Hi, I am using phenix to refine a low resolution structure. The problem I had is that the geometry of disulfide and NAG in the refined structure is not right. I did use a very tight geometry restrains. Both wxc_scale and wxu_scale are set to 0.05. In the refined structures, the sulfur of one cys is very close to the Cb of its disulfide partner. For NAG part, C2-N2-C7-O7-C8 should be in the same plane. But they are not. Is there a way to adjust these violations? Thanks in advance for the helps, Li-Zhi Mi,
Hi Li-Zhi Mi, - make sure that the restraints are actually used: look ".geo" file - it contains a list of all geometry restraints used in refinement; - changing the wxc_scale will not necessarily help (although it might) since it is a global weight used for the whole target; - try idealizing the geometry of this problem fragment before refinement; - you can also edit the corresponding CIF file to decrease the sigmas for these particular restraints. Pavel. On 1/22/2009 7:06 AM, Li-Zhi Mi wrote:
Hi, I am using phenix to refine a low resolution structure. The problem I had is that the geometry of disulfide and NAG in the refined structure is not right. I did use a very tight geometry restrains. Both wxc_scale and wxu_scale are set to 0.05. In the refined structures, the sulfur of one cys is very close to the Cb of its disulfide partner. For NAG part, C2-N2-C7-O7-C8 should be in the same plane. But they are not. Is there a way to adjust these violations? Thanks in advance for the helps, Li-Zhi Mi,
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Hi Pavel, It has been a while since our last communication. I'm writing to you to in an attempt to exploit once used possibility to refine structure with your help in Phenix while I'm not a Phenix subscriber. The structure is at low 3.o A resolution and includes antibody Fab fragment and an Antigen. My primary interest is to try SA option in Phenix and to build missing several residues in chains C and D both belonging to antigen. In addition, there are 2 complexes per a.u., i.e. I have 2 Fab-Antigen complexes in a.u. Each Fab consists of two chains: light and heavy. So, there are 6 protein chains in the a.u. Will you be kind enough to give it a try in Phenix with SA option active? Thank you. _______ Vaheh To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation.
Sorry, this was not intended for mailing list. _______ Vaheh -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Oganesyan, Vaheh Sent: Thursday, January 22, 2009 2:59 PM To: PHENIX user mailing list Subject: [phenixbb] S Novym Godom Hi Pavel, It has been a while since our last communication. I'm writing to you to in an attempt to exploit once used possibility to refine structure with your help in Phenix while I'm not a Phenix subscriber. The structure is at low 3.o A resolution and includes antibody Fab fragment and an Antigen. My primary interest is to try SA option in Phenix and to build missing several residues in chains C and D both belonging to antigen. In addition, there are 2 complexes per a.u., i.e. I have 2 Fab-Antigen complexes in a.u. Each Fab consists of two chains: light and heavy. So, there are 6 protein chains in the a.u. Will you be kind enough to give it a try in Phenix with SA option active? Thank you. _______ Vaheh To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation. _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation.
SA: Simulated Annealing. Pavel. On 1/22/2009 1:09 PM, Maia Cherney wrote:
What is SA option? _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Li-Zhi In addition to what Pavel said, the monomer library entry for NAG has N2, C7, O7 and C8 in a plane. C2 is not necessarily in the same plane. Nigel On 1/22/09 7:06 AM, Li-Zhi Mi wrote:
Hi, I am using phenix to refine a low resolution structure. The problem I had is that the geometry of disulfide and NAG in the refined structure is not right. I did use a very tight geometry restrains. Both wxc_scale and wxu_scale are set to 0.05. In the refined structures, the sulfur of one cys is very close to the Cb of its disulfide partner. For NAG part, C2-N2-C7-O7-C8 should be in the same plane. But they are not. Is there a way to adjust these violations? Thanks in advance for the helps, Li-Zhi Mi,
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
-- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Fax : 510-486-5909 Email : [email protected] Web : CCI.LBL.gov
Hi Pavel and Nigel, Thanks very much for the help. I will check ".geo" file to make sure the restraints are used. In addition, I will try other tips mentioned by Pavel. Nigel, as you mentioned, the monomer library only define N2, C7, O7 and C8 in the same plane. But just like Ca, C, O, N, Ca' in peptide bond need to be in the same plane, all these five atoms (C8, C7, O, N and C2) should be in the same plane. May I give a temporary name for NAG and provide corresponding cif file in the refinement? Li-Zhi, On Thu, 2009-01-22 at 08:59 -0800, Nigel W Moriarty wrote:
Li-Zhi
In addition to what Pavel said, the monomer library entry for NAG has N2, C7, O7 and C8 in a plane. C2 is not necessarily in the same plane.
Nigel
On 1/22/09 7:06 AM, Li-Zhi Mi wrote:
Hi, I am using phenix to refine a low resolution structure. The problem I had is that the geometry of disulfide and NAG in the refined structure is not right. I did use a very tight geometry restrains. Both wxc_scale and wxu_scale are set to 0.05. In the refined structures, the sulfur of one cys is very close to the Cb of its disulfide partner. For NAG part, C2-N2-C7-O7-C8 should be in the same plane. But they are not. Is there a way to adjust these violations? Thanks in advance for the helps, Li-Zhi Mi,
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Hi Li-Zhi,
Nigel, as you mentioned, the monomer library only define N2, C7, O7 and C8 in the same plane. But just like Ca, C, O, N, Ca' in peptide bond need to be in the same plane, all these five atoms (C8, C7, O, N and C2) should be in the same plane. May I give a temporary name for NAG and provide corresponding cif file in the refinement?
You can copy the NAG.cif file, make modifications, and add it to the phenix.refine command line. The modified file will override the standard file from the mon_lib directory. I.e. you don't have to change the residue name. But you can change the file name for clarity if you like, e.g. to NAG_customized.cif. Ralf
Hi Ralf, Thanks very much for the help. I will try that. Li-Zhi, On Thu, 2009-01-22 at 10:22 -0800, Ralf W. Grosse-Kunstleve wrote:
Hi Li-Zhi,
Nigel, as you mentioned, the monomer library only define N2, C7, O7 and C8 in the same plane. But just like Ca, C, O, N, Ca' in peptide bond need to be in the same plane, all these five atoms (C8, C7, O, N and C2) should be in the same plane. May I give a temporary name for NAG and provide corresponding cif file in the refinement?
You can copy the NAG.cif file, make modifications, and add it to the phenix.refine command line. The modified file will override the standard file from the mon_lib directory. I.e. you don't have to change the residue name. But you can change the file name for clarity if you like, e.g. to NAG_customized.cif.
Ralf _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
participants (7)
-
Li-Zhi Mi -
Maia Cherney -
Nigel W Moriarty -
Oganesyan, Vaheh -
Pavel Afonine -
Pavel Afonine
-
Ralf W. Grosse-Kunstleve