March 2025 - Chimera-users - RBVI Mailing Lists

registration
by YELIZ KAYA 11 Mar '25

11 Mar '25

I registered to the Chimera program with my address yeliz.kaya(a)iuc.edu.tr. Can I find out if I am registered to the Chimera program? Thank you. Assoc. Prof. Dr. Yeliz KAYA IUC Chemistry Department -- *İSTANBUL ÜNİVERSİTESİ-CERRAHPAŞA <https://www.iuc.edu.tr/tr/_>* Yasal Uyarı: <https://bilgiislem.iuc.edu.tr/tr/content/e-posta-hizmetleri/%E2%96%BA-e-pos…> Bu e-posta ve beraberinde iletilen bütün dosyalar sadece göndericisi tarafından alınması amaçlanan yetkili gerçek ya da tüzel kişinin kullanımı içindir. Eğer söz konusu yetkili alıcı değilseniz bu e-postanın içeriğini açıklamanız, kopyalamanız, yönlendirmeniz ve kullanmanız kesinlikle yasaktır ve bu e-postayı derhal silmeniz gerekmektedir. İSTANBUL ÜNİVERSİTESİ-CERRAHPAŞA bu e-postanın içerdiği bilgilerin doğruluğu veya eksiksiz olduğu konusunda herhangi bir garanti vermemektedir. Bu nedenle bu bilgilerin ne şekilde olursa olsun içeriğinden, iletilmesinden, alınmasından ve saklanmasından sorumlu değildir. Bu e-postadaki görüşler yalnızca gönderen kişiye aittir ve İSTANBUL ÜNİVERSİTESİ-CERRAHPAŞA'nın görüşlerini yansıtmayabilir. *ISTANBUL UNIVERSITY-CERRAHPASA <https://www.iuc.edu.tr/tr/_>* Disclaimer <https://bilgiislem.iuc.edu.tr/tr/content/e-posta-hizmetleri/%E2%96%BA-e-pos…>: This e-mail and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the intended recipient you are hereby notified that any dissemination, forwarding, copying or use of any of the information is strictly prohibited, and the e-mail should immediately be deleted. ISTANBUL UNIVERSITY-CERRAHPASA makes no warranty as to the accuracy or completeness of any information contained in this e-mail and hereby excludes any liability of any kind for the information contained therein or for the information transmission, reception, storage or use of such in any way whatsoever. The opinions expressed in this e-mail may belong to the sender alone and may not necessarily reflect the opinions of ISTANBUL UNIVERSITY-CERRAHPASA.

2 1

Problem downloading PDBs in Chimera
by Clarke, Oliver 10 Mar '25

10 Mar '25

Hi, Since this weekend, I have been unable to download PDBs from within Chimera (using "open" or Fetch by ID). The same PDBs load fine in ChimeraX or when downloaded manually. Cached PDBs load fine. Cheers Oli

4 3

Setting partial charges to a protein gives same charges in both Gasteiger and AM1-BCC methods. Is that corrects?
by teralexei＠proton.me 03 Mar '25

03 Mar '25

Dear colleagues, calculation of partial charges in Chimera looks to work improperly in my hands. After addcharge or dokprep procedures, independent on method used (am1-bcc or Gasteiger), mol2 files are just the same: @<TRIPOS>MOLECULE .... PROTEIN AMBER ff14SB @<TRIPOS>ATOM 1 N -76.5030 6.5380 -16.5070 N.4 1 ARG 0.1305 2 CA -75.2450 7.2900 -16.2110 C.3 1 ARG -0.0223 .... The problem persist in both Chimera 1.17.3 and ChimeraX. The latter gives even "NO_CHARGES" comment in both (am1-bcc and Gasteiger) cases: @<TRIPOS>MOLECULE .... PROTEIN NO_CHARGES @<TRIPOS>ATOM 1 N -76.5030 6.5380 -16.5070 N.4 1 ARG 0.1305 2 CA -75.2450 7.2900 -16.2110 C.3 1 ARG -0.0223 .... I am not an expert in molecular modeling, sorry. But I think that I am doing something wrong. Could you please help me with setting charges properly? Thank you in advance! PS. I am a newbie here. Please don't hurt me too much. Yours sincerely, Al.

2 1