Re: [ccp4bb] disordered helix
This looks to me like a good attempt for GraphEnt. Give it a shot and you might be positively surprised. Jürgen Sent from my iPad On May 13, 2013, at 21:26, Dale Tronrud det...@uoxray.uoregon.edu wrote: Sometimes a floppy bit of a protein is even more floppy in a particular crystal form. Your maps do not appear to support your model of a helix in this location. I would not build it unless maps based on later refinement show something reasonable in the omit map. (Of course if you leave out the helix, all your maps will be omit maps.) It is quite common to submit models to the PDB that do not contain all of the amino acids expected based on the sequence. If you can't see where the chain goes you certainly can't be expected to build it. Dale Tronrud On 05/13/2013 04:23 AM, atul kumar wrote: I have attached the map and omit map(after deleting helix) images. 2Fo-Fc(1 sigma) Fo-Fc(3sigma) On 5/13/13, Eleanor Dodson eleanor.dod...@york.ac.uk wrote: Hard to say without seeing the maps and experimenting. My first check would be to set the NTD occupancies to 0.0 - refine the CTD alone, then look at the maps in COOT. Or maybe let an automatic modelling building program such as Buccaneer try to rebuild the NTD section, with starting phases from the CTD. Eleanor On 13 May 2013 09:04, atul kumar atulsingh21...@gmail.com wrote: Dear all, I have solved the structure of my protein by molecular replacement at 2.9A, with Rfactor and Rfree 18 and 22 respectively. Overall everything seems fine, its a two domain protein NTD and CTD, the NTD have high average B factor compared to CTD. A helix of NTD seems to be disordered, I tried different geometric weights but the refined structure does not seem to follow proper geometry for this helix. The B-factor of this helix is very high compared to overall B factor for NTD and omit map shows only some partial density in this region( off course not conclusive). All the homologous structure have helix in this region although with high B-factor. Should I submit the current pdb or need more refinement? thanks and regards Atul Kumar
Re: [ccp4bb] reference for true multiplicity?
Dear Frank, We did extensive testing of this approach at the beginning of this millenium - see Acta Cryst. D59 (2003) 393 and 688 - but never claimed that it was our idea. Best wishes, George On 05/14/2013 06:50 AM, Frank von Delft wrote: Hi, I'm meant to know this but I'm blanking, so I'll crowdsource instead: Anybody know a (the) reference where it was showed that the best SAD data is obtained by collecting multiple revolutions at different crystal offsets (kappa settings)? It's axiomatic now (I hope!), but I remember seeing someone actually show this. I thought Sheldrick early tweens, but PubMed is not being useful. (Oh dear, this will unleash references from the 60s, won't it.) phx -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-33021 or -33068 Fax. +49-551-39-22582
Re: [ccp4bb] reference for true multiplicity?
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Frank, I would not call it 'axiomatic' but 'statistics' to reduce the (stochastic) error by several independent measurements. You can probably give any statistics textbook as a reference. In real life, though, you have to compromise with radiation damage, though. For references I recommend searching journals.iucr.org for 'Garman' as author. If you add 'radiation damaga' as keywords, the result reduces to 37 hits of choice. Best, Tim On 05/14/2013 06:50 AM, Frank von Delft wrote: Hi, I'm meant to know this but I'm blanking, so I'll crowdsource instead: Anybody know a (the) reference where it was showed that the best SAD data is obtained by collecting multiple revolutions at different crystal offsets (kappa settings)? It's axiomatic now (I hope!), but I remember seeing someone actually show this. I thought Sheldrick early tweens, but PubMed is not being useful. (Oh dear, this will unleash references from the 60s, won't it.) phx - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFRkfN7UxlJ7aRr7hoRAnlWAJ9T4MvGHUGA+HRwOL2i/6rU7KW1xwCcDsAq KAvPG9FqtNYO2kLqmh7wIZI= =MNNU -END PGP SIGNATURE-
Re: [ccp4bb] reference for true multiplicity?
It's not about multiplicity, it's about scaling. See quote I sent earlier. phx. On 14/05/2013 10:40, Felix Frolow wrote: I guess that in a standpoint to reduce errors it is easy to improve statistical errors by longer counting or by using multiple observations. However the real enemy at the gate is a systematic error which require special skills and experience to detect and to eliminate. I never understood why to measure not very good data trying to recover anomalous signal by improving statistics using very high redundancy instead of trying to collect data which are perfect by minimising systematics errors and of course increasing counting time, but with minimum redundancy of only 2 ? Like in good old times with 4 circle diffractometers and good scintillation counters that produced true counting statistics: 10 counts - 30% precision 100 counts - 10% precision 1000 counts - 3% precision 1 counts - 1% precision Canonising and worshipping redundancy looking for true holy multiplicity on my taste is counterproductive….. My 2 NIS :-) And of corse - one of the systematic errors is the radiation damage…... FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il mailto:mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On May 14, 2013, at 11:19 , Tim Gruene t...@shelx.uni-ac.gwdg.de mailto:t...@shelx.uni-ac.gwdg.de wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Frank, I would not call it 'axiomatic' but 'statistics' to reduce the (stochastic) error by several independent measurements. You can probably give any statistics textbook as a reference. In real life, though, you have to compromise with radiation damage, though. For references I recommend searching journals.iucr.org http://journals.iucr.org for 'Garman' as author. If you add 'radiation damaga' as keywords, the result reduces to 37 hits of choice. Best, Tim On 05/14/2013 06:50 AM, Frank von Delft wrote: Hi, I'm meant to know this but I'm blanking, so I'll crowdsource instead: Anybody know a (the) reference where it was showed that the best SAD data is obtained by collecting multiple revolutions at different crystal offsets (kappa settings)? It's axiomatic now (I hope!), but I remember seeing someone actually show this. I thought Sheldrick early tweens, but PubMed is not being useful. (Oh dear, this will unleash references from the 60s, won't it.) phx - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFRkfN7UxlJ7aRr7hoRAnlWAJ9T4MvGHUGA+HRwOL2i/6rU7KW1xwCcDsAq KAvPG9FqtNYO2kLqmh7wIZI= =MNNU -END PGP SIGNATURE-
Re: [ccp4bb] reference for true multiplicity?
We know that our scaling models do not completely describe and compensate for all systematic errors, for various reasons including radiation damage (which is hard to model). This can be seen by scaling together data collected about different axes, where typically the merging statistics between different sweeps are worse than those within a sweep. Nevertheless, we would expect that averaging the somewhat disparate data should produce a more accurate estimate of the true intensity, provided that the underlying true intensities are really the same (isomorphism): merging statistics measure precision (internal agreement) rather than accuracy. For measurement of anomalous differences, we should aim to measure the Bijvoet reflection pairs in as similar way as possible so that they are likely to have the same uncorrected systematic errors, most importantly to collect them close together in time, to minimise differences in radiation damage. However it is clearly also true that high multiplicity is extremely valuable, indeed essential for S-SAD, presumably just to average out errors, both random and systematic. Scala has an option to use matched pairs for estimation of anomalous differences (ANOMALOUS MATCH) but all the tests I've done using this option gave worse results than just merging everything. For this reason I haven't implemented the option in Aimless. Phil On 14 May 2013, at 12:07, Frank von Delft frank.vonde...@sgc.ox.ac.uk wrote: It's not about multiplicity, it's about scaling. See quote I sent earlier. phx. On 14/05/2013 10:40, Felix Frolow wrote: I guess that in a standpoint to reduce errors it is easy to improve statistical errors by longer counting or by using multiple observations. However the real enemy at the gate is a systematic error which require special skills and experience to detect and to eliminate. I never understood why to measure not very good data trying to recover anomalous signal by improving statistics using very high redundancy instead of trying to collect data which are perfect by minimising systematics errors and of course increasing counting time, but with minimum redundancy of only 2 ? Like in good old times with 4 circle diffractometers and good scintillation counters that produced true counting statistics: 10 counts - 30% precision 100 counts - 10% precision 1000 counts - 3% precision 1 counts - 1% precision Canonising and worshipping redundancy looking for true holy multiplicity on my taste is counterproductive….. My 2 NIS :-) And of corse - one of the systematic errors is the radiation damage…... FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On May 14, 2013, at 11:19 , Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Frank, I would not call it 'axiomatic' but 'statistics' to reduce the (stochastic) error by several independent measurements. You can probably give any statistics textbook as a reference. In real life, though, you have to compromise with radiation damage, though. For references I recommend searching journals.iucr.org for 'Garman' as author. If you add 'radiation damaga' as keywords, the result reduces to 37 hits of choice. Best, Tim On 05/14/2013 06:50 AM, Frank von Delft wrote: Hi, I'm meant to know this but I'm blanking, so I'll crowdsource instead: Anybody know a (the) reference where it was showed that the best SAD data is obtained by collecting multiple revolutions at different crystal offsets (kappa settings)? It's axiomatic now (I hope!), but I remember seeing someone actually show this. I thought Sheldrick early tweens, but PubMed is not being useful. (Oh dear, this will unleash references from the 60s, won't it.) phx - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFRkfN7UxlJ7aRr7hoRAnlWAJ9T4MvGHUGA+HRwOL2i/6rU7KW1xwCcDsAq KAvPG9FqtNYO2kLqmh7wIZI= =MNNU -END PGP SIGNATURE-
Re: [ccp4bb] reference for true multiplicity?
Precision does not trump accuracy is something Michael Blum told me. Also Charles Wheelan wrote in his recently published Naked Statistics: “But no amount of precision can make up for inaccuracy.” I myself have been pleasantly surprised at how low multiplicity can be nowadays and still do S-SAD phasing. And If one uses iodide, the quality of diffraction data does not need to be as high as with sulfur-SAD phasing. Does one need to collect about different rotation axes? Not always. I wonder now if it would even hide a signal. Does one need multiplicity of more than 6 to 8? Not always. Be careful about radiation damage with increasing multiplicity and exposure. Does one need to minimize radation damage? I definitely think so. Does one need ot make sure the cryostream is not moving or vibrating your sample? Definitely yes. Does one need enough counting statistics to tease out the signal? Yes, but this depends on the expected signal. And so on. I can provide datasets of images if anyone likes. Jim
[ccp4bb] Fwd: Re: [ccp4bb] reference for true multiplicity?
George points out that the quote I referred to did not make it to the BB -- here we go, read below and learn, it is a most succinct summary. phx Original Message Subject:Re: [ccp4bb] reference for true multiplicity? Date: Tue, 14 May 2013 09:25:22 +0100 From: Frank von Delft frank.vonde...@sgc.ox.ac.uk To: George Sheldrick gshe...@shelx.uni-ac.gwdg.de Thanks! It's the Acta D59 p688 I was thinking of - start of discussion: The results presented here show that it is possible to solve protein structures using the anomalous scattering from native S atoms measured on a laboratory instrument in a careful but relatively routine manner, provided that a sufficiently high real redundancy is obtained (ranging from 16 to 44 in these experiments). Real redundancy implies measurement of equivalent or identical re¯ections with different paths through the crystal, not just repeated measurements; this is expedited by high crystal symmetry and by the use of a three-circle (or ) goniometer. Wise words... phx On 14/05/2013 08:06, George Sheldrick wrote: Dear Frank, We did extensive testing of this approach at the beginning of this millenium - see Acta Cryst. D59 (2003) 393 and 688 - but never claimed that it was our idea. Best wishes, George On 05/14/2013 06:50 AM, Frank von Delft wrote: Hi, I'm meant to know this but I'm blanking, so I'll crowdsource instead: Anybody know a (the) reference where it was showed that the best SAD data is obtained by collecting multiple revolutions at different crystal offsets (kappa settings)? It's axiomatic now (I hope!), but I remember seeing someone actually show this. I thought Sheldrick early tweens, but PubMed is not being useful. (Oh dear, this will unleash references from the 60s, won't it.) phx
Re: [ccp4bb] Fwd: Re: [ccp4bb] reference for true multiplicity?
Yes, a good summary. The use of the term redundancy (real or otherwise!) in crystallography is potentially misleading as the normal usages means superfluous/ surplus to requirements. The closest usage I can find from elsewhere is in information theory where it is applied for purposes of error detection when communicating over a noisy channel. Seems similar to the crystallographic use. The more relevant point is what sort of errors would be mitigated by having different paths through the crystal. The obvious ones are absorption errors and errors in detector calibration. Inverse beam methods can mitigate these by ensuring the systematic errors are similar for the reflections being compared. However, my interpretation of the Acta D59 paper is that it is accepted that systematic errors are present and, by making multiple measurements under different conditions, the effect of these systematic errors will be minimised. Can anyone suggest other sources of error which would be mitigated by having different paths through the crystal. I don't think radiation damage (mentioned by several people) is one. Colin From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Frank von Delft Sent: 14 May 2013 14:23 To: ccp4bb Subject: [ccp4bb] Fwd: Re: [ccp4bb] reference for true multiplicity? George points out that the quote I referred to did not make it to the BB -- here we go, read below and learn, it is a most succinct summary. phx Original Message Subject: Re: [ccp4bb] reference for true multiplicity? Date: Tue, 14 May 2013 09:25:22 +0100 From: Frank von Delft frank.vonde...@sgc.ox.ac.ukmailto:%3cfrank.vonde...@sgc.ox.ac.uk%3e To: George Sheldrick gshe...@shelx.uni-ac.gwdg.demailto:gshe...@shelx.uni-ac.gwdg.de Thanks! It's the Acta D59 p688 I was thinking of - start of discussion: The results presented here show that it is possible to solve protein structures using the anomalous scattering from native S atoms measured on a laboratory instrument in a careful but relatively routine manner, provided that a sufficiently high real redundancy is obtained (ranging from 16 to 44 in these experiments). Real redundancy implies measurement of equivalent or identical re¯ections with different paths through the crystal, not just repeated measurements; this is expedited by high crystal symmetry and by the use of a three-circle (or ) goniometer. Wise words... phx On 14/05/2013 08:06, George Sheldrick wrote: Dear Frank, We did extensive testing of this approach at the beginning of this millenium - see Acta Cryst. D59 (2003) 393 and 688 - but never claimed that it was our idea. Best wishes, George On 05/14/2013 06:50 AM, Frank von Delft wrote: Hi, I'm meant to know this but I'm blanking, so I'll crowdsource instead: Anybody know a (the) reference where it was showed that the best SAD data is obtained by collecting multiple revolutions at different crystal offsets (kappa settings)? It's axiomatic now (I hope!), but I remember seeing someone actually show this. I thought Sheldrick early tweens, but PubMed is not being useful. (Oh dear, this will unleash references from the 60s, won't it.) phx -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
Re: [ccp4bb] Fwd: Re: [ccp4bb] reference for true multiplicity?
On Tuesday, May 14, 2013 01:58:06 pm Colin Nave wrote: The use of the term redundancy (real or otherwise!) in crystallography is potentially misleading as the normal usages means superfluous/ surplus to requirements. That may be true in the UK, but on this side of the pond redundancy normally refers to ensuring a safety margin by having more of whatever than is strictly needed for functionality, so that even if some of the whatsits fail you have enough remaining to go on with. The use of the term in crystallography is perfectly normal to American ears. Here's a definition from Wikipedia redundancy is the duplication of critical components or functions of a system with the intention of increasing reliability of the system... just another tidbit of cross-pond difference in language. Ethan The closest usage I can find from elsewhere is in information theory where it is applied for purposes of error detection when communicating over a noisy channel. Seems similar to the crystallographic use. The more relevant point is what sort of errors would be mitigated by having different paths through the crystal. The obvious ones are absorption errors and errors in detector calibration. Inverse beam methods can mitigate these by ensuring the systematic errors are similar for the reflections being compared. However, my interpretation of the Acta D59 paper is that it is accepted that systematic errors are present and, by making multiple measurements under different conditions, the effect of these systematic errors will be minimised. Can anyone suggest other sources of error which would be mitigated by having different paths through the crystal. I don't think radiation damage (mentioned by several people) is one. Colin From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Frank von Delft Sent: 14 May 2013 14:23 To: ccp4bb Subject: [ccp4bb] Fwd: Re: [ccp4bb] reference for true multiplicity? George points out that the quote I referred to did not make it to the BB -- here we go, read below and learn, it is a most succinct summary. phx Original Message Subject: Re: [ccp4bb] reference for true multiplicity? Date: Tue, 14 May 2013 09:25:22 +0100 From: Frank von Delft frank.vonde...@sgc.ox.ac.ukmailto:%3cfrank.vonde...@sgc.ox.ac.uk%3e To: George Sheldrick gshe...@shelx.uni-ac.gwdg.demailto:gshe...@shelx.uni-ac.gwdg.de Thanks! It's the Acta D59 p688 I was thinking of - start of discussion: The results presented here show that it is possible to solve protein structures using the anomalous scattering from native S atoms measured on a laboratory instrument in a careful but relatively routine manner, provided that a sufficiently high real redundancy is obtained (ranging from 16 to 44 in these experiments). Real redundancy implies measurement of equivalent or identical re�ections with different paths through the crystal, not just repeated measurements; this is expedited by high crystal symmetry and by the use of a three-circle (or ) goniometer. Wise words... phx On 14/05/2013 08:06, George Sheldrick wrote: Dear Frank, We did extensive testing of this approach at the beginning of this millenium - see Acta Cryst. D59 (2003) 393 and 688 - but never claimed that it was our idea. Best wishes, George On 05/14/2013 06:50 AM, Frank von Delft wrote: Hi, I'm meant to know this but I'm blanking, so I'll crowdsource instead: Anybody know a (the) reference where it was showed that the best SAD data is obtained by collecting multiple revolutions at different crystal offsets (kappa settings)? It's axiomatic now (I hope!), but I remember seeing someone actually show this. I thought Sheldrick early tweens, but PubMed is not being useful. (Oh dear, this will unleash references from the 60s, won't it.) phx -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
[ccp4bb] deleted font settings for ccp4i--how to have ccp4i use Ubuntu fonts
After an Ubuntu 13.04 reboot I noticed that all my ccp4i fonts looked very jagged and illegible. The preferences have the font assigned to be -Adobe-Helvetica-Medium-R-Normal--*-120-*-*-*-*-*-* Is there a way to have ccp4i use the Ubuntu fonts ? Thanks for your help Hari
Re: [ccp4bb] Fwd: Re: [ccp4bb] reference for true multiplicity?
The idea of RAID (redundant array of inexpensive disks) must seem pretty silly to the Brits- disks may be inexpensive but they're not free- why waste money on a redundant system? Ethan Merritt wrote: On Tuesday, May 14, 2013 01:58:06 pm Colin Nave wrote: The use of the term redundancy (real or otherwise!) in crystallography is potentially misleading as the normal usages means superfluous/ surplus to requirements. That may be true in the UK, but on this side of the pond redundancy normally refers to ensuring a safety margin by having more of whatever than is strictly needed for functionality, so that even if some of the whatsits fail you have enough remaining to go on with. The use of the term in crystallography is perfectly normal to American ears. Here's a definition from Wikipedia redundancy is the duplication of critical components or functions of a system with the intention of increasing reliability of the system... just another tidbit of cross-pond difference in language. Ethan The closest usage I can find from elsewhere is in information theory where it is applied for purposes of error detection when communicating over a noisy channel. Seems similar to the crystallographic use. The more relevant point is what sort of errors would be mitigated by having different paths through the crystal. The obvious ones are absorption errors and errors in detector calibration. Inverse beam methods can mitigate these by ensuring the systematic errors are similar for the reflections being compared. However, my interpretation of the Acta D59 paper is that it is accepted that systematic errors are present and, by making multiple measurements under different conditions, the effect of these systematic errors will be minimised. Can anyone suggest other sources of error which would be mitigated by having different paths through the crystal. I don't think radiation damage (mentioned by several people) is one. Colin From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Frank von Delft Sent: 14 May 2013 14:23 To: ccp4bb Subject: [ccp4bb] Fwd: Re: [ccp4bb] reference for true multiplicity? George points out that the quote I referred to did not make it to the BB -- here we go, read below and learn, it is a most succinct summary. phx Original Message Subject: Re: [ccp4bb] reference for true multiplicity? Date: Tue, 14 May 2013 09:25:22 +0100 From: Frank von Delft frank.vonde...@sgc.ox.ac.ukmailto:%3cfrank.vonde...@sgc.ox.ac.uk%3e To: George Sheldrick gshe...@shelx.uni-ac.gwdg.demailto:gshe...@shelx.uni-ac.gwdg.de Thanks! It's the Acta D59 p688 I was thinking of - start of discussion: The results presented here show that it is possible to solve protein structures using the anomalous scattering from native S atoms measured on a laboratory instrument in a careful but relatively routine manner, provided that a sufficiently high real redundancy is obtained (ranging from 16 to 44 in these experiments). Real redundancy implies measurement of equivalent or identical re�ections with different paths through the crystal, not just repeated measurements; this is expedited by high crystal symmetry and by the use of a three-circle (or ) goniometer. Wise words... phx On 14/05/2013 08:06, George Sheldrick wrote: Dear Frank, We did extensive testing of this approach at the beginning of this millenium - see Acta Cryst. D59 (2003) 393 and 688 - but never claimed that it was our idea. Best wishes, George On 05/14/2013 06:50 AM, Frank von Delft wrote: Hi, I'm meant to know this but I'm blanking, so I'll crowdsource instead: Anybody know a (the) reference where it was showed that the best SAD data is obtained by collecting multiple revolutions at different crystal offsets (kappa settings)? It's axiomatic now (I hope!), but I remember seeing someone actually show this. I thought Sheldrick early tweens, but PubMed is not being useful. (Oh dear, this will unleash references from the 60s, won't it.) phx
Re: [ccp4bb] deleted font settings for ccp4i--how to have ccp4i use Ubuntu fonts
In 12.04LTS I install X-fonts, and font servers e.g., sudo apt-get install xfonts-75dpi xfonts-100dpi xfs xfstt This allows ccp4i to display the fonts I remember. X-fonts are not installed by default in Ubuntu 12.04 and probably 13.04 as well. There may be a more elegant way to customize ccp4i but this works for me and is legible. Roger Rowlett On May 14, 2013 6:49 PM, hari jayaram hari...@gmail.com wrote: After an Ubuntu 13.04 reboot I noticed that all my ccp4i fonts looked very jagged and illegible. The preferences have the font assigned to be -Adobe-Helvetica-Medium-R-Normal--*-120-*-*-*-*-*-* Is there a way to have ccp4i use the Ubuntu fonts ? Thanks for your help Hari
