[ccp4bb] Determining number of surface atoms with AREAIMOL
Dear all, This is more of a scientific question than a technical one - I hope this is the right place to ask. I'm new to the CCP4 bundle. So far I've only used the AREAIMOL tool, which determines the accessible surface area of a system. My system is an irregular periodic slab and so I have used the following options: SMODE IMOL TRANS PROBE 0.75 OUTPUT END I have used such a small probe sphere radius because it's half of the first peak in the radial distribution function, that is, more or less half of the average first nearest-neighbor distance. I'm doing this because my slab being amorphous I want to have a systematic and unambiguous way of determining the number of surface atoms. Using the settings above, AREAIMOL produces a number of surface atoms in good agreement with a naive visual interpretation of the structure, which feels right. My question is if this is a sound approach and what alternative criteria for computing the number of surface atoms are available/used by the community. Many thanks, Miguel -- *Dr. Miguel Caro* /Postdoctoral researcher/ Department of Electrical Engineering and Automation, and COMP Centre of Excellence in Computational Nanoscience Aalto University, Finland Personal email: *mcar...@gmail.com* Work: *miguel.c...@aalto.fi* Website: http://mcaroba.dyndns.org
Re: [ccp4bb] CCP4: scalepack2mtz problem
I suspect this is an external problem - there is no failure message in the P212121 case.. Obviously the input data is different for the 2 sets, do you know why? The integration should be identical. And you have NCS translation at 0,0,0.5 which makes it hard to be sure if the SG is P21212 or P212121 That gives the (probably incorrect) suggestion that the data might be twinned Not sure why there are differences in the log files and the tasks - scale[pack2mtz and ctruncate should run more or less identically for these two cases. I suggest checking your input, and trying again Eleanor On 8 December 2014 at 21:51, Uma Ratu rosiso2...@gmail.com wrote: Dear All: I try to import the .sca file from hkl2000. The data was scaled as P212121 from HKL2000. In ccp4, I used scalepack2mtz from Scalepack(Denzo) into MTZ format, run as Ctruncate. The import stopped at Twin fractione estimates exluding operators and didn't go any further. I scaled the data as P222, and imported it using scalepack2mtz. It went through without problem. I have the log files from both imports attached. Could you advice why the P212121 can't go through? Thank you Uma
[ccp4bb] Open positions in chromatin biology and gene silencing at the University of Geneva, Switzerland
Two positions at PhD student or postdoctoral level are available for highly motivated, creative individuals at the Department of Molecular Biology of the University of Geneva in Switzerland. The laboratory of Thomas Schalch (http://www.molbio.unige.ch/eng/research_groups/schalch/lab) is seeking candidates with a strong interest in understanding mechanisms underlying chromatin structure, associated macromolecular complexes and gene silencing by structure-function analysis. Our research efforts are targeted towards macromolecular assemblies relevant to chromatin biology in the fission yeast S. Pombe. Formation of specialized chromatin environments plays important roles in development and disease, and it is our goal to understand the molecular details in the context of well tractable model organisms. The Department of Molecular Biology at the University of Geneva is one of the oldest molecular biology departments in the world and was home to the discovery of restriction enzymes. Today, the department's research program focuses on gene expression, replication and signaling, and it provides access to state of the art equipment for X-ray crystallography, microscopy, molecular biology and biophysical analyses. The candidate has to have an excellent command of spoken and written English. Previous experience with protein X-ray crystallography, protein production or experience with S.pombe is a plus. Most importantly, a strong interest in the mechanistic understanding of chromatin biology and gene silencing is required. Candidates should contact Thomas Schalch at thomas.scha...@unige.ch. To apply, please send a letter of motivation, a Curriculum Vitae (CV) detailing your publications and past research experiences. PhD students will be part of the International PhD program in Basic and Applied Molecular Life Sciences (http://lifesciencesphd.unige.ch, next deadline for PhD applicants is Dec. 15. 2014!). Thank you for forwarding this announcement to interested candidates. Best regards, Thomas Schalch -- Thomas Schalch, PhD Professeur boursier FNS Department of Molecular Biology University of Geneva
[ccp4bb] pdb2pqr generation
Dear All, I wish to generate electrostatics surface cartoon for a protein, which is a tetramer. I am using pdb to pqr server (http://nbcr-222.ucsd.edu/pdb2pqr_1.8/) to generate .pqr files as part of this process. I find that server is able to genetrate .pqr file contents, only when input pdb file contains a single chain (monomer), it is failing to do the same when I give it tetramer pdb co-ordinates, why is that ? and how can I generate a .pqr file for teramer...what other options do I have ? many thanks in adavnce abhishek
Re: [ccp4bb] unknown densities
Yamei, This is not unusual, particularly for many proteins that bind nucleotide derivatives, especially GDP/GTP binding proteins, as Nat said. If it is GDP that is tightly bound at high occupancy, it should be quite easy to identify because of the pyrophosphates and the guanine ring. To build into, pop in a GDP molecule from another GDP/GTP binding protein structure; there is GDP .cif files in the CCP4 and Phenix libraries. Just be aware that there are at least two major conformers seen regarding the guanine ring (syn and anti). While in GDP/GTP binding proteins the ring conformer I believe is anti (the ring not over the ribose), in GDP-sugar enzymes, it can be syn (the ring over the ribose). Michael R. Michael Garavito, Ph.D. Professor of Biochemistry Molecular Biology 603 Wilson Rd., Rm. 513 Michigan State University East Lansing, MI 48824-1319 Office: (517) 355-9724 Lab: (517) 353-9125 FAX: (517) 353-9334Email: rmgarav...@gmail.com On Dec 8, 2014, at 10:15 PM, Yamei Yu ymyux...@gmail.com wrote: Hi all, We crystallised a small GTPase expressed in E. Coli and found some densities in GDP/GTP binding site. We didn’t add any GDP/GTP or GDP/GPD homologues during protein expression, purification and crystallisation. The resolution is not high, we couldn’t tell what it is. Is there any method to detect what it is? Thanks! Best wishes! yamei Yamei Yu State Key Laboratory of Biotherapy／Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University,Chengdu,610041, P.R.China Tel: 15882013485 Email: ymyux...@gmail.com ymyux...@163.com yamei...@scu.edu.cn
Re: [ccp4bb] pdb2pqr generation
Dear abhishek, one work-around is to split the PDB-file into four different PDB-files, one per chain, and concatenate the results back together. Alternatively you can try Coot to calculate the ESP. Bst, Tim On 12/09/2014 02:23 PM, abhishek jamwal wrote: Dear All, I wish to generate electrostatics surface cartoon for a protein, which is a tetramer. I am using pdb to pqr server (http://nbcr-222.ucsd.edu/pdb2pqr_1.8/) to generate .pqr files as part of this process. I find that server is able to genetrate .pqr file contents, only when input pdb file contains a single chain (monomer), it is failing to do the same when I give it tetramer pdb co-ordinates, why is that ? and how can I generate a .pqr file for teramer...what other options do I have ? many thanks in adavnce abhishek -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: OpenPGP digital signature
Re: [ccp4bb] CCP4: scalepack2mtz problem
Hi, Eleanor: Thank you for your suggestions. In HKL, I integrated the data set with P222, and scaled it with P222 and P212121. From pointless, it says the data better fit with P212121. So I would like to process the data with P212121 as well. And you have NCS translation at 0,0,0.5 which makes it hard to be sure if the SG is P21212 or P212121 That gives the (probably incorrect) suggestion that the data might be twinned This might be the reason that import failed with P212121. Regard Uma On Tue, Dec 9, 2014 at 6:31 AM, Eleanor Dodson eleanor.dod...@york.ac.uk wrote: I suspect this is an external problem - there is no failure message in the P212121 case.. Obviously the input data is different for the 2 sets, do you know why? The integration should be identical. And you have NCS translation at 0,0,0.5 which makes it hard to be sure if the SG is P21212 or P212121 That gives the (probably incorrect) suggestion that the data might be twinned Not sure why there are differences in the log files and the tasks - scale[pack2mtz and ctruncate should run more or less identically for these two cases. I suggest checking your input, and trying again Eleanor On 8 December 2014 at 21:51, Uma Ratu rosiso2...@gmail.com wrote: Dear All: I try to import the .sca file from hkl2000. The data was scaled as P212121 from HKL2000. In ccp4, I used scalepack2mtz from Scalepack(Denzo) into MTZ format, run as Ctruncate. The import stopped at Twin fractione estimates exluding operators and didn't go any further. I scaled the data as P222, and imported it using scalepack2mtz. It went through without problem. I have the log files from both imports attached. Could you advice why the P212121 can't go through? Thank you Uma
[ccp4bb] Ramachandran maps
Hi guys, Sorry for the repost in COOT/CCP4/PHENIX. It is possible on of the users in one of these communities might know the answer I was wondering if there is a small script I can use to generate the outline of the allowed regions of Ramachandran map on to which I can superimpose my coordinates phi and psi? Something like what appears in COOT-Validate-Ramachandran Plot. How does one generate such images for publications? Thank you, Patrick FREE 3D EARTH SCREENSAVER - Watch the Earth right on your desktop! Check it out at http://www.inbox.com/earth
Re: [ccp4bb] CCP4: scalepack2mtz problem
Processing (integration and scaling) only depends on the point group, not the space group, so it is the same in P222 and P212121. Structure solution is different so you may need to try different space groups Phil On 9 Dec 2014, at 14:36, Uma Ratu rosiso2...@gmail.com wrote: Hi, Eleanor: Thank you for your suggestions. In HKL, I integrated the data set with P222, and scaled it with P222 and P212121. From pointless, it says the data better fit with P212121. So I would like to process the data with P212121 as well. And you have NCS translation at 0,0,0.5 which makes it hard to be sure if the SG is P21212 or P212121 That gives the (probably incorrect) suggestion that the data might be twinned This might be the reason that import failed with P212121. Regard Uma On Tue, Dec 9, 2014 at 6:31 AM, Eleanor Dodson eleanor.dod...@york.ac.uk wrote: I suspect this is an external problem - there is no failure message in the P212121 case.. Obviously the input data is different for the 2 sets, do you know why? The integration should be identical. And you have NCS translation at 0,0,0.5 which makes it hard to be sure if the SG is P21212 or P212121 That gives the (probably incorrect) suggestion that the data might be twinned Not sure why there are differences in the log files and the tasks - scale[pack2mtz and ctruncate should run more or less identically for these two cases. I suggest checking your input, and trying again Eleanor On 8 December 2014 at 21:51, Uma Ratu rosiso2...@gmail.com wrote: Dear All: I try to import the .sca file from hkl2000. The data was scaled as P212121 from HKL2000. In ccp4, I used scalepack2mtz from Scalepack(Denzo) into MTZ format, run as Ctruncate. The import stopped at Twin fractione estimates exluding operators and didn't go any further. I scaled the data as P222, and imported it using scalepack2mtz. It went through without problem. I have the log files from both imports attached. Could you advice why the P212121 can't go through? Thank you Uma
Re: [ccp4bb] CCP4: scalepack2mtz problem
No - no - failure has nothing to do with the SG - only the point group matters.. You dont need to reintegrate - integration only requires knowledge of thecrystal class. That must be why you get some different results. If you like to send me the 2 sca files I can check more carefully. Eleanor On 9 December 2014 at 15:03, Phil Evans p...@mrc-lmb.cam.ac.uk wrote: Processing (integration and scaling) only depends on the point group, not the space group, so it is the same in P222 and P212121. Structure solution is different so you may need to try different space groups Phil On 9 Dec 2014, at 14:36, Uma Ratu rosiso2...@gmail.com wrote: Hi, Eleanor: Thank you for your suggestions. In HKL, I integrated the data set with P222, and scaled it with P222 and P212121. From pointless, it says the data better fit with P212121. So I would like to process the data with P212121 as well. And you have NCS translation at 0,0,0.5 which makes it hard to be sure if the SG is P21212 or P212121 That gives the (probably incorrect) suggestion that the data might be twinned This might be the reason that import failed with P212121. Regard Uma On Tue, Dec 9, 2014 at 6:31 AM, Eleanor Dodson eleanor.dod...@york.ac.uk wrote: I suspect this is an external problem - there is no failure message in the P212121 case.. Obviously the input data is different for the 2 sets, do you know why? The integration should be identical. And you have NCS translation at 0,0,0.5 which makes it hard to be sure if the SG is P21212 or P212121 That gives the (probably incorrect) suggestion that the data might be twinned Not sure why there are differences in the log files and the tasks - scale[pack2mtz and ctruncate should run more or less identically for these two cases. I suggest checking your input, and trying again Eleanor On 8 December 2014 at 21:51, Uma Ratu rosiso2...@gmail.com wrote: Dear All: I try to import the .sca file from hkl2000. The data was scaled as P212121 from HKL2000. In ccp4, I used scalepack2mtz from Scalepack(Denzo) into MTZ format, run as Ctruncate. The import stopped at Twin fractione estimates exluding operators and didn't go any further. I scaled the data as P222, and imported it using scalepack2mtz. It went through without problem. I have the log files from both imports attached. Could you advice why the P212121 can't go through? Thank you Uma
[ccp4bb] השב: [ccp4bb] pdb2pqr generation
Hi, I don't recall having this problem with pdb2pqr through the apps link. Did you try it? If all fails I suggest that contact the apbs/pd2pqr support. They're very helpful. Boaz הודעה מקורית מאת abhishek jamwal jamwalabhis...@gmail.com תאריך: 09/12/2014 8:29 (GMT-05:00) אל CCP4BB@JISCMAIL.AC.UK נושא [ccp4bb] pdb2pqr generation Dear All, I wish to generate electrostatics surface cartoon for a protein, which is a tetramer. I am using pdb to pqr server (http://nbcr-222.ucsd.edu/pdb2pqr_1.8/) to generate .pqr files as part of this process. I find that server is able to genetrate .pqr file contents, only when input pdb file contains a single chain (monomer), it is failing to do the same when I give it tetramer pdb co-ordinates, why is that ? and how can I generate a .pqr file for teramer...what other options do I have ? many thanks in adavnce abhishek
Re: [ccp4bb] Ramachandran maps
The UCSF Chimera program does this very well. I don’t know about script based, but the GUI is very good and plots are publication quality. David Da-Neng Wang Lab Structural Biology Program New York University School of Medicine Publications via Google Scholarhttp://scholar.google.com/citations?user=F9G61tAJhl=enoi=ao On 12/9/14, 9:47 AM, PC patrick.coss...@inbox.commailto:patrick.coss...@inbox.com wrote: Hi guys, Sorry for the repost in COOT/CCP4/PHENIX. It is possible on of the users in one of these communities might know the answer I was wondering if there is a small script I can use to generate the outline of the allowed regions of Ramachandran map on to which I can superimpose my coordinates phi and psi? Something like what appears in COOT-Validate-Ramachandran Plot. How does one generate such images for publications? Thank you, Patrick FREE 3D EARTH SCREENSAVER - Watch the Earth right on your desktop! Check it out at http://www.inbox.com/earth
Re: [ccp4bb] Challenging Mol.Rep. Problem
Generally fab geometry presents problems for mr due to variable interdomain angle. Assuming your sg is correct and this is not a twin, i would try searching at 4 or even 5 a resolution. I would not reject the chance that you have high solvent content, so you might have fewer molecules in au than expected from vm estimates. We recently solved a whole bunch of structures with large unit cell dimensions and high solvent content in the 75% or even 82% range. All had issues with resolution, freezing, and twinning - similar to shat you describe. In a few cases we screened over 35 crystals (of the same protein variant, same condition, just repeats) to find one that diffracted beyond 4a. Don't give up! May the pork be with you. Artem On Dec 9, 2014 12:32 PM, Mo Wong mowon...@gmail.com wrote: Hi all, I’m stuck on a rather complex molecular replacement problem. The crystals are of an antigen-Fab complex totaling ~67 kDa (waiting to confirm using PAGE gel). They diffract to ~3.5A at the synchrotron and process in C2 with dimensions 220x130x230 and beta at 103 so it looks like there are round 9to12-ish copies in the ASU. The overall Rmerge is high at ~25% with I/sig cutoff ~2 and redundancy of 5; however, at 4.5A this drops to ~15%. Furthermore, processing in P1 gives similar Rmerge values too. Self-Patterson doesn’t suggest translational symmetry, but the self-rotation function (SRF) suggests high NCS (see below/attached). I’m hoping the SRF might be helpful in trying to confirm/dismiss C2 is the likely space group, and perhaps suggest a logical assembly with the ASU (I see strong 2-fold and 3-fold NCS operators suggesting to me dimeric trimers or vice versa - however, I’ve never had to really analyze SRFs in the absence of a mol. rep. solution so my interpretation could be wrong). Anyway, any help to bringing a molecular replacement solution closer to reality would be appreciated. Thanks! [image: Inline image 1]
Re: [ccp4bb] Challenging Mol.Rep. Problem
Thank you cell phone typing for the inadvertent prophanity. Sorry! On Dec 9, 2014 1:00 PM, Artem Evdokimov artem.evdoki...@gmail.com wrote: Generally fab geometry presents problems for mr due to variable interdomain angle. Assuming your sg is correct and this is not a twin, i would try searching at 4 or even 5 a resolution. I would not reject the chance that you have high solvent content, so you might have fewer molecules in au than expected from vm estimates. We recently solved a whole bunch of structures with large unit cell dimensions and high solvent content in the 75% or even 82% range. All had issues with resolution, freezing, and twinning - similar to shat you describe. In a few cases we screened over 35 crystals (of the same protein variant, same condition, just repeats) to find one that diffracted beyond 4a. Don't give up! May the pork be with you. Artem On Dec 9, 2014 12:32 PM, Mo Wong mowon...@gmail.com wrote: Hi all, I’m stuck on a rather complex molecular replacement problem. The crystals are of an antigen-Fab complex totaling ~67 kDa (waiting to confirm using PAGE gel). They diffract to ~3.5A at the synchrotron and process in C2 with dimensions 220x130x230 and beta at 103 so it looks like there are round 9to12-ish copies in the ASU. The overall Rmerge is high at ~25% with I/sig cutoff ~2 and redundancy of 5; however, at 4.5A this drops to ~15%. Furthermore, processing in P1 gives similar Rmerge values too. Self-Patterson doesn’t suggest translational symmetry, but the self-rotation function (SRF) suggests high NCS (see below/attached). I’m hoping the SRF might be helpful in trying to confirm/dismiss C2 is the likely space group, and perhaps suggest a logical assembly with the ASU (I see strong 2-fold and 3-fold NCS operators suggesting to me dimeric trimers or vice versa - however, I’ve never had to really analyze SRFs in the absence of a mol. rep. solution so my interpretation could be wrong). Anyway, any help to bringing a molecular replacement solution closer to reality would be appreciated. Thanks! [image: Inline image 1]
Re: [ccp4bb] Challenging Mol.Rep. Problem
Try othercell to look for other indexing - C2 is a possible alternate SG to H32. And have you run pointless to check on symmetry operators? You certainly have 4 independent 3 fold rotations which would generate 12 mols per ASU. But first think about higher symmetry SGs - that will make the whole problem easier! Eleanor On 9 December 2014 at 19:00, Artem Evdokimov artem.evdoki...@gmail.com wrote: Generally fab geometry presents problems for mr due to variable interdomain angle. Assuming your sg is correct and this is not a twin, i would try searching at 4 or even 5 a resolution. I would not reject the chance that you have high solvent content, so you might have fewer molecules in au than expected from vm estimates. We recently solved a whole bunch of structures with large unit cell dimensions and high solvent content in the 75% or even 82% range. All had issues with resolution, freezing, and twinning - similar to shat you describe. In a few cases we screened over 35 crystals (of the same protein variant, same condition, just repeats) to find one that diffracted beyond 4a. Don't give up! May the pork be with you. Artem On Dec 9, 2014 12:32 PM, Mo Wong mowon...@gmail.com wrote: Hi all, I’m stuck on a rather complex molecular replacement problem. The crystals are of an antigen-Fab complex totaling ~67 kDa (waiting to confirm using PAGE gel). They diffract to ~3.5A at the synchrotron and process in C2 with dimensions 220x130x230 and beta at 103 so it looks like there are round 9to12-ish copies in the ASU. The overall Rmerge is high at ~25% with I/sig cutoff ~2 and redundancy of 5; however, at 4.5A this drops to ~15%. Furthermore, processing in P1 gives similar Rmerge values too. Self-Patterson doesn’t suggest translational symmetry, but the self-rotation function (SRF) suggests high NCS (see below/attached). I’m hoping the SRF might be helpful in trying to confirm/dismiss C2 is the likely space group, and perhaps suggest a logical assembly with the ASU (I see strong 2-fold and 3-fold NCS operators suggesting to me dimeric trimers or vice versa - however, I’ve never had to really analyze SRFs in the absence of a mol. rep. solution so my interpretation could be wrong). Anyway, any help to bringing a molecular replacement solution closer to reality would be appreciated. Thanks! [image: Inline image 1]
Re: [ccp4bb] unknown densities
Hi Yamei, Depending on your dataset and collection, if you have collected any anomalous data, you can check for peaks that indicate phosphorus atoms in anomalous maps. It might even be worth feeding into ANoDe ( http://shelx.uni-ac.gwdg.de/SHELX/anode.php) if you have sufficiently high multiplicity on e.g. a Cu source. (Disclaimer: I'm no expert. Others here know how this works much better than I do) Shane Caldwell McGill University On Tue, Dec 9, 2014 at 8:35 AM, R. M. Garavito rmgarav...@gmail.com wrote: Yamei, This is not unusual, particularly for many proteins that bind nucleotide derivatives, especially GDP/GTP binding proteins, as Nat said. If it is GDP that is tightly bound at high occupancy, it should be quite easy to identify because of the pyrophosphates and the guanine ring. To build into, pop in a GDP molecule from another GDP/GTP binding protein structure; there is GDP .cif files in the CCP4 and Phenix libraries. Just be aware that there are at least two major conformers seen regarding the guanine ring (syn and anti). While in GDP/GTP binding proteins the ring conformer I believe is anti (the ring not over the ribose), in GDP-sugar enzymes, it can be syn (the ring over the ribose). Michael ** *R. Michael Garavito, Ph.D.* *Professor of Biochemistry Molecular Biology* *603 Wilson Rd., Rm. 513* *Michigan State University * *East Lansing, MI 48824-1319* *Office:* *(517) 355-9724 %28517%29%20355-9724 Lab: (517) 353-9125 %28517%29%20353-9125* *FAX: (517) 353-9334 %28517%29%20353-9334 Email: rmgarav...@gmail.com garav...@gmail.com* ** On Dec 8, 2014, at 10:15 PM, Yamei Yu ymyux...@gmail.com wrote: Hi all, We crystallised a small GTPase expressed in E. Coli and found some densities in GDP/GTP binding site. We didn’t add any GDP/GTP or GDP/GPD homologues during protein expression, purification and crystallisation. The resolution is not high, we couldn’t tell what it is. Is there any method to detect what it is? Thanks! Best wishes! yamei Yamei Yu State Key Laboratory of Biotherapy／Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University,Chengdu,610041, P.R.China Tel: 15882013485 Email: ymyux...@gmail.com ymyux...@163.com yamei...@scu.edu.cn
Re: [ccp4bb] Challenging Mol.Rep. Problem
Hi, We’ve had good luck with Phaser in placing many copies of proteins or domains, if the model is reasonably good. Because of the variable elbow angle, you probably want to place the domains separately. However, as soon as you find one convincing assembly you can switch to searching for the whole Fab. Alternatively, you can try a bunch of different models and hope that one is right. Something that might be useful is a new “MR_GYRE feature in Phaser. This is a likelihood-based version of the PC refinement that can be done in CNS, to optimise the relative orientations of domains between the rotation and translation searches. If you get stuck, we might be able to give a hand — we haven’t had much experience ourselves with using this on unsolved structures. Of course, the advice you’ve had from others to be certain first of the space group is very good! Best wishes, Randy Read - Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical ResearchTel: +44 1223 336500 Wellcome Trust/MRC Building Fax: +44 1223 336827 Hills RoadE-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk On 9 Dec 2014, at 18:31, Mo Wong mowon...@gmail.com wrote: Hi all, I’m stuck on a rather complex molecular replacement problem. The crystals are of an antigen-Fab complex totaling ~67 kDa (waiting to confirm using PAGE gel). They diffract to ~3.5A at the synchrotron and process in C2 with dimensions 220x130x230 and beta at 103 so it looks like there are round 9to12-ish copies in the ASU. The overall Rmerge is high at ~25% with I/sig cutoff ~2 and redundancy of 5; however, at 4.5A this drops to ~15%. Furthermore, processing in P1 gives similar Rmerge values too. Self-Patterson doesn’t suggest translational symmetry, but the self-rotation function (SRF) suggests high NCS (see below/attached). I’m hoping the SRF might be helpful in trying to confirm/dismiss C2 is the likely space group, and perhaps suggest a logical assembly with the ASU (I see strong 2-fold and 3-fold NCS operators suggesting to me dimeric trimers or vice versa - however, I’ve never had to really analyze SRFs in the absence of a mol. rep. solution so my interpretation could be wrong). Anyway, any help to bringing a molecular replacement solution closer to reality would be appreciated. Thanks! SELF_RF.gif
Re: [ccp4bb] pdb2pqr generation
Hi Tim, You have sparked my interest in Coot ESP. Do you know of a link to explain how to display/export it? I can generate it but nothing happens (other than the protein disappearing Cheers Joel -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim Gruene Sent: Wednesday, 10 December 2014 3:07 a.m. To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] pdb2pqr generation Dear abhishek, one work-around is to split the PDB-file into four different PDB-files, one per chain, and concatenate the results back together. Alternatively you can try Coot to calculate the ESP. Bst, Tim On 12/09/2014 02:23 PM, abhishek jamwal wrote: Dear All, I wish to generate electrostatics surface cartoon for a protein, which is a tetramer. I am using pdb to pqr server (http://nbcr-222.ucsd.edu/pdb2pqr_1.8/) to generate .pqr files as part of this process. I find that server is able to genetrate .pqr file contents, only when input pdb file contains a single chain (monomer), it is failing to do the same when I give it tetramer pdb co-ordinates, why is that ? and how can I generate a .pqr file for teramer...what other options do I have ? many thanks in adavnce abhishek -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
