Re: [ccp4bb] jligand help

2016-12-16 Thread Robbie Joosten
com> Verzonden: vrijdag 16 december 2016 18:35 Aan: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Onderwerp: [ccp4bb] jligand help Dear All, I have CCP4 6.5.0 installed on my laptop PC. Everything runs fine, to my knowledge, except JLigand. When I click this program from the

[ccp4bb] jligand help

2016-12-16 Thread Nicholas Larsen
Dear All, I have CCP4 6.5.0 installed on my laptop PC. Everything runs fine, to my knowledge, except JLigand. When I click this program from the program list, absolutely nothing happens. No error message, nothing. It doesn't launch. Do I need to reinstall cpp4 or is JLigand a separate

[ccp4bb] AW: [ccp4bb] Jligand help

2014-08-08 Thread Herman . Schreuder
, Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Prem Prakash Gesendet: Freitag, 8. August 2014 07:32 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] Jligand help With due respect ! I want to ask that, If it is protonated at neutral pH, what about the local pka

[ccp4bb] Jligand help

2014-08-07 Thread Abhinav Kumar
Hi, I am making a ligand in Jligand (figure attached) and have a question about valency of nitrogen. Jligand puts three hydrogens on nitrogen N1 when the ligand is regularized. Should there be two hydrogens or three? -- Thanks, Abhinav __ Abhinav Kumar,

Re: [ccp4bb] Jligand help

2014-08-07 Thread Ian Tickle
Hi, I would say three: aliphatic amines such as the one you show are weak bases so at neutral pH the protonated form predominates. Aromatic amines are obviously trickier. Cheers -- Ian On 7 August 2014 17:37, Abhinav Kumar abhin...@slac.stanford.edu wrote: Hi, I am making a ligand in

Re: [ccp4bb] Jligand help

2014-08-07 Thread Abhinav Kumar
Thanks Ian. Is it possible to force Jligand to keep only two hydrogens in this case? I tried setting the N's charge to 0, but it reverts back to 1 after regularization. Thanks, Abhinav __ Abhinav Kumar, Ph.D. The Joint Center for Structural Genomics MS99,

Re: [ccp4bb] Jligand help

2014-08-07 Thread Boaz Shaanan
: Thursday, August 07, 2014 8:04 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Jligand help Thanks Ian. Is it possible to force Jligand to keep only two hydrogens in this case? I tried setting the N's charge to 0, but it reverts back to 1 after regularization. Thanks, Abhinav

Re: [ccp4bb] Jligand help

2014-08-07 Thread Prem Prakash
[abhin...@slac.stanford.edu] *Sent:* Thursday, August 07, 2014 8:04 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] Jligand help Thanks Ian. Is it possible to force Jligand to keep only two hydrogens in this case? I tried setting the N's charge to 0, but it reverts back to 1 after