molecules and common additives used in purification and crystallization. I found that the structure of bis-tris-propane is similar to the target

Re: [ccp4bb] Dose anyone see this ligand before?

2013-07-17 Thread p...@uni-greifswald.de
and Regards   -- Sonali Dhindwal “Live as if you were to die tomorrow. Learn as if you were to live forever.” - From: sonali dhindwal To: ccp4...@hotmail.com Sent: Wednesday, 17 July 2013 9:44 AM Subject: Re: [ccp4bb] Dose anyone see this ligand before? hi Wei

Re: [ccp4bb] Dose anyone see this ligand before?

2013-07-17 Thread Bosch, Juergen
Try here: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=8031loc=ec_rcs download the sdf and use the sdf to pdb converter Or I think phenix can read in sdf and convert them Jürgen On Jul 17, 2013, at 9:35 AM, Wei Feng wrote: Dear all, Thank you for your advices. I had tried to use MPD

Re: [ccp4bb] Dose anyone see this ligand before?

2013-07-17 Thread Dale Tronrud
Do you have any reason to expect either of these molecules would be in your crystal? The model you build has to fit the density, be consistent with the surrounding environment (which you haven't shared with us) and you have to have some story for how that molecule got in your crystal.

Re: [ccp4bb] Dose anyone see this ligand before?

2013-07-17 Thread R. M. Garavito
Wei I heartily second Dale's comment. Since you do know what has been in contact with your protein, you should be able to make a list of ALL POSSIBLE compounds your protein has been exposed to. However, don't go off the deep end. You say that We guess that the molecular formula should be

Re: [ccp4bb] Dose anyone see this ligand before?

2013-07-16 Thread Bosch, Juergen
Special position ? sulfate-size ? Jürgen On Jul 16, 2013, at 11:35 AM, Wei Feng wrote: Dear all, I found some redundant density in my structure beween two molecule. (see picture 1 and 2) But I am not sure which ligand will be. Dose everyone see this ligand before? If so, can you tell the PDB

Re: [ccp4bb] Dose anyone see this ligand before?

2013-07-16 Thread Oganesyan, Vaheh
Of Bosch, Juergen Sent: Tuesday, July 16, 2013 11:53 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Dose anyone see this ligand before? Special position ? sulfate-size ? Jürgen On Jul 16, 2013, at 11:35 AM, Wei Feng wrote: Dear all, I found some redundant density in my structure beween two

Re: [ccp4bb] Dose anyone see this ligand before?

2013-07-16 Thread Nicolas Foos
/*/ *From:*CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Bosch, Juergen *Sent:* Tuesday, July 16, 2013 11:53 AM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] Dose anyone see this ligand before? Special position ? sulfate-size ? Jürgen On Jul 16, 2013, at 11:35 AM, Wei

Re: [ccp4bb] Dose anyone see this ligand before?

2013-07-16 Thread Bosch, Juergen
product of reaction. Vaheh From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Bosch, Juergen Sent: Tuesday, July 16, 2013 11:53 AM To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Dose anyone see this ligand

Re: [ccp4bb] Dose anyone see this ligand before?

2013-07-16 Thread Vandna Kukshal
[mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Bosch, Juergen *Sent:* Tuesday, July 16, 2013 11:53 AM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] Dose anyone see this ligand before? Special position ? sulfate-size ? Jürgen On Jul 16, 2013, at 11:35 AM, Wei Feng wrote: Dear all, I found

Re: [ccp4bb] Dose anyone see this ligand before?

2013-07-16 Thread sonali dhindwal
...@yahoo.co.in To: ccp4...@hotmail.com ccp4...@hotmail.com Sent: Wednesday, 17 July 2013 9:44 AM Subject: Re: [ccp4bb] Dose anyone see this ligand before? hi Wei, This looks like MPD, 2-Methyl-2,4-pentanediol. May b u have added it as ur cryo-protectant. Thanks and Regards   -- Sonali